nohup: ignoring input file: /data/arabidopsis/xiang/magic_founder/Col_0_R1/R38_L1_Col_0_sdlg_R1_nss_barcode_GTA.unmap_1.fq file: /data/arabidopsis/xiang/magic_founder/Bur_0_R1/R38_L1_Bur_0_sdlg_R1_nss_barcode_ACG.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Bur_0_R2/R38_L2_Bur_0_sdlg_R2_nss_barcode_ACG.unmap_1.fq $RNAGI/rnagi.sh -o ./Col_0 -n ngene.fa Col_0.Tongene.merge.fq reference: ngene.fa file: /data/arabidopsis/xiang/magic_founder/Can_0_R1/R38_L1_Can_0_sdlg_R1_nss_barcode_CAT.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Can_0_R2/R38_L2_Can_0_sdlg_R2_nss_barcode_CAT.unmap_1.fq $RNAGI/rnagi.sh -o ./Bur_0 -n ngene.fa Bur_0.Tongene.merge.fq reference: ngene.fa file: /data/arabidopsis/xiang/magic_founder/Ct_1_R2/R38_L2_Ct_1_sdlg_R2_nss_barcode_TGC.unmap_1.fq $RNAGI/rnagi.sh -o ./Ct_1 -n ngene.fa Ct_1.Tongene.merge.fq reference: ngene.fa $RNAGI/rnagi.sh -o ./Can_0 -n ngene.fa Can_0.Tongene.merge.fq reference: ngene.fa file: /data/arabidopsis/xiang/magic_founder/Edi_0_R1/R38_L3_Edi_0_sdlg_R1_nss_barcode_ACG.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Edi_0_R2/R38_L4_Edi_0_sdlg_R2_nss_barcode_ACG.unmap_1.fq $RNAGI/rnagi.sh -o ./Edi_0 -n ngene.fa Edi_0.Tongene.merge.fq reference: ngene.fa Settings: Output files: "ngene.fa.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: default Max bucket size, sqrt multiplier: default Max bucket size, len divisor: 4 Difference-cover sample period: 1024 Endianness: little Actual local endianness: little Sanity checking: disabled Assertions: disabled Random seed: 0 Sizeofs: void*:8, int:4, long:8, size_t:8 Input files DNA, FASTA: ngene.fa Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 33565 Using parameters --bmax 25174 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 25174 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 5; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 14917.2 (target: 25173) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 11812 (Using difference cover) Sorting block time: 00:00:00 Returning block of 11813 Getting block 2 of 9 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 14037 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14038 Getting block 3 of 9 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 23148 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23149 Getting block 4 of 9 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 4498 (Using difference cover) Sorting block time: 00:00:00 Returning block of 4499 Getting block 5 of 9 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 24267 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24268 Getting block 6 of 9 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 5947 (Using difference cover) Sorting block time: 00:00:00 Returning block of 5948 Getting block 7 of 9 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 20388 (Using difference cover) Sorting block time: 00:00:00 Returning block of 20389 Getting block 8 of 9 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 24685 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24686 Getting block 9 of 9 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 5473 (Using difference cover) Sorting block time: 00:00:00 Returning block of 5474 Exited Ebwt loop fchr[A]: 0 fchr[C]: 38070 fchr[G]: 67162 fchr[T]: 96010 fchr[$]: 134263 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4243591 bytes to primary EBWT file: ngene.fa.1.ebwt Wrote 16788 bytes to secondary EBWT file: ngene.fa.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 134263 bwtLen: 134264 sz: 33566 bwtSz: 33566 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4196 offsSz: 16784 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 300 numSides: 600 numLines: 600 ebwtTotLen: 38400 ebwtTotSz: 38400 reverse: 0 Total time for call to driver() for forward index: 00:00:00 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length Writing header Reserving space for joined string Joining reference sequences Time to join reference sequences: 00:00:00 bmax according to bmaxDivN setting: 33565 Using parameters --bmax 25174 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 25174 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:00 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:00 Invoking Larsson-Sadakane on ranks Invoking Larsson-Sadakane on ranks time: 00:00:00 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates QSorting sample offsets, eliminating duplicates time: 00:00:00 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 Calculating bucket sizes Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Binary sorting into buckets 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Binary sorting into buckets time: 00:00:00 Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 19179.6 (target: 25173) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 14379 (Using difference cover) Sorting block time: 00:00:00 Returning block of 14380 Getting block 2 of 7 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 22666 (Using difference cover) Sorting block time: 00:00:00 Returning block of 22667 Getting block 3 of 7 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 22284 (Using difference cover) Sorting block time: 00:00:00 Returning block of 22285 Getting block 4 of 7 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 15389 (Using difference cover) Sorting block time: 00:00:00 Returning block of 15390 Getting block 5 of 7 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 24719 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24720 Getting block 6 of 7 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 19531 (Using difference cover) Sorting block time: 00:00:00 Returning block of 19532 Getting block 7 of 7 Reserving size (25174) for bucket Calculating Z arrays Calculating Z arrays time: 00:00:00 Entering block accumulator loop: 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Block accumulator loop time: 00:00:00 Sorting block of length 15289 (Using difference cover) Sorting block time: 00:00:00 Returning block of 15290 Exited Ebwt loop fchr[A]: 0 fchr[C]: 38070 fchr[G]: 67162 fchr[T]: 96010 fchr[$]: 134263 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4243591 bytes to primary EBWT file: ngene.fa.rev.1.ebwt Wrote 16788 bytes to secondary EBWT file: ngene.fa.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 134263 bwtLen: 134264 sz: 33566 bwtSz: 33566 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 4196 offsSz: 16784 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 300 numSides: 600 numLines: 600 ebwtTotLen: 38400 ebwtTotSz: 38400 reverse: 0 Total time for backward call to driver() for mirror index: 00:00:01 tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Col_0 ngene.fa ./Col_0/Col_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:17:29 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:17:29 2011] Preparing output location ./Col_0// [Mon Apr 4 16:17:29 2011] Checking for Bowtie index files [Mon Apr 4 16:17:29 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:17:29 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:17:29 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:17:29 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:17:30 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Ct_1 ngene.fa ./Ct_1/Ct_1.Tongene.merge.flt_1.fq [Mon Apr 4 16:17:33 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:17:33 2011] Preparing output location ./Ct_1// [Mon Apr 4 16:17:33 2011] Checking for Bowtie index files [Mon Apr 4 16:17:33 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:17:33 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:17:33 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:17:33 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:17:33 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Edi_0 ngene.fa ./Edi_0/Edi_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:17:36 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:17:36 2011] Preparing output location ./Edi_0// [Mon Apr 4 16:17:36 2011] Checking for Bowtie index files [Mon Apr 4 16:17:36 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:17:36 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:17:36 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:17:36 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:17:36 2011] Checking reads min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:17:39 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:17:42 2011] Joining segment hits tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Can_0 ngene.fa ./Can_0/Can_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:17:44 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:17:44 2011] Preparing output location ./Can_0// [Mon Apr 4 16:17:44 2011] Checking for Bowtie index files [Mon Apr 4 16:17:44 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:17:44 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:17:44 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:17:44 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:17:44 2011] Checking reads min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:17:47 2011] Mapping reads against ngene.fa with Bowtie tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Bur_0 ngene.fa ./Bur_0/Bur_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:17:50 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:17:50 2011] Preparing output location ./Bur_0// [Mon Apr 4 16:17:50 2011] Checking for Bowtie index files [Mon Apr 4 16:17:50 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:17:50 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:17:50 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:17:50 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:17:50 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:17:50 2011] Checking reads [Mon Apr 4 16:17:52 2011] Joining segment hits [Mon Apr 4 16:17:53 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:17:56 2011] Mapping reads against ngene.fa with Bowtie(3/3) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:17:59 2011] Searching for junctions via segment mapping [Mon Apr 4 16:18:01 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:18:04 2011] Mapping reads against ngene.fa with Bowtie(1/3) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:18:05 2011] Joining segment hits [Mon Apr 4 16:18:06 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:18:08 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:18:08 2011] Retrieving sequences for splices [Mon Apr 4 16:18:08 2011] Indexing splices [Mon Apr 4 16:18:09 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:18:09 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:18:10 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:18:10 2011] Searching for junctions via segment mapping [Mon Apr 4 16:18:11 2011] Mapping reads against segment_juncs with Bowtie min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:18:12 2011] Joining segment hits [Mon Apr 4 16:18:13 2011] Reporting output tracks ----------------------------------------------- Run complete [00:00:45 elapsed] [Mon Apr 4 16:18:16 2011] Joining segment hits [Mon Apr 4 16:18:17 2011] Mapping reads against ngene.fa with Bowtie cufflinks -p 4 -o ./Col_0 -r ngene.fa ./Col_0/accepted_hits.bam [16:18:19] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.575_From_ct_1_3082021_± [ ] > Processing Locus CUFF.583_From_ct_1_3302721_± [ ] > Processing Locus CUFF.595_From_ct_1_3302721_± [ ] > Processing Locus CUFF.663_From_kn_0_3613403_± [ ] > Processing Locus CUFF.679_From_ler_0_3998410± [ ] > Processing Locus CUFF.689_From_ler_0_4018856± [ ] > Processing Locus CUFF.699_From_no_0_2905273_± [ ] > Processing Locus CUFF.703_From_no_0_2885444_± [ ] > Processing Locus CUFF.733_From_no_0_2956652_± [ ] > Processing Locus CUFF.763_From_rsch_4_403203± [ ] > Processing Locus CUFF.913_From_wil_2_2834553± [* ] > Processing Locus CUFF.945_From_wu_0_2678387_± [* ] > Processed 12 loci. [*************************] 100% > Map Properties: > Total Map Mass: 151.00 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:18:19] Assembling transcripts and estimating abundances. > Processing Locus CUFF.575_From_ct_1_3082021_ [ ] 0% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 8% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 16% > Processing Locus CUFF.663_From_kn_0_3613403_ [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [******** ] 33% > Processing Locus CUFF.689_From_ler_0_4018856 [********** ] 41% > Processing Locus CUFF.699_From_no_0_2905273_ [************ ] 50% > Processing Locus CUFF.703_From_no_0_2885444_ [************** ] 58% > Processing Locus CUFF.733_From_no_0_2956652_ [**************** ] 66% > Processing Locus CUFF.763_From_rsch_4_403203 [****************** ] 75% > Processing Locus CUFF.913_From_wil_2_2834553 [******************** ] 83% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************** ] 91% > Processed 12 loci. [*************************] 100% [16:18:19] Loading reference annotation and sequence No fasta index found for ngene.fa. Rebuilding, please wait.. Fasta index rebuilt. [16:18:19] Learning bias parameters. > Processing Locus CUFF.575_From_ct_1_3082021_ [ ] 0% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 8% > Processing Locus CUFF.663_From_kn_0_3613403_ [**** ] 16% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 25% > Processing Locus CUFF.689_From_ler_0_4018856 [******** ] 33% > Processing Locus CUFF.733_From_no_0_2956652_ [********** ] 41% > Processing Locus CUFF.763_From_rsch_4_403203 [************ ] 50% > Processed 7 loci. [*************************] 100% [16:18:19] Assembling transcripts and estimating abundances. > Processing Locus CUFF.575_From_ct_1_3082021_ [ ] 0% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 8% > Processing Locus CUFF.663_From_kn_0_3613403_ [**** ] 16% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 25% > Processing Locus CUFF.689_From_ler_0_4018856 [******** ] 33% > Processing Locus CUFF.733_From_no_0_2956652_ [********** ] 41% > Processing Locus CUFF.763_From_rsch_4_403203 [************ ] 50% > Processed 7 loci. [*************************] 100% [Mon Apr 4 16:18:21 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:18:27 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:18:27 2011] Joining segment hits [Mon Apr 4 16:18:30 2011] Retrieving sequences for splices [Mon Apr 4 16:18:30 2011] Indexing splices [Mon Apr 4 16:18:31 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:18:31 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:18:33 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:18:35 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:18:37 2011] Searching for junctions via segment mapping [Mon Apr 4 16:18:37 2011] Joining segment hits [Mon Apr 4 16:18:38 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:06 elapsed] [Mon Apr 4 16:18:42 2011] Mapping reads against ngene.fa with Bowtie(1/3) cufflinks -p 4 -o ./Ct_1 -r ngene.fa ./Ct_1/accepted_hits.bam [16:18:43] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399. [ ] > Processing Locus CUFF.529_From_bur_0_1873494. [ ] > Processing Locus CUFF.551_From_can_0_3122480. [ ] > Processing Locus CUFF.561_From_can_0_3189753. [ ] > Processing Locus CUFF.571_From_can_0_3076940. [ ] > Processing Locus CUFF.575_From_ct_1_3082021_. [ ] > Processing Locus CUFF.577_From_ct_1_3125173_. [ ] > Processing Locus CUFF.579_From_ct_1_3133451_. [ ] > Processing Locus CUFF.581_From_can_0_3218459. [ ] > Processing Locus CUFF.581_From_can_0_3218459. [ ] > Processing Locus CUFF.583_From_ct_1_3302721_. [ ] > Processing Locus CUFF.585_From_ct_1_3247037_. [* ] > Processing Locus CUFF.593_From_can_0_3270131. [* ] > Processing Locus CUFF.595_From_ct_1_3302721_. [* ] > Processing Locus CUFF.607_From_edi_0_2891226. [* ] > Processing Locus CUFF.607_From_edi_0_2891226. [* ] > Processing Locus CUFF.615_From_edi_0_2932438. [* ] > Processing Locus CUFF.619_From_edi_0_2871668. [* ] > Processing Locus CUFF.629_From_kn_0_3594465_. [* ] > Processing Locus CUFF.635_From_ct_1_3241157_. [* ] > Processing Locus CUFF.655_From_hi_0_2795398_. [* ] > Processing Locus CUFF.663_From_kn_0_3613403_. [** ] > Processing Locus CUFF.665_From_hi_0_2939638_. [** ] > Processing Locus CUFF.669_From_ler_0_4225073. [** ] > Processing Locus CUFF.671_From_edi_0_2859720. [** ] > Processing Locus CUFF.673_From_ler_0_4224097. [** ] > Processing Locus CUFF.677_From_ct_1_3133995_. [** ] > Processing Locus CUFF.679_From_ler_0_3998410. [** ] > Processing Locus CUFF.685_From_mt_0_4231054_. [** ] > Processing Locus CUFF.687_From_mt_0_4230874_. [** ] > Processing Locus CUFF.689_From_ler_0_4018856. [** ] > Processing Locus CUFF.691_From_hi_0_2961678_. [*** ] > Processing Locus CUFF.693_From_no_0_2934639_. [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_. [*** ] > Processing Locus CUFF.697_From_mt_0_4229662_. [*** ] > Processing Locus CUFF.699_From_no_0_2905273_. [*** ] > Processing Locus CUFF.703_From_no_0_2885444_. [*** ] > Processing Locus CUFF.723_From_po_0_3306688_. [*** ] > Processing Locus CUFF.727_From_hi_0_2953648_. [*** ] > Processing Locus CUFF.729_From_oy_0_3001818_. [*** ] > Processing Locus CUFF.731_From_po_0_3324652_. [**** ] > Processing Locus CUFF.733_From_no_0_2956652_. [**** ] > Processing Locus CUFF.737_From_ct_1_3132277_. [**** ] > Processing Locus CUFF.739_From_po_0_3340213_. [**** ] > Processing Locus CUFF.741_From_po_0_3382155_. [**** ] > Processing Locus CUFF.743_From_po_0_3330421_. [**** ] > Processing Locus CUFF.747_From_po_0_3299272_. [**** ] > Processing Locus CUFF.753_From_oy_0_3121110_. [**** ] > Processing Locus CUFF.763_From_rsch_4_403203. [**** ] > Processing Locus CUFF.771_From_po_0_3332479_. [**** ] > Processing Locus CUFF.785_From_no_0_3128142_. [***** ] > Processing Locus CUFF.803_From_po_0_3573778_. [***** ] > Processing Locus CUFF.809_From_sf_2_2682779_. [***** ] > Processing Locus CUFF.809_From_sf_2_2682779_. [***** ] > Processing Locus CUFF.827_From_rsch_4_427728. [***** ] > Processing Locus CUFF.833_From_tsu_0_3208747. [***** ] > Processing Locus CUFF.861_From_mt_0_4528444_. [***** ] > Processing Locus CUFF.861_From_mt_0_4528444_. [***** ] > Processing Locus CUFF.871_From_rsch_4_426655. [***** ] > Processing Locus CUFF.877_From_sf_2_2687786_. [***** ] > Processing Locus CUFF.879_From_rsch_4_405516. [***** ] > Processing Locus CUFF.881_From_wil_2_2925323. [****** ] > Processing Locus CUFF.899_From_ws_0_3190963_. [****** ] > Processing Locus CUFF.913_From_wil_2_2834553. [****** ] > Processing Locus CUFF.917_From_ws_0_3371988_. [****** ] > Processing Locus CUFF.919_From_ws_0_3347582_. [****** ] > Processing Locus CUFF.919_From_ws_0_3347582_. [****** ] > Processing Locus CUFF.919_From_ws_0_3347582_. [****** ] > Processing Locus CUFF.921_From_wil_2_3077447. [****** ] > Processing Locus CUFF.925_From_ws_0_3371988_. [****** ] > Processing Locus CUFF.935_From_ws_0_3380934_. [****** ] > Processing Locus CUFF.937_From_ws_0_3373604_. [****** ] > Processing Locus CUFF.945_From_wu_0_2678387_. [****** ] > Processing Locus CUFF.947_From_wu_0_2654219_. [******* ] > Processing Locus CUFF.955_From_ws_0_3340488_. [******* ] > Processing Locus CUFF.957_From_ws_0_3381390_. [******* ] > Processing Locus CUFF.975_From_zu_0_3259399_. [******* ] > Processing Locus CUFF.983_From_zu_0_3243571_. [******* ] > Processed 78 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5434.91 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:18:43] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 2% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 6% > Processing Locus CUFF.577_From_ct_1_3125173_ [* ] 7% > Processing Locus CUFF.579_From_ct_1_3133451_ [** ] 8% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 10% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 11% > Processing Locus CUFF.583_From_ct_1_3302721_ [*** ] 12% > Processing Locus CUFF.585_From_ct_1_3247037_ [*** ] 14% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 15% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 16% > Processing Locus CUFF.607_From_edi_0_2891226 [**** ] 17% > Processing Locus CUFF.607_From_edi_0_2891226 [**** ] 19% > Processing Locus CUFF.615_From_edi_0_2932438 [***** ] 20% > Processing Locus CUFF.619_From_edi_0_2871668 [***** ] 21% > Processing Locus CUFF.629_From_kn_0_3594465_ [***** ] 23% > Processing Locus CUFF.635_From_ct_1_3241157_ [****** ] 24% > Processing Locus CUFF.655_From_hi_0_2795398_ [****** ] 25% > Processing Locus CUFF.663_From_kn_0_3613403_ [****** ] 26% > Processing Locus CUFF.665_From_hi_0_2939638_ [******* ] 28% > Processing Locus CUFF.669_From_ler_0_4225073 [******* ] 29% > Processing Locus CUFF.671_From_edi_0_2859720 [******* ] 30% > Processing Locus CUFF.673_From_ler_0_4224097 [******** ] 32% > Processing Locus CUFF.677_From_ct_1_3133995_ [******** ] 33% > Processing Locus CUFF.679_From_ler_0_3998410 [******** ] 34% > Processing Locus CUFF.685_From_mt_0_4231054_ [******** ] 35% > Processing Locus CUFF.687_From_mt_0_4230874_ [********* ] 37% > Processing Locus CUFF.689_From_ler_0_4018856 [********* ] 38% > Processing Locus CUFF.691_From_hi_0_2961678_ [********* ] 39% > Processing Locus CUFF.693_From_no_0_2934639_ [********** ] 41% > Processing Locus CUFF.695_From_mt_0_4217716_ [********** ] 42% > Processing Locus CUFF.697_From_mt_0_4229662_ [********** ] 43% > Processing Locus CUFF.699_From_no_0_2905273_ [*********** ] 44% > Processing Locus CUFF.703_From_no_0_2885444_ [*********** ] 46% > Processing Locus CUFF.723_From_po_0_3306688_ [*********** ] 47% > Processing Locus CUFF.727_From_hi_0_2953648_ [************ ] 48% > Processing Locus CUFF.729_From_oy_0_3001818_ [************ ] 50% > Processing Locus CUFF.731_From_po_0_3324652_ [************ ] 51% > Processing Locus CUFF.733_From_no_0_2956652_ [************* ] 52% > Processing Locus CUFF.737_From_ct_1_3132277_ [************* ] 53% > Processing Locus CUFF.739_From_po_0_3340213_ [************* ] 55% > Processing Locus CUFF.741_From_po_0_3382155_ [************** ] 56% > Processing Locus CUFF.743_From_po_0_3330421_ [************** ] 57% > Processing Locus CUFF.747_From_po_0_3299272_ [************** ] 58% > Processing Locus CUFF.753_From_oy_0_3121110_ [*************** ] 60% > Processing Locus CUFF.763_From_rsch_4_403203 [*************** ] 61% > Processing Locus CUFF.771_From_po_0_3332479_ [*************** ] 62% > Processing Locus CUFF.785_From_no_0_3128142_ [**************** ] 64% > Processing Locus CUFF.803_From_po_0_3573778_ [**************** ] 65% > Processing Locus CUFF.809_From_sf_2_2682779_ [**************** ] 66% > Processing Locus CUFF.809_From_sf_2_2682779_ [**************** ] 67% > Processing Locus CUFF.827_From_rsch_4_427728 [***************** ] 69% > Processing Locus CUFF.833_From_tsu_0_3208747 [***************** ] 70% > Processing Locus CUFF.861_From_mt_0_4528444_ [***************** ] 71% > Processing Locus CUFF.861_From_mt_0_4528444_ [****************** ] 73% > Processing Locus CUFF.871_From_rsch_4_426655 [****************** ] 74% > Processing Locus CUFF.877_From_sf_2_2687786_ [****************** ] 75% > Processing Locus CUFF.879_From_rsch_4_405516 [******************* ] 76% > Processing Locus CUFF.881_From_wil_2_2925323 [******************* ] 78% > Processing Locus CUFF.899_From_ws_0_3190963_ [******************* ] 79% > Processing Locus CUFF.913_From_wil_2_2834553 [******************** ] 80% > Processing Locus CUFF.917_From_ws_0_3371988_ [******************** ] 82% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 83% > Processing Locus CUFF.919_From_ws_0_3347582_ [********************* ] 84% > Processing Locus CUFF.919_From_ws_0_3347582_ [********************* ] 85% > Processing Locus CUFF.921_From_wil_2_3077447 [********************* ] 87% > Processing Locus CUFF.925_From_ws_0_3371988_ [********************** ] 88% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************** ] 89% > Processing Locus CUFF.937_From_ws_0_3373604_ [********************** ] 91% > Processing Locus CUFF.945_From_wu_0_2678387_ [*********************** ] 92% > Processing Locus CUFF.947_From_wu_0_2654219_ [*********************** ] 93% > Processing Locus CUFF.955_From_ws_0_3340488_ [*********************** ] 94% > Processing Locus CUFF.957_From_ws_0_3381390_ [************************ ] 96% > Processing Locus CUFF.975_From_zu_0_3259399_ [************************ ] 97% > Processing Locus CUFF.983_From_zu_0_3243571_ [************************ ] 98% > Processed 78 loci. [*************************] 100% [16:18:44] Loading reference annotation and sequence [16:18:44] Learning bias parameters. > Processing Locus CUFF.551_From_can_0_3122480 [ ] 0% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 1% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 2% > Processing Locus CUFF.575_From_ct_1_3082021_ [ ] 3% > Processing Locus CUFF.577_From_ct_1_3125173_ [* ] 5% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 6% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 7% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 8% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 10% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 11% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 12% > Processing Locus CUFF.615_From_edi_0_2932438 [*** ] 14% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 15% > Processing Locus CUFF.629_From_kn_0_3594465_ [**** ] 16% > Processing Locus CUFF.635_From_ct_1_3241157_ [**** ] 17% > Processing Locus CUFF.655_From_hi_0_2795398_ [**** ] 19% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 20% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 21% > Processing Locus CUFF.673_From_ler_0_4224097 [***** ] 23% > Processing Locus CUFF.677_From_ct_1_3133995_ [****** ] 24% > Processing Locus CUFF.687_From_mt_0_4230874_ [****** ] 25% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 26% > Processing Locus CUFF.691_From_hi_0_2961678_ [******* ] 28% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 29% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 30% > Processing Locus CUFF.723_From_po_0_3306688_ [******** ] 32% > Processing Locus CUFF.729_From_oy_0_3001818_ [******** ] 33% > Processing Locus CUFF.731_From_po_0_3324652_ [******** ] 34% > Processing Locus CUFF.737_From_ct_1_3132277_ [******** ] 35% > Processing Locus CUFF.741_From_po_0_3382155_ [********* ] 37% > Processing Locus CUFF.743_From_po_0_3330421_ [********* ] 38% > Processing Locus CUFF.747_From_po_0_3299272_ [********* ] 39% > Processing Locus CUFF.753_From_oy_0_3121110_ [********** ] 41% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 42% > Processing Locus CUFF.771_From_po_0_3332479_ [********** ] 43% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 44% > Processing Locus CUFF.803_From_po_0_3573778_ [*********** ] 46% > Processing Locus CUFF.827_From_rsch_4_427728 [*********** ] 47% > Processing Locus CUFF.833_From_tsu_0_3208747 [************ ] 48% > Processing Locus CUFF.861_From_mt_0_4528444_ [************ ] 50% > Processing Locus CUFF.871_From_rsch_4_426655 [************ ] 51% > Processing Locus CUFF.877_From_sf_2_2687786_ [************* ] 52% > Processing Locus CUFF.879_From_rsch_4_405516 [************* ] 53% > Processing Locus CUFF.881_From_wil_2_2925323 [************* ] 55% > Processing Locus CUFF.919_From_ws_0_3347582_ [************** ] 56% > Processing Locus CUFF.925_From_ws_0_3371988_ [************** ] 57% > Processing Locus CUFF.935_From_ws_0_3380934_ [************** ] 58% > Processing Locus CUFF.937_From_ws_0_3373604_ [*************** ] 60% > Processing Locus CUFF.955_From_ws_0_3340488_ [*************** ] 61% > Processing Locus CUFF.957_From_ws_0_3381390_ [*************** ] 62% > Processing Locus CUFF.975_From_zu_0_3259399_ [**************** ] 64% > Processing Locus CUFF.983_From_zu_0_3243571_ [**************** ] 65% > Processed 52 loci. [*************************] 100% [16:18:44] Assembling transcripts and estimating abundances. > Processing Locus CUFF.551_From_can_0_3122480 [ ] 0% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 1% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 2% > Processing Locus CUFF.575_From_ct_1_3082021_ [ ] 3% > Processing Locus CUFF.577_From_ct_1_3125173_ [* ] 5% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 6% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 7% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 8% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 10% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 11% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 12% > Processing Locus CUFF.615_From_edi_0_2932438 [*** ] 14% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 15% > Processing Locus CUFF.629_From_kn_0_3594465_ [**** ] 16% > Processing Locus CUFF.635_From_ct_1_3241157_ [**** ] 17% > Processing Locus CUFF.655_From_hi_0_2795398_ [**** ] 19% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 20% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 21% > Processing Locus CUFF.673_From_ler_0_4224097 [***** ] 23% > Processing Locus CUFF.677_From_ct_1_3133995_ [****** ] 24% > Processing Locus CUFF.687_From_mt_0_4230874_ [****** ] 25% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 26% > Processing Locus CUFF.691_From_hi_0_2961678_ [******* ] 28% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 29% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 30% > Processing Locus CUFF.723_From_po_0_3306688_ [******** ] 32% > Processing Locus CUFF.729_From_oy_0_3001818_ [******** ] 33% > Processing Locus CUFF.731_From_po_0_3324652_ [******** ] 34% > Processing Locus CUFF.737_From_ct_1_3132277_ [******** ] 35% > Processing Locus CUFF.741_From_po_0_3382155_ [********* ] 37% > Processing Locus CUFF.743_From_po_0_3330421_ [********* ] 38% > Processing Locus CUFF.747_From_po_0_3299272_ [********* ] 39% > Processing Locus CUFF.753_From_oy_0_3121110_ [********** ] 41% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 42% > Processing Locus CUFF.771_From_po_0_3332479_ [********** ] 43% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 44% > Processing Locus CUFF.803_From_po_0_3573778_ [*********** ] 46% > Processing Locus CUFF.827_From_rsch_4_427728 [*********** ] 47% > Processing Locus CUFF.833_From_tsu_0_3208747 [************ ] 48% > Processing Locus CUFF.861_From_mt_0_4528444_ [************ ] 50% > Processing Locus CUFF.871_From_rsch_4_426655 [************ ] 51% > Processing Locus CUFF.877_From_sf_2_2687786_ [************* ] 52% > Processing Locus CUFF.879_From_rsch_4_405516 [************* ] 53% > Processing Locus CUFF.881_From_wil_2_2925323 [************* ] 55% > Processing Locus CUFF.919_From_ws_0_3347582_ [************** ] 56% > Processing Locus CUFF.925_From_ws_0_3371988_ [************** ] 57% > Processing Locus CUFF.935_From_ws_0_3380934_ [************** ] 58% > Processing Locus CUFF.937_From_ws_0_3373604_ [*************** ] 60% > Processing Locus CUFF.955_From_ws_0_3340488_ [*************** ] 61% > Processing Locus CUFF.957_From_ws_0_3381390_ [*************** ] 62% > Processing Locus CUFF.975_From_zu_0_3259399_ [**************** ] 64% > Processing Locus CUFF.983_From_zu_0_3243571_ [**************** ] 65% > Processed 52 loci. [*************************] 100% [Mon Apr 4 16:18:46 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:18:49 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:18:50 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:18:56 2011] Searching for junctions via segment mapping [Mon Apr 4 16:18:56 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:18:59 2011] Retrieving sequences for splices [Mon Apr 4 16:18:59 2011] Indexing splices [Mon Apr 4 16:19:00 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:19:02 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:19:03 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:19:06 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:19:09 2011] Joining segment hits [Mon Apr 4 16:19:11 2011] Searching for junctions via segment mapping [Mon Apr 4 16:19:12 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:37 elapsed] cufflinks -p 4 -o ./Edi_0 -r ngene.fa ./Edi_0/accepted_hits.bam [16:19:19] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399W [ ] > Processing Locus CUFF.551_From_can_0_3122480W [ ] > Processing Locus CUFF.567_From_can_0_3258779W [ ] > Processing Locus CUFF.571_From_can_0_3076940W [ ] > Processing Locus CUFF.575_From_ct_1_3082021_W [ ] > Processing Locus CUFF.583_From_ct_1_3302721_W [ ] > Processing Locus CUFF.589_From_edi_0_2723255W [ ] > Processing Locus CUFF.593_From_can_0_3270131W [ ] > Processing Locus CUFF.595_From_ct_1_3302721_W [ ] > Processing Locus CUFF.597_From_edi_0_2759827W [ ] > Processing Locus CUFF.599_From_edi_0_2744702W [* ] > Processing Locus CUFF.609_From_hi_0_2755116_W [* ] > Processing Locus CUFF.611_From_edi_0_2921730W [* ] > Processing Locus CUFF.619_From_edi_0_2871668W [* ] > Processing Locus CUFF.623_From_hi_0_2778596_W [* ] > Processing Locus CUFF.627_From_edi_0_2889434W [* ] > Processing Locus CUFF.627_From_edi_0_2889434W [* ] > Processing Locus CUFF.629_From_kn_0_3594465_W [* ] > Processing Locus CUFF.637_From_kn_0_3626969_W [* ] > Processing Locus CUFF.639_From_hi_0_2916184_W [* ] > Processing Locus CUFF.641_From_kn_0_3605300_W [** ] > Processing Locus CUFF.643_From_kn_0_3799876_W [** ] > Processing Locus CUFF.645_From_edi_0_2888586W [** ] > Processing Locus CUFF.649_From_kn_0_3617271_W [** ] > Processing Locus CUFF.663_From_kn_0_3613403_W [** ] > Processing Locus CUFF.665_From_hi_0_2939638_W [** ] > Processing Locus CUFF.666_From_ler_0_4004770W [** ] > Processing Locus CUFF.671_From_edi_0_2859720W [** ] > Processing Locus CUFF.679_From_ler_0_3998410W [** ] > Processing Locus CUFF.685_From_mt_0_4231054_W [** ] > Processing Locus CUFF.687_From_mt_0_4230874_W [*** ] > Processing Locus CUFF.689_From_ler_0_4018856W [*** ] > Processing Locus CUFF.691_From_hi_0_2961678_W [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_W [*** ] > Processing Locus CUFF.699_From_no_0_2905273_W [*** ] > Processing Locus CUFF.701_From_no_0_2951521_W [*** ] > Processing Locus CUFF.703_From_no_0_2885444_W [*** ] > Processing Locus CUFF.707_From_no_0_2959683_W [*** ] > Processing Locus CUFF.711_From_no_0_3088052_W [*** ] > Processing Locus CUFF.721_From_no_0_3120392_W [**** ] > Processing Locus CUFF.721_From_no_0_3120392_W [**** ] > Processing Locus CUFF.721_From_no_0_3120392_W [**** ] > Processing Locus CUFF.721_From_no_0_3120392_W [**** ] > Processing Locus CUFF.721_From_no_0_3120392_W [**** ] > Processing Locus CUFF.727_From_hi_0_2953648_W [**** ] > Processing Locus CUFF.733_From_no_0_2956652_W [**** ] > Processing Locus CUFF.737_From_ct_1_3132277_W [**** ] > Processing Locus CUFF.743_From_po_0_3330421_W [**** ] > Processing Locus CUFF.755_From_mt_0_4193196_W [**** ] > Processing Locus CUFF.763_From_rsch_4_403203W [**** ] > Processing Locus CUFF.767_From_rsch_4_411814W [**** ] > Processing Locus CUFF.769_From_rsch_4_410762W [**** ] > Processing Locus CUFF.775_From_rsch_4_409124W [**** ] > Processing Locus CUFF.777_From_rsch_4_408506W [***** ] > Processing Locus CUFF.779_From_rsch_4_421454W [***** ] > Processing Locus CUFF.783_From_oy_0_2965192_W [***** ] > Processing Locus CUFF.791_From_rsch_4_425553W [***** ] > Processing Locus CUFF.795_From_rsch_4_429714W [***** ] > Processing Locus CUFF.801_From_sf_2_2532172_W [***** ] > Processing Locus CUFF.811_From_sf_2_2459023_W [***** ] > Processing Locus CUFF.819_From_tsu_0_3036945W [***** ] > Processing Locus CUFF.827_From_rsch_4_427728W [***** ] > Processing Locus CUFF.839_From_sf_2_2680171_W [****** ] > Processing Locus CUFF.843_From_rsch_4_429219W [****** ] > Processing Locus CUFF.843_From_rsch_4_429219W [****** ] > Processing Locus CUFF.855_From_wil_2_2915899W [****** ] > Processing Locus CUFF.861_From_mt_0_4528444_W [****** ] > Processing Locus CUFF.871_From_rsch_4_426655W [****** ] > Processing Locus CUFF.873_From_wil_2_3050523W [****** ] > Processing Locus CUFF.877_From_sf_2_2687786_W [****** ] > Processing Locus CUFF.879_From_rsch_4_405516W [****** ] > Processing Locus CUFF.881_From_wil_2_2925323W [****** ] > Processing Locus CUFF.893_From_ws_0_3190679_W [****** ] > Processing Locus CUFF.907_From_ws_0_3182508_W [******* ] > Processing Locus CUFF.913_From_wil_2_2834553W [******* ] > Processing Locus CUFF.927_From_wu_0_2655481_W [******* ] > Processing Locus CUFF.935_From_ws_0_3380934_W [******* ] > Processing Locus CUFF.937_From_ws_0_3373604_W [******* ] > Processing Locus CUFF.945_From_wu_0_2678387_W [******* ] > Processing Locus CUFF.947_From_wu_0_2654219_W [******* ] > Processing Locus CUFF.955_From_ws_0_3340488_W [******* ] > Processing Locus CUFF.967_From_zu_0_3022629_W [******* ] > Processing Locus CUFF.969_From_zu_0_3190435_W [******** ] > Processing Locus CUFF.971_From_zu_0_3255169_W [******** ] > Processing Locus CUFF.977_From_zu_0_3255503_W [******** ] > Processing Locus CUFF.991_From_zu_0_3277661_W [******** ] > Processing Locus CUFF.993_From_zu_0_3082201_W [******** ] > Processed 87 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5522.80 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:19:19] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 1% > Processing Locus CUFF.567_From_can_0_3258779 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.583_From_ct_1_3302721_ [* ] 5% > Processing Locus CUFF.589_From_edi_0_2723255 [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 8% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.597_From_edi_0_2759827 [** ] 10% > Processing Locus CUFF.599_From_edi_0_2744702 [** ] 11% > Processing Locus CUFF.609_From_hi_0_2755116_ [*** ] 12% > Processing Locus CUFF.611_From_edi_0_2921730 [*** ] 13% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 14% > Processing Locus CUFF.623_From_hi_0_2778596_ [**** ] 16% > Processing Locus CUFF.627_From_edi_0_2889434 [**** ] 17% > Processing Locus CUFF.627_From_edi_0_2889434 [**** ] 18% > Processing Locus CUFF.629_From_kn_0_3594465_ [**** ] 19% > Processing Locus CUFF.637_From_kn_0_3626969_ [***** ] 20% > Processing Locus CUFF.639_From_hi_0_2916184_ [***** ] 21% > Processing Locus CUFF.641_From_kn_0_3605300_ [***** ] 22% > Processing Locus CUFF.643_From_kn_0_3799876_ [****** ] 24% > Processing Locus CUFF.645_From_edi_0_2888586 [****** ] 25% > Processing Locus CUFF.649_From_kn_0_3617271_ [****** ] 26% > Processing Locus CUFF.663_From_kn_0_3613403_ [****** ] 27% > Processing Locus CUFF.665_From_hi_0_2939638_ [******* ] 28% > Processing Locus CUFF.666_From_ler_0_4004770 [******* ] 29% > Processing Locus CUFF.671_From_edi_0_2859720 [******* ] 31% > Processing Locus CUFF.679_From_ler_0_3998410 [******** ] 32% > Processing Locus CUFF.685_From_mt_0_4231054_ [******** ] 33% > Processing Locus CUFF.687_From_mt_0_4230874_ [******** ] 34% > Processing Locus CUFF.689_From_ler_0_4018856 [******** ] 35% > Processing Locus CUFF.691_From_hi_0_2961678_ [********* ] 36% > Processing Locus CUFF.695_From_mt_0_4217716_ [********* ] 37% > Processing Locus CUFF.699_From_no_0_2905273_ [********* ] 39% > Processing Locus CUFF.701_From_no_0_2951521_ [********** ] 40% > Processing Locus CUFF.703_From_no_0_2885444_ [********** ] 41% > Processing Locus CUFF.707_From_no_0_2959683_ [********** ] 42% > Processing Locus CUFF.711_From_no_0_3088052_ [********** ] 43% > Processing Locus CUFF.721_From_no_0_3120392_ [*********** ] 44% > Processing Locus CUFF.721_From_no_0_3120392_ [*********** ] 45% > Processing Locus CUFF.721_From_no_0_3120392_ [*********** ] 47% > Processing Locus CUFF.721_From_no_0_3120392_ [************ ] 48% > Processing Locus CUFF.721_From_no_0_3120392_ [************ ] 49% > Processing Locus CUFF.727_From_hi_0_2953648_ [************ ] 50% > Processing Locus CUFF.733_From_no_0_2956652_ [************ ] 51% > Processing Locus CUFF.737_From_ct_1_3132277_ [************* ] 52% > Processing Locus CUFF.743_From_po_0_3330421_ [************* ] 54% > Processing Locus CUFF.755_From_mt_0_4193196_ [************* ] 55% > Processing Locus CUFF.763_From_rsch_4_403203 [************** ] 56% > Processing Locus CUFF.767_From_rsch_4_411814 [************** ] 57% > Processing Locus CUFF.769_From_rsch_4_410762 [************** ] 58% > Processing Locus CUFF.775_From_rsch_4_409124 [************** ] 59% > Processing Locus CUFF.777_From_rsch_4_408506 [*************** ] 60% > Processing Locus CUFF.779_From_rsch_4_421454 [*************** ] 62% > Processing Locus CUFF.783_From_oy_0_2965192_ [*************** ] 63% > Processing Locus CUFF.791_From_rsch_4_425553 [**************** ] 64% > Processing Locus CUFF.795_From_rsch_4_429714 [**************** ] 65% > Processing Locus CUFF.801_From_sf_2_2532172_ [**************** ] 66% > Processing Locus CUFF.811_From_sf_2_2459023_ [**************** ] 67% > Processing Locus CUFF.819_From_tsu_0_3036945 [***************** ] 68% > Processing Locus CUFF.827_From_rsch_4_427728 [***************** ] 70% > Processing Locus CUFF.839_From_sf_2_2680171_ [***************** ] 71% > Processing Locus CUFF.843_From_rsch_4_429219 [****************** ] 72% > Processing Locus CUFF.843_From_rsch_4_429219 [****************** ] 73% > Processing Locus CUFF.855_From_wil_2_2915899 [****************** ] 74% > Processing Locus CUFF.861_From_mt_0_4528444_ [****************** ] 75% > Processing Locus CUFF.871_From_rsch_4_426655 [******************* ] 77% > Processing Locus CUFF.873_From_wil_2_3050523 [******************* ] 78% > Processing Locus CUFF.877_From_sf_2_2687786_ [******************* ] 79% > Processing Locus CUFF.879_From_rsch_4_405516 [******************** ] 80% > Processing Locus CUFF.881_From_wil_2_2925323 [******************** ] 81% > Processing Locus CUFF.893_From_ws_0_3190679_ [******************** ] 82% > Processing Locus CUFF.907_From_ws_0_3182508_ [******************** ] 83% > Processing Locus CUFF.913_From_wil_2_2834553 [********************* ] 85% > Processing Locus CUFF.927_From_wu_0_2655481_ [********************* ] 86% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************* ] 87% > Processing Locus CUFF.937_From_ws_0_3373604_ [********************** ] 88% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************** ] 89% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************** ] 90% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************** ] 91% > Processing Locus CUFF.967_From_zu_0_3022629_ [*********************** ] 93% > Processing Locus CUFF.969_From_zu_0_3190435_ [*********************** ] 94% > Processing Locus CUFF.971_From_zu_0_3255169_ [*********************** ] 95% > Processing Locus CUFF.977_From_zu_0_3255503_ [************************ ] 96% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 97% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 98% > Processed 87 loci. [*************************] 100% [16:19:19] Loading reference annotation and sequence [16:19:19] Learning bias parameters. > Processing Locus CUFF.551_From_can_0_3122480 [ ] 0% > Processing Locus CUFF.567_From_can_0_3258779 [ ] 1% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 2% > Processing Locus CUFF.575_From_ct_1_3082021_ [ ] 3% > Processing Locus CUFF.589_From_edi_0_2723255 [* ] 4% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 5% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 6% > Processing Locus CUFF.597_From_edi_0_2759827 [** ] 8% > Processing Locus CUFF.599_From_edi_0_2744702 [** ] 9% > Processing Locus CUFF.611_From_edi_0_2921730 [** ] 10% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 11% > Processing Locus CUFF.623_From_hi_0_2778596_ [*** ] 12% > Processing Locus CUFF.627_From_edi_0_2889434 [*** ] 13% > Processing Locus CUFF.627_From_edi_0_2889434 [*** ] 14% > Processing Locus CUFF.629_From_kn_0_3594465_ [**** ] 16% > Processing Locus CUFF.637_From_kn_0_3626969_ [**** ] 17% > Processing Locus CUFF.641_From_kn_0_3605300_ [**** ] 18% > Processing Locus CUFF.643_From_kn_0_3799876_ [**** ] 19% > Processing Locus CUFF.645_From_edi_0_2888586 [***** ] 20% > Processing Locus CUFF.649_From_kn_0_3617271_ [***** ] 21% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 22% > Processing Locus CUFF.665_From_hi_0_2939638_ [****** ] 24% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 26% > Processing Locus CUFF.685_From_mt_0_4231054_ [****** ] 27% > Processing Locus CUFF.687_From_mt_0_4230874_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.691_From_hi_0_2961678_ [******* ] 31% > Processing Locus CUFF.695_From_mt_0_4217716_ [******** ] 32% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 33% > Processing Locus CUFF.701_From_no_0_2951521_ [******** ] 34% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 35% > Processing Locus CUFF.707_From_no_0_2959683_ [********* ] 36% > Processing Locus CUFF.711_From_no_0_3088052_ [********* ] 37% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 39% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 40% > Processing Locus CUFF.743_From_po_0_3330421_ [********** ] 41% > Processing Locus CUFF.755_From_mt_0_4193196_ [********** ] 42% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 43% > Processing Locus CUFF.767_From_rsch_4_411814 [*********** ] 44% > Processing Locus CUFF.769_From_rsch_4_410762 [*********** ] 45% > Processing Locus CUFF.777_From_rsch_4_408506 [*********** ] 47% > Processing Locus CUFF.779_From_rsch_4_421454 [************ ] 48% > Processing Locus CUFF.783_From_oy_0_2965192_ [************ ] 49% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 50% > Processing Locus CUFF.795_From_rsch_4_429714 [************ ] 51% > Processing Locus CUFF.801_From_sf_2_2532172_ [************* ] 52% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 54% > Processing Locus CUFF.827_From_rsch_4_427728 [************* ] 55% > Processing Locus CUFF.839_From_sf_2_2680171_ [************** ] 56% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 57% > Processing Locus CUFF.861_From_mt_0_4528444_ [************** ] 58% > Processing Locus CUFF.873_From_wil_2_3050523 [************** ] 59% > Processing Locus CUFF.877_From_sf_2_2687786_ [*************** ] 60% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 62% > Processing Locus CUFF.881_From_wil_2_2925323 [*************** ] 63% > Processing Locus CUFF.927_From_wu_0_2655481_ [**************** ] 64% > Processing Locus CUFF.935_From_ws_0_3380934_ [**************** ] 65% > Processing Locus CUFF.937_From_ws_0_3373604_ [**************** ] 66% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 67% > Processing Locus CUFF.947_From_wu_0_2654219_ [***************** ] 68% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 70% > Processing Locus CUFF.971_From_zu_0_3255169_ [***************** ] 71% > Processing Locus CUFF.977_From_zu_0_3255503_ [****************** ] 72% > Processing Locus CUFF.991_From_zu_0_3277661_ [****************** ] 73% > Processing Locus CUFF.993_From_zu_0_3082201_ [****************** ] 74% > Processed 66 loci. [*************************] 100% [16:19:19] Assembling transcripts and estimating abundances. > Processing Locus CUFF.551_From_can_0_3122480 [ ] 0% > Processing Locus CUFF.567_From_can_0_3258779 [ ] 1% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 2% > Processing Locus CUFF.575_From_ct_1_3082021_ [ ] 3% > Processing Locus CUFF.589_From_edi_0_2723255 [* ] 4% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 5% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 6% > Processing Locus CUFF.597_From_edi_0_2759827 [** ] 8% > Processing Locus CUFF.599_From_edi_0_2744702 [** ] 9% > Processing Locus CUFF.611_From_edi_0_2921730 [** ] 10% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 11% > Processing Locus CUFF.623_From_hi_0_2778596_ [*** ] 12% > Processing Locus CUFF.627_From_edi_0_2889434 [*** ] 13% > Processing Locus CUFF.627_From_edi_0_2889434 [*** ] 14% > Processing Locus CUFF.629_From_kn_0_3594465_ [**** ] 16% > Processing Locus CUFF.637_From_kn_0_3626969_ [**** ] 17% > Processing Locus CUFF.641_From_kn_0_3605300_ [**** ] 18% > Processing Locus CUFF.643_From_kn_0_3799876_ [**** ] 19% > Processing Locus CUFF.645_From_edi_0_2888586 [***** ] 20% > Processing Locus CUFF.649_From_kn_0_3617271_ [***** ] 21% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 22% > Processing Locus CUFF.665_From_hi_0_2939638_ [****** ] 24% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 26% > Processing Locus CUFF.685_From_mt_0_4231054_ [****** ] 27% > Processing Locus CUFF.687_From_mt_0_4230874_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.691_From_hi_0_2961678_ [******* ] 31% > Processing Locus CUFF.695_From_mt_0_4217716_ [******** ] 32% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 33% > Processing Locus CUFF.701_From_no_0_2951521_ [******** ] 34% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 35% > Processing Locus CUFF.707_From_no_0_2959683_ [********* ] 36% > Processing Locus CUFF.711_From_no_0_3088052_ [********* ] 37% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 39% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 40% > Processing Locus CUFF.743_From_po_0_3330421_ [********** ] 41% > Processing Locus CUFF.755_From_mt_0_4193196_ [********** ] 42% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 43% > Processing Locus CUFF.767_From_rsch_4_411814 [*********** ] 44% > Processing Locus CUFF.769_From_rsch_4_410762 [*********** ] 45% > Processing Locus CUFF.777_From_rsch_4_408506 [*********** ] 47% > Processing Locus CUFF.779_From_rsch_4_421454 [************ ] 48% > Processing Locus CUFF.783_From_oy_0_2965192_ [************ ] 49% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 50% > Processing Locus CUFF.795_From_rsch_4_429714 [************ ] 51% > Processing Locus CUFF.801_From_sf_2_2532172_ [************* ] 52% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 54% > Processing Locus CUFF.827_From_rsch_4_427728 [************* ] 55% > Processing Locus CUFF.839_From_sf_2_2680171_ [************** ] 56% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 57% > Processing Locus CUFF.861_From_mt_0_4528444_ [************** ] 58% > Processing Locus CUFF.873_From_wil_2_3050523 [************** ] 59% > Processing Locus CUFF.877_From_sf_2_2687786_ [*************** ] 60% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 62% > Processing Locus CUFF.881_From_wil_2_2925323 [*************** ] 63% > Processing Locus CUFF.927_From_wu_0_2655481_ [**************** ] 64% > Processing Locus CUFF.935_From_ws_0_3380934_ [**************** ] 65% > Processing Locus CUFF.937_From_ws_0_3373604_ [**************** ] 66% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 67% > Processing Locus CUFF.947_From_wu_0_2654219_ [***************** ] 68% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 70% > Processing Locus CUFF.971_From_zu_0_3255169_ [***************** ] 71% > Processing Locus CUFF.977_From_zu_0_3255503_ [****************** ] 72% > Processing Locus CUFF.991_From_zu_0_3277661_ [****************** ] 73% > Processing Locus CUFF.993_From_zu_0_3082201_ [****************** ] 74% > Processed 66 loci. [*************************] 100% [Mon Apr 4 16:19:30 2011] Retrieving sequences for splices [Mon Apr 4 16:19:30 2011] Indexing splices [Mon Apr 4 16:19:30 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:19:33 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:19:36 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:19:39 2011] Joining segment hits [Mon Apr 4 16:19:41 2011] Retrieving sequences for splices [Mon Apr 4 16:19:41 2011] Indexing splices [Mon Apr 4 16:19:42 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:19:42 2011] Reporting output tracks [Mon Apr 4 16:19:44 2011] Mapping reads against segment_juncs with Bowtie ----------------------------------------------- Run complete [00:02:01 elapsed] [Mon Apr 4 16:19:46 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:19:49 2011] Joining segment hits [Mon Apr 4 16:19:51 2011] Reporting output tracks cufflinks -p 4 -o ./Can_0 -r ngene.fa ./Can_0/accepted_hits.bam [16:19:52] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.525_From_bur_0_1863298Û [ ] > Processing Locus CUFF.527_From_bur_0_1967596Û [ ] > Processing Locus CUFF.531_From_bur_0_1868430Û [ ] > Processing Locus CUFF.535_From_bur_0_1969548Û [ ] > Processing Locus CUFF.537_From_bur_0_1999718Û [ ] > Processing Locus CUFF.541_From_can_0_3059433Û [ ] > Processing Locus CUFF.543_From_can_0_3017860Û [ ] > Processing Locus CUFF.545_From_bur_0_1856286Û [ ] > Processing Locus CUFF.549_From_can_0_3216099Û [ ] > Processing Locus CUFF.551_From_can_0_3122480Û [ ] > Processing Locus CUFF.553_From_can_0_3223655Û [* ] > Processing Locus CUFF.555_From_can_0_3217045Û [* ] > Processing Locus CUFF.557_From_can_0_3234869Û [* ] > Processing Locus CUFF.559_From_can_0_3231205Û [* ] > Processing Locus CUFF.565_From_can_0_3257137Û [* ] > Processing Locus CUFF.567_From_can_0_3258779Û [* ] > Processing Locus CUFF.569_From_can_0_3263637Û [* ] > Processing Locus CUFF.571_From_can_0_3076940Û [* ] > Processing Locus CUFF.573_From_can_0_3233581Û [* ] > Processing Locus CUFF.575_From_ct_1_3082021_Û [** ] > Processing Locus CUFF.581_From_can_0_3218459Û [** ] > Processing Locus CUFF.583_From_ct_1_3302721_Û [** ] > Processing Locus CUFF.585_From_ct_1_3247037_Û [** ] > Processing Locus CUFF.587_From_ct_1_3277323_Û [** ] > Processing Locus CUFF.589_From_edi_0_2723255Û [** ] > Processing Locus CUFF.591_From_can_0_3239881Û [** ] > Processing Locus CUFF.593_From_can_0_3270131Û [** ] > Processing Locus CUFF.595_From_ct_1_3302721_Û [** ] > Processing Locus CUFF.603_From_bur_0_2025286Û [** ] > Processing Locus CUFF.609_From_hi_0_2755116_Û [*** ] > Processing Locus CUFF.611_From_edi_0_2921730Û [*** ] > Processing Locus CUFF.613_From_hi_0_2773206_Û [*** ] > Processing Locus CUFF.619_From_edi_0_2871668Û [*** ] > Processing Locus CUFF.621_From_edi_0_2934714Û [*** ] > Processing Locus CUFF.621_From_edi_0_2934714Û [*** ] > Processing Locus CUFF.623_From_hi_0_2778596_Û [*** ] > Processing Locus CUFF.629_From_kn_0_3594465_Û [*** ] > Processing Locus CUFF.635_From_ct_1_3241157_Û [*** ] > Processing Locus CUFF.637_From_kn_0_3626969_Û [*** ] > Processing Locus CUFF.645_From_edi_0_2888586Û [**** ] > Processing Locus CUFF.649_From_kn_0_3617271_Û [**** ] > Processing Locus CUFF.653_From_kn_0_3751597_Û [**** ] > Processing Locus CUFF.663_From_kn_0_3613403_Û [**** ] > Processing Locus CUFF.665_From_hi_0_2939638_Û [**** ] > Processing Locus CUFF.666_From_ler_0_4004770Û [**** ] > Processing Locus CUFF.671_From_edi_0_2859720Û [**** ] > Processing Locus CUFF.677_From_ct_1_3133995_Û [**** ] > Processing Locus CUFF.679_From_ler_0_3998410Û [**** ] > Processing Locus CUFF.685_From_mt_0_4231054_Û [**** ] > Processing Locus CUFF.689_From_ler_0_4018856Û [***** ] > Processing Locus CUFF.691_From_hi_0_2961678_Û [***** ] > Processing Locus CUFF.695_From_mt_0_4217716_Û [***** ] > Processing Locus CUFF.697_From_mt_0_4229662_Û [***** ] > Processing Locus CUFF.699_From_no_0_2905273_Û [***** ] > Processing Locus CUFF.701_From_no_0_2951521_Û [***** ] > Processing Locus CUFF.703_From_no_0_2885444_Û [***** ] > Processing Locus CUFF.707_From_no_0_2959683_Û [***** ] > Processing Locus CUFF.725_From_no_0_3116640_Û [***** ] > Processing Locus CUFF.729_From_oy_0_3001818_Û [****** ] > Processing Locus CUFF.733_From_no_0_2956652_Û [****** ] > Processing Locus CUFF.737_From_ct_1_3132277_Û [****** ] > Processing Locus CUFF.739_From_po_0_3340213_Û [****** ] > Processing Locus CUFF.741_From_po_0_3382155_Û [****** ] > Processing Locus CUFF.743_From_po_0_3330421_Û [****** ] > Processing Locus CUFF.747_From_po_0_3299272_Û [****** ] > Processing Locus CUFF.749_From_oy_0_3162092_Û [****** ] > Processing Locus CUFF.751_From_rsch_4_403485Û [****** ] > Processing Locus CUFF.755_From_mt_0_4193196_Û [****** ] > Processing Locus CUFF.763_From_rsch_4_403203Û [******* ] > Processing Locus CUFF.767_From_rsch_4_411814Û [******* ] > Processing Locus CUFF.769_From_rsch_4_410762Û [******* ] > Processing Locus CUFF.771_From_po_0_3332479_Û [******* ] > Processing Locus CUFF.775_From_rsch_4_409124Û [******* ] > Processing Locus CUFF.777_From_rsch_4_408506Û [******* ] > Processing Locus CUFF.779_From_rsch_4_421454Û [******* ] > Processing Locus CUFF.785_From_no_0_3128142_Û [******* ] > Processing Locus CUFF.785_From_no_0_3128142_Û [******* ] > Processing Locus CUFF.791_From_rsch_4_425553Û [******* ] > Processing Locus CUFF.795_From_rsch_4_429714Û [******** ] > Processing Locus CUFF.801_From_sf_2_2532172_Û [******** ] > Processing Locus CUFF.805_From_sf_2_2486157_Û [******** ] > Processing Locus CUFF.809_From_sf_2_2682779_Û [******** ] > Processing Locus CUFF.811_From_sf_2_2459023_Û [******** ] > Processing Locus CUFF.819_From_tsu_0_3036945Û [******** ] > Processing Locus CUFF.829_From_tsu_0_3135135Û [******** ] > Processing Locus CUFF.831_From_sf_2_2687774_Û [******** ] > Processing Locus CUFF.839_From_sf_2_2680171_Û [******** ] > Processing Locus CUFF.843_From_rsch_4_429219Û [********* ] > Processing Locus CUFF.843_From_rsch_4_429219Û [********* ] > Processing Locus CUFF.855_From_wil_2_2915899Û [********* ] > Processing Locus CUFF.861_From_mt_0_4528444_Û [********* ] > Processing Locus CUFF.861_From_mt_0_4528444_Û [********* ] > Processing Locus CUFF.865_From_wil_2_2892485Û [********* ] > Processing Locus CUFF.873_From_wil_2_3050523Û [********* ] > Processing Locus CUFF.877_From_sf_2_2687786_Û [********* ] > Processing Locus CUFF.879_From_rsch_4_405516Û [********* ] > Processing Locus CUFF.881_From_wil_2_2925323Û [********* ] > Processing Locus CUFF.883_From_wil_2_3066229Û [********* ] > Processing Locus CUFF.893_From_ws_0_3190679_Û [********* ] > Processing Locus CUFF.895_From_tsu_0_3215821Û [********** ] > Processing Locus CUFF.907_From_ws_0_3182508_Û [********** ] > Processing Locus CUFF.909_From_wil_2_3052273Û [********** ] > Processing Locus CUFF.913_From_wil_2_2834553Û [********** ] > Processing Locus CUFF.935_From_ws_0_3380934_Û [********** ] > Processing Locus CUFF.943_From_zu_0_3075813_Û [********** ] > Processing Locus CUFF.945_From_wu_0_2678387_Û [********** ] > Processing Locus CUFF.947_From_wu_0_2654219_Û [********** ] > Processing Locus CUFF.955_From_ws_0_3340488_Û [********** ] > Processing Locus CUFF.957_From_ws_0_3381390_Û [*********** ] > Processing Locus CUFF.961_From_wu_0_2837848_Û [*********** ] > Processing Locus CUFF.963_From_zu_0_3092045_Û [*********** ] > Processing Locus CUFF.965_From_zu_0_3238769_Û [*********** ] > Processing Locus CUFF.965_From_zu_0_3238769_Û [*********** ] > Processing Locus CUFF.967_From_zu_0_3022629_Û [*********** ] > Processing Locus CUFF.971_From_zu_0_3255169_Û [*********** ] > Processing Locus CUFF.971_From_zu_0_3255169_Û [*********** ] > Processing Locus CUFF.973_From_zu_0_3242889_Û [*********** ] > Processing Locus CUFF.977_From_zu_0_3255503_Û [*********** ] > Processing Locus CUFF.979_From_zu_0_3278243_Û [*********** ] > Processing Locus CUFF.987_From_zu_0_3118546_Û [*********** ] > Processing Locus CUFF.991_From_zu_0_3277661_Û [************ ] > Processing Locus CUFF.993_From_zu_0_3082201_Û [************ ] > Processed 122 loci. [*************************] 100% > Map Properties: > Total Map Mass: 10769.79 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:19:52] Assembling transcripts and estimating abundances. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.527_From_bur_0_1967596 [ ] 0% > Processing Locus CUFF.531_From_bur_0_1868430 [ ] 1% > Processing Locus CUFF.535_From_bur_0_1969548 [ ] 2% > Processing Locus CUFF.537_From_bur_0_1999718 [ ] 3% > Processing Locus CUFF.541_From_can_0_3059433 [* ] 4% > Processing Locus CUFF.543_From_can_0_3017860 [* ] 4% > Processing Locus CUFF.545_From_bur_0_1856286 [* ] 5% > Processing Locus CUFF.549_From_can_0_3216099 [* ] 6% > Processing Locus CUFF.551_From_can_0_3122480 [* ] 7% > Processing Locus CUFF.553_From_can_0_3223655 [** ] 8% > Processing Locus CUFF.555_From_can_0_3217045 [** ] 9% > Processing Locus CUFF.557_From_can_0_3234869 [** ] 9% > Processing Locus CUFF.559_From_can_0_3231205 [** ] 10% > Processing Locus CUFF.565_From_can_0_3257137 [** ] 11% > Processing Locus CUFF.567_From_can_0_3258779 [*** ] 12% > Processing Locus CUFF.569_From_can_0_3263637 [*** ] 13% > Processing Locus CUFF.571_From_can_0_3076940 [*** ] 13% > Processing Locus CUFF.573_From_can_0_3233581 [*** ] 14% > Processing Locus CUFF.575_From_ct_1_3082021_ [*** ] 15% > Processing Locus CUFF.581_From_can_0_3218459 [**** ] 16% > Processing Locus CUFF.583_From_ct_1_3302721_ [**** ] 17% > Processing Locus CUFF.585_From_ct_1_3247037_ [**** ] 18% > Processing Locus CUFF.587_From_ct_1_3277323_ [**** ] 18% > Processing Locus CUFF.589_From_edi_0_2723255 [**** ] 19% > Processing Locus CUFF.591_From_can_0_3239881 [***** ] 20% > Processing Locus CUFF.593_From_can_0_3270131 [***** ] 21% > Processing Locus CUFF.595_From_ct_1_3302721_ [***** ] 22% > Processing Locus CUFF.603_From_bur_0_2025286 [***** ] 22% > Processing Locus CUFF.609_From_hi_0_2755116_ [***** ] 23% > Processing Locus CUFF.611_From_edi_0_2921730 [****** ] 24% > Processing Locus CUFF.613_From_hi_0_2773206_ [****** ] 25% > Processing Locus CUFF.619_From_edi_0_2871668 [****** ] 26% > Processing Locus CUFF.621_From_edi_0_2934714 [****** ] 27% > Processing Locus CUFF.621_From_edi_0_2934714 [****** ] 27% > Processing Locus CUFF.623_From_hi_0_2778596_ [******* ] 28% > Processing Locus CUFF.629_From_kn_0_3594465_ [******* ] 29% > Processing Locus CUFF.635_From_ct_1_3241157_ [******* ] 30% > Processing Locus CUFF.637_From_kn_0_3626969_ [******* ] 31% > Processing Locus CUFF.645_From_edi_0_2888586 [******* ] 31% > Processing Locus CUFF.649_From_kn_0_3617271_ [******** ] 32% > Processing Locus CUFF.653_From_kn_0_3751597_ [******** ] 33% > Processing Locus CUFF.663_From_kn_0_3613403_ [******** ] 34% > Processing Locus CUFF.665_From_hi_0_2939638_ [******** ] 35% > Processing Locus CUFF.666_From_ler_0_4004770 [********* ] 36% > Processing Locus CUFF.671_From_edi_0_2859720 [********* ] 36% > Processing Locus CUFF.677_From_ct_1_3133995_ [********* ] 37% > Processing Locus CUFF.679_From_ler_0_3998410 [********* ] 38% > Processing Locus CUFF.685_From_mt_0_4231054_ [********* ] 39% > Processing Locus CUFF.689_From_ler_0_4018856 [********** ] 40% > Processing Locus CUFF.691_From_hi_0_2961678_ [********** ] 40% > Processing Locus CUFF.695_From_mt_0_4217716_ [********** ] 41% > Processing Locus CUFF.697_From_mt_0_4229662_ [********** ] 42% > Processing Locus CUFF.699_From_no_0_2905273_ [********** ] 43% > Processing Locus CUFF.701_From_no_0_2951521_ [*********** ] 44% > Processing Locus CUFF.703_From_no_0_2885444_ [*********** ] 45% > Processing Locus CUFF.707_From_no_0_2959683_ [*********** ] 45% > Processing Locus CUFF.725_From_no_0_3116640_ [*********** ] 46% > Processing Locus CUFF.729_From_oy_0_3001818_ [*********** ] 47% > Processing Locus CUFF.733_From_no_0_2956652_ [************ ] 48% > Processing Locus CUFF.737_From_ct_1_3132277_ [************ ] 49% > Processing Locus CUFF.739_From_po_0_3340213_ [************ ] 50% > Processing Locus CUFF.741_From_po_0_3382155_ [************ ] 50% > Processing Locus CUFF.743_From_po_0_3330421_ [************ ] 51% > Processing Locus CUFF.747_From_po_0_3299272_ [************* ] 52% > Processing Locus CUFF.749_From_oy_0_3162092_ [************* ] 53% > Processing Locus CUFF.751_From_rsch_4_403485 [************* ] 54% > Processing Locus CUFF.755_From_mt_0_4193196_ [************* ] 54% > Processing Locus CUFF.763_From_rsch_4_403203 [************* ] 55% > Processing Locus CUFF.767_From_rsch_4_411814 [************** ] 56% > Processing Locus CUFF.769_From_rsch_4_410762 [************** ] 57% > Processing Locus CUFF.771_From_po_0_3332479_ [************** ] 58% > Processing Locus CUFF.775_From_rsch_4_409124 [************** ] 59% > Processing Locus CUFF.777_From_rsch_4_408506 [************** ] 59% > Processing Locus CUFF.779_From_rsch_4_421454 [*************** ] 60% > Processing Locus CUFF.785_From_no_0_3128142_ [*************** ] 61% > Processing Locus CUFF.785_From_no_0_3128142_ [*************** ] 62% > Processing Locus CUFF.791_From_rsch_4_425553 [*************** ] 63% > Processing Locus CUFF.795_From_rsch_4_429714 [*************** ] 63% > Processing Locus CUFF.801_From_sf_2_2532172_ [**************** ] 64% > Processing Locus CUFF.805_From_sf_2_2486157_ [**************** ] 65% > Processing Locus CUFF.809_From_sf_2_2682779_ [**************** ] 66% > Processing Locus CUFF.811_From_sf_2_2459023_ [**************** ] 67% > Processing Locus CUFF.819_From_tsu_0_3036945 [***************** ] 68% > Processing Locus CUFF.829_From_tsu_0_3135135 [***************** ] 68% > Processing Locus CUFF.831_From_sf_2_2687774_ [***************** ] 69% > Processing Locus CUFF.839_From_sf_2_2680171_ [***************** ] 70% > Processing Locus CUFF.843_From_rsch_4_429219 [***************** ] 71% > Processing Locus CUFF.843_From_rsch_4_429219 [****************** ] 72% > Processing Locus CUFF.855_From_wil_2_2915899 [****************** ] 72% > Processing Locus CUFF.861_From_mt_0_4528444_ [****************** ] 73% > Processing Locus CUFF.861_From_mt_0_4528444_ [****************** ] 74% > Processing Locus CUFF.865_From_wil_2_2892485 [****************** ] 75% > Processing Locus CUFF.873_From_wil_2_3050523 [******************* ] 76% > Processing Locus CUFF.877_From_sf_2_2687786_ [******************* ] 77% > Processing Locus CUFF.879_From_rsch_4_405516 [******************* ] 77% > Processing Locus CUFF.881_From_wil_2_2925323 [******************* ] 78% > Processing Locus CUFF.883_From_wil_2_3066229 [******************* ] 79% > Processing Locus CUFF.893_From_ws_0_3190679_ [******************** ] 80% > Processing Locus CUFF.895_From_tsu_0_3215821 [******************** ] 81% > Processing Locus CUFF.907_From_ws_0_3182508_ [******************** ] 81% > Processing Locus CUFF.909_From_wil_2_3052273 [******************** ] 82% > Processing Locus CUFF.913_From_wil_2_2834553 [******************** ] 83% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************* ] 84% > Processing Locus CUFF.943_From_zu_0_3075813_ [********************* ] 85% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************* ] 86% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************* ] 86% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************* ] 87% > Processing Locus CUFF.957_From_ws_0_3381390_ [********************** ] 88% > Processing Locus CUFF.961_From_wu_0_2837848_ [********************** ] 89% > Processing Locus CUFF.963_From_zu_0_3092045_ [********************** ] 90% > Processing Locus CUFF.965_From_zu_0_3238769_ [********************** ] 90% > Processing Locus CUFF.965_From_zu_0_3238769_ [********************** ] 91% > Processing Locus CUFF.967_From_zu_0_3022629_ [*********************** ] 92% > Processing Locus CUFF.971_From_zu_0_3255169_ [*********************** ] 93% > Processing Locus CUFF.971_From_zu_0_3255169_ [*********************** ] 94% > Processing Locus CUFF.973_From_zu_0_3242889_ [*********************** ] 95% > Processing Locus CUFF.977_From_zu_0_3255503_ [*********************** ] 95% > Processing Locus CUFF.979_From_zu_0_3278243_ [************************ ] 96% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 97% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 98% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 99% > Processed 122 loci. [*************************] 100% [16:19:52] Loading reference annotation and sequence [16:19:52] Learning bias parameters. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.535_From_bur_0_1969548 [ ] 0% > Processing Locus CUFF.541_From_can_0_3059433 [ ] 1% > Processing Locus CUFF.543_From_can_0_3017860 [ ] 2% > Processing Locus CUFF.549_From_can_0_3216099 [ ] 3% > Processing Locus CUFF.551_From_can_0_3122480 [* ] 4% > Processing Locus CUFF.553_From_can_0_3223655 [* ] 4% > Processing Locus CUFF.555_From_can_0_3217045 [* ] 5% > Processing Locus CUFF.557_From_can_0_3234869 [* ] 6% > Processing Locus CUFF.559_From_can_0_3231205 [* ] 7% > Processing Locus CUFF.565_From_can_0_3257137 [** ] 8% > Processing Locus CUFF.567_From_can_0_3258779 [** ] 9% > Processing Locus CUFF.569_From_can_0_3263637 [** ] 9% > Processing Locus CUFF.571_From_can_0_3076940 [** ] 10% > Processing Locus CUFF.573_From_can_0_3233581 [** ] 11% > Processing Locus CUFF.575_From_ct_1_3082021_ [*** ] 12% > Processing Locus CUFF.581_From_can_0_3218459 [*** ] 13% > Processing Locus CUFF.587_From_ct_1_3277323_ [*** ] 13% > Processing Locus CUFF.589_From_edi_0_2723255 [*** ] 14% > Processing Locus CUFF.591_From_can_0_3239881 [*** ] 15% > Processing Locus CUFF.593_From_can_0_3270131 [**** ] 16% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 17% > Processing Locus CUFF.603_From_bur_0_2025286 [**** ] 18% > Processing Locus CUFF.609_From_hi_0_2755116_ [**** ] 18% > Processing Locus CUFF.619_From_edi_0_2871668 [**** ] 19% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 20% > Processing Locus CUFF.629_From_kn_0_3594465_ [***** ] 21% > Processing Locus CUFF.635_From_ct_1_3241157_ [***** ] 22% > Processing Locus CUFF.637_From_kn_0_3626969_ [***** ] 22% > Processing Locus CUFF.645_From_edi_0_2888586 [***** ] 23% > Processing Locus CUFF.649_From_kn_0_3617271_ [****** ] 24% > Processing Locus CUFF.663_From_kn_0_3613403_ [****** ] 25% > Processing Locus CUFF.665_From_hi_0_2939638_ [****** ] 26% > Processing Locus CUFF.666_From_ler_0_4004770 [****** ] 27% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 27% > Processing Locus CUFF.679_From_ler_0_3998410 [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 30% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 31% > Processing Locus CUFF.699_From_no_0_2905273_ [******* ] 31% > Processing Locus CUFF.701_From_no_0_2951521_ [******** ] 32% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 33% > Processing Locus CUFF.707_From_no_0_2959683_ [******** ] 34% > Processing Locus CUFF.725_From_no_0_3116640_ [******** ] 35% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 36% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 36% > Processing Locus CUFF.737_From_ct_1_3132277_ [********* ] 37% > Processing Locus CUFF.743_From_po_0_3330421_ [********* ] 38% > Processing Locus CUFF.747_From_po_0_3299272_ [********* ] 39% > Processing Locus CUFF.751_From_rsch_4_403485 [********** ] 40% > Processing Locus CUFF.755_From_mt_0_4193196_ [********** ] 40% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 41% > Processing Locus CUFF.767_From_rsch_4_411814 [********** ] 42% > Processing Locus CUFF.769_From_rsch_4_410762 [********** ] 43% > Processing Locus CUFF.771_From_po_0_3332479_ [*********** ] 44% > Processing Locus CUFF.775_From_rsch_4_409124 [*********** ] 45% > Processing Locus CUFF.777_From_rsch_4_408506 [*********** ] 45% > Processing Locus CUFF.779_From_rsch_4_421454 [*********** ] 46% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 47% > Processing Locus CUFF.785_From_no_0_3128142_ [************ ] 48% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 49% > Processing Locus CUFF.795_From_rsch_4_429714 [************ ] 50% > Processing Locus CUFF.801_From_sf_2_2532172_ [************ ] 50% > Processing Locus CUFF.805_From_sf_2_2486157_ [************ ] 51% > Processing Locus CUFF.809_From_sf_2_2682779_ [************* ] 52% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 53% > Processing Locus CUFF.819_From_tsu_0_3036945 [************* ] 54% > Processing Locus CUFF.829_From_tsu_0_3135135 [************* ] 54% > Processing Locus CUFF.831_From_sf_2_2687774_ [************* ] 55% > Processing Locus CUFF.839_From_sf_2_2680171_ [************** ] 56% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 57% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 58% > Processing Locus CUFF.855_From_wil_2_2915899 [************** ] 59% > Processing Locus CUFF.861_From_mt_0_4528444_ [************** ] 59% > Processing Locus CUFF.865_From_wil_2_2892485 [*************** ] 60% > Processing Locus CUFF.873_From_wil_2_3050523 [*************** ] 61% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 62% > Processing Locus CUFF.895_From_tsu_0_3215821 [*************** ] 63% > Processing Locus CUFF.907_From_ws_0_3182508_ [*************** ] 63% > Processing Locus CUFF.909_From_wil_2_3052273 [**************** ] 64% > Processing Locus CUFF.913_From_wil_2_2834553 [**************** ] 65% > Processing Locus CUFF.943_From_zu_0_3075813_ [**************** ] 66% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 67% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 68% > Processing Locus CUFF.957_From_ws_0_3381390_ [***************** ] 68% > Processing Locus CUFF.961_From_wu_0_2837848_ [***************** ] 69% > Processing Locus CUFF.967_From_zu_0_3022629_ [***************** ] 70% > Processing Locus CUFF.971_From_zu_0_3255169_ [***************** ] 71% > Processing Locus CUFF.971_From_zu_0_3255169_ [****************** ] 72% > Processing Locus CUFF.973_From_zu_0_3242889_ [****************** ] 72% > Processing Locus CUFF.977_From_zu_0_3255503_ [****************** ] 73% > Processing Locus CUFF.979_From_zu_0_3278243_ [****************** ] 74% > Processing Locus CUFF.987_From_zu_0_3118546_ [****************** ] 75% > Processing Locus CUFF.991_From_zu_0_3277661_ [******************* ] 76% > Processing Locus CUFF.993_From_zu_0_3082201_ [******************* ] 77% > Processed 95 loci. [*************************] 100% [16:19:53] Assembling transcripts and estimating abundances. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.535_From_bur_0_1969548 [ ] 0% > Processing Locus CUFF.541_From_can_0_3059433 [ ] 1% > Processing Locus CUFF.543_From_can_0_3017860 [ ] 2% > Processing Locus CUFF.549_From_can_0_3216099 [ ] 3% > Processing Locus CUFF.551_From_can_0_3122480 [* ] 4% > Processing Locus CUFF.553_From_can_0_3223655 [* ] 4% > Processing Locus CUFF.555_From_can_0_3217045 [* ] 5% > Processing Locus CUFF.557_From_can_0_3234869 [* ] 6% > Processing Locus CUFF.559_From_can_0_3231205 [* ] 7% > Processing Locus CUFF.565_From_can_0_3257137 [** ] 8% > Processing Locus CUFF.567_From_can_0_3258779 [** ] 9% > Processing Locus CUFF.569_From_can_0_3263637 [** ] 9% > Processing Locus CUFF.571_From_can_0_3076940 [** ] 10% > Processing Locus CUFF.573_From_can_0_3233581 [** ] 11% > Processing Locus CUFF.575_From_ct_1_3082021_ [*** ] 12% > Processing Locus CUFF.581_From_can_0_3218459 [*** ] 13% > Processing Locus CUFF.587_From_ct_1_3277323_ [*** ] 13% > Processing Locus CUFF.589_From_edi_0_2723255 [*** ] 14% > Processing Locus CUFF.591_From_can_0_3239881 [*** ] 15% > Processing Locus CUFF.593_From_can_0_3270131 [**** ] 16% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 17% > Processing Locus CUFF.603_From_bur_0_2025286 [**** ] 18% > Processing Locus CUFF.609_From_hi_0_2755116_ [**** ] 18% > Processing Locus CUFF.619_From_edi_0_2871668 [**** ] 19% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 20% > Processing Locus CUFF.629_From_kn_0_3594465_ [***** ] 21% > Processing Locus CUFF.635_From_ct_1_3241157_ [***** ] 22% > Processing Locus CUFF.637_From_kn_0_3626969_ [***** ] 22% > Processing Locus CUFF.645_From_edi_0_2888586 [***** ] 23% > Processing Locus CUFF.649_From_kn_0_3617271_ [****** ] 24% > Processing Locus CUFF.663_From_kn_0_3613403_ [****** ] 25% > Processing Locus CUFF.665_From_hi_0_2939638_ [****** ] 26% > Processing Locus CUFF.666_From_ler_0_4004770 [****** ] 27% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 27% > Processing Locus CUFF.679_From_ler_0_3998410 [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 30% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 31% > Processing Locus CUFF.699_From_no_0_2905273_ [******* ] 31% > Processing Locus CUFF.701_From_no_0_2951521_ [******** ] 32% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 33% > Processing Locus CUFF.707_From_no_0_2959683_ [******** ] 34% > Processing Locus CUFF.725_From_no_0_3116640_ [******** ] 35% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 36% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 36% > Processing Locus CUFF.737_From_ct_1_3132277_ [********* ] 37% > Processing Locus CUFF.743_From_po_0_3330421_ [********* ] 38% > Processing Locus CUFF.747_From_po_0_3299272_ [********* ] 39% > Processing Locus CUFF.751_From_rsch_4_403485 [********** ] 40% > Processing Locus CUFF.755_From_mt_0_4193196_ [********** ] 40% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 41% > Processing Locus CUFF.767_From_rsch_4_411814 [********** ] 42% > Processing Locus CUFF.769_From_rsch_4_410762 [********** ] 43% > Processing Locus CUFF.771_From_po_0_3332479_ [*********** ] 44% > Processing Locus CUFF.775_From_rsch_4_409124 [*********** ] 45% > Processing Locus CUFF.777_From_rsch_4_408506 [*********** ] 45% > Processing Locus CUFF.779_From_rsch_4_421454 [*********** ] 46% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 47% > Processing Locus CUFF.785_From_no_0_3128142_ [************ ] 48% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 49% > Processing Locus CUFF.795_From_rsch_4_429714 [************ ] 50% > Processing Locus CUFF.801_From_sf_2_2532172_ [************ ] 50% > Processing Locus CUFF.805_From_sf_2_2486157_ [************ ] 51% > Processing Locus CUFF.809_From_sf_2_2682779_ [************* ] 52% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 53% > Processing Locus CUFF.819_From_tsu_0_3036945 [************* ] 54% > Processing Locus CUFF.829_From_tsu_0_3135135 [************* ] 54% > Processing Locus CUFF.831_From_sf_2_2687774_ [************* ] 55% > Processing Locus CUFF.839_From_sf_2_2680171_ [************** ] 56% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 57% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 58% > Processing Locus CUFF.855_From_wil_2_2915899 [************** ] 59% > Processing Locus CUFF.861_From_mt_0_4528444_ [************** ] 59% > Processing Locus CUFF.865_From_wil_2_2892485 [*************** ] 60% > Processing Locus CUFF.873_From_wil_2_3050523 [*************** ] 61% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 62% > Processing Locus CUFF.895_From_tsu_0_3215821 [*************** ] 63% > Processing Locus CUFF.907_From_ws_0_3182508_ [*************** ] 63% > Processing Locus CUFF.909_From_wil_2_3052273 [**************** ] 64% > Processing Locus CUFF.913_From_wil_2_2834553 [**************** ] 65% > Processing Locus CUFF.943_From_zu_0_3075813_ [**************** ] 66% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 67% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 68% > Processing Locus CUFF.957_From_ws_0_3381390_ [***************** ] 68% > Processing Locus CUFF.961_From_wu_0_2837848_ [***************** ] 69% > Processing Locus CUFF.967_From_zu_0_3022629_ [***************** ] 70% > Processing Locus CUFF.971_From_zu_0_3255169_ [***************** ] 71% > Processing Locus CUFF.971_From_zu_0_3255169_ [****************** ] 72% > Processing Locus CUFF.973_From_zu_0_3242889_ [****************** ] 72% > Processing Locus CUFF.977_From_zu_0_3255503_ [****************** ] 73% > Processing Locus CUFF.979_From_zu_0_3278243_ [****************** ] 74% > Processing Locus CUFF.987_From_zu_0_3118546_ [****************** ] 75% > Processing Locus CUFF.991_From_zu_0_3277661_ [******************* ] 76% > Processing Locus CUFF.993_From_zu_0_3082201_ [******************* ] 77% > Processed 95 loci. [*************************] 100% ----------------------------------------------- Run complete [00:02:04 elapsed] cufflinks -p 4 -o ./Bur_0 -r ngene.fa ./Bur_0/accepted_hits.bam [16:20:06] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399]à [ ] > Processing Locus CUFF.525_From_bur_0_1863298]à [ ] > Processing Locus CUFF.527_From_bur_0_1967596]à [ ] > Processing Locus CUFF.529_From_bur_0_1873494]à [ ] > Processing Locus CUFF.531_From_bur_0_1868430]à [ ] > Processing Locus CUFF.533_From_bur_0_2020452]à [ ] > Processing Locus CUFF.535_From_bur_0_1969548]à [ ] > Processing Locus CUFF.537_From_bur_0_1999718]à [ ] > Processing Locus CUFF.539_From_bur_0_2021834]à [ ] > Processing Locus CUFF.545_From_bur_0_1856286]à [ ] > Processing Locus CUFF.557_From_can_0_3234869]à [* ] > Processing Locus CUFF.563_From_bur_0_2020452]à [* ] > Processing Locus CUFF.563_From_bur_0_2020452]à [* ] > Processing Locus CUFF.569_From_can_0_3263637]à [* ] > Processing Locus CUFF.571_From_can_0_3076940]à [* ] > Processing Locus CUFF.573_From_can_0_3233581]à [* ] > Processing Locus CUFF.575_From_ct_1_3082021_]à [* ] > Processing Locus CUFF.577_From_ct_1_3125173_]à [* ] > Processing Locus CUFF.583_From_ct_1_3302721_]à [* ] > Processing Locus CUFF.585_From_ct_1_3247037_]à [* ] > Processing Locus CUFF.587_From_ct_1_3277323_]à [** ] > Processing Locus CUFF.593_From_can_0_3270131]à [** ] > Processing Locus CUFF.595_From_ct_1_3302721_]à [** ] > Processing Locus CUFF.603_From_bur_0_2025286]à [** ] > Processing Locus CUFF.607_From_edi_0_2891226]à [** ] > Processing Locus CUFF.611_From_edi_0_2921730]à [** ] > Processing Locus CUFF.613_From_hi_0_2773206_]à [** ] > Processing Locus CUFF.615_From_edi_0_2932438]à [** ] > Processing Locus CUFF.617_From_edi_0_2918156]à [** ] > Processing Locus CUFF.623_From_hi_0_2778596_]à [** ] > Processing Locus CUFF.641_From_kn_0_3605300_]à [*** ] > Processing Locus CUFF.653_From_kn_0_3751597_]à [*** ] > Processing Locus CUFF.663_From_kn_0_3613403_]à [*** ] > Processing Locus CUFF.665_From_hi_0_2939638_]à [*** ] > Processing Locus CUFF.671_From_edi_0_2859720]à [*** ] > Processing Locus CUFF.677_From_ct_1_3133995_]à [*** ] > Processing Locus CUFF.679_From_ler_0_3998410]à [*** ] > Processing Locus CUFF.685_From_mt_0_4231054_]à [*** ] > Processing Locus CUFF.687_From_mt_0_4230874_]à [*** ] > Processing Locus CUFF.689_From_ler_0_4018856]à [**** ] > Processing Locus CUFF.691_From_hi_0_2961678_]à [**** ] > Processing Locus CUFF.695_From_mt_0_4217716_]à [**** ] > Processing Locus CUFF.699_From_no_0_2905273_]à [**** ] > Processing Locus CUFF.703_From_no_0_2885444_]à [**** ] > Processing Locus CUFF.721_From_no_0_3120392_]à [**** ] > Processing Locus CUFF.725_From_no_0_3116640_]à [**** ] > Processing Locus CUFF.729_From_oy_0_3001818_]à [**** ] > Processing Locus CUFF.731_From_po_0_3324652_]à [**** ] > Processing Locus CUFF.733_From_no_0_2956652_]à [**** ] > Processing Locus CUFF.737_From_ct_1_3132277_]à [***** ] > Processing Locus CUFF.741_From_po_0_3382155_]à [***** ] > Processing Locus CUFF.753_From_oy_0_3121110_]à [***** ] > Processing Locus CUFF.755_From_mt_0_4193196_]à [***** ] > Processing Locus CUFF.759_From_no_0_2936769_]à [***** ] > Processing Locus CUFF.761_From_po_0_3606391_]à [***** ] > Processing Locus CUFF.763_From_rsch_4_403203]à [***** ] > Processing Locus CUFF.773_From_po_0_3606391_]à [***** ] > Processing Locus CUFF.783_From_oy_0_2965192_]à [***** ] > Processing Locus CUFF.785_From_no_0_3128142_]à [****** ] > Processing Locus CUFF.785_From_no_0_3128142_]à [****** ] > Processing Locus CUFF.789_From_rsch_4_427544]à [****** ] > Processing Locus CUFF.799_From_sf_2_2662232_]à [****** ] > Processing Locus CUFF.803_From_po_0_3573778_]à [****** ] > Processing Locus CUFF.811_From_sf_2_2459023_]à [****** ] > Processing Locus CUFF.817_From_sf_2_2524453_]à [****** ] > Processing Locus CUFF.825_From_sf_2_2700286_]à [****** ] > Processing Locus CUFF.825_From_sf_2_2700286_]à [****** ] > Processing Locus CUFF.839_From_sf_2_2680171_]à [****** ] > Processing Locus CUFF.847_From_tsu_0_3242833]à [****** ] > Processing Locus CUFF.861_From_mt_0_4528444_]à [****** ] > Processing Locus CUFF.873_From_wil_2_3050523]à [******* ] > Processing Locus CUFF.877_From_sf_2_2687786_]à [******* ] > Processing Locus CUFF.879_From_rsch_4_405516]à [******* ] > Processing Locus CUFF.881_From_wil_2_2925323]à [******* ] > Processing Locus CUFF.895_From_tsu_0_3215821]à [******* ] > Processing Locus CUFF.907_From_ws_0_3182508_]à [******* ] > Processing Locus CUFF.913_From_wil_2_2834553]à [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_]à [******* ] > Processing Locus CUFF.925_From_ws_0_3371988_]à [******* ] > Processing Locus CUFF.945_From_wu_0_2678387_]à [******** ] > Processing Locus CUFF.947_From_wu_0_2654219_]à [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_]à [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_]à [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_]à [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_]à [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_]à [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_]à [******** ] > Processing Locus CUFF.955_From_ws_0_3340488_]à [******** ] > Processing Locus CUFF.957_From_ws_0_3381390_]à [******** ] > Processing Locus CUFF.963_From_zu_0_3092045_]à [******** ] > Processing Locus CUFF.965_From_zu_0_3238769_]à [******** ] > Processing Locus CUFF.967_From_zu_0_3022629_]à [******** ] > Processing Locus CUFF.975_From_zu_0_3259399_]à [******** ] > Processing Locus CUFF.983_From_zu_0_3243571_]à [********* ] > Processing Locus CUFF.983_From_zu_0_3243571_]à [********* ] > Processing Locus CUFF.985_From_zu_0_3280213_]à [********* ] > Processing Locus CUFF.985_From_zu_0_3280213_]à [********* ] > Processing Locus CUFF.985_From_zu_0_3280213_]à [********* ] > Processing Locus CUFF.985_From_zu_0_3280213_]à [********* ] > Processing Locus CUFF.987_From_zu_0_3118546_]à [********* ] > Processing Locus CUFF.989_From_zu_0_3289907_]à [********* ] > Processing Locus CUFF.993_From_zu_0_3082201_]à [********* ] > Processed 102 loci. [*************************] 100% > Map Properties: > Total Map Mass: 10167.96 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:20:06] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.527_From_bur_0_1967596 [ ] 1% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 2% > Processing Locus CUFF.531_From_bur_0_1868430 [ ] 3% > Processing Locus CUFF.533_From_bur_0_2020452 [* ] 4% > Processing Locus CUFF.535_From_bur_0_1969548 [* ] 5% > Processing Locus CUFF.537_From_bur_0_1999718 [* ] 6% > Processing Locus CUFF.539_From_bur_0_2021834 [* ] 7% > Processing Locus CUFF.545_From_bur_0_1856286 [** ] 8% > Processing Locus CUFF.557_From_can_0_3234869 [** ] 9% > Processing Locus CUFF.563_From_bur_0_2020452 [** ] 10% > Processing Locus CUFF.563_From_bur_0_2020452 [** ] 11% > Processing Locus CUFF.569_From_can_0_3263637 [*** ] 12% > Processing Locus CUFF.571_From_can_0_3076940 [*** ] 13% > Processing Locus CUFF.573_From_can_0_3233581 [*** ] 14% > Processing Locus CUFF.575_From_ct_1_3082021_ [*** ] 15% > Processing Locus CUFF.577_From_ct_1_3125173_ [**** ] 16% > Processing Locus CUFF.583_From_ct_1_3302721_ [**** ] 17% > Processing Locus CUFF.585_From_ct_1_3247037_ [**** ] 18% > Processing Locus CUFF.587_From_ct_1_3277323_ [**** ] 19% > Processing Locus CUFF.593_From_can_0_3270131 [***** ] 20% > Processing Locus CUFF.595_From_ct_1_3302721_ [***** ] 21% > Processing Locus CUFF.603_From_bur_0_2025286 [***** ] 22% > Processing Locus CUFF.607_From_edi_0_2891226 [***** ] 23% > Processing Locus CUFF.611_From_edi_0_2921730 [****** ] 24% > Processing Locus CUFF.613_From_hi_0_2773206_ [****** ] 25% > Processing Locus CUFF.615_From_edi_0_2932438 [****** ] 26% > Processing Locus CUFF.617_From_edi_0_2918156 [****** ] 27% > Processing Locus CUFF.623_From_hi_0_2778596_ [******* ] 28% > Processing Locus CUFF.641_From_kn_0_3605300_ [******* ] 29% > Processing Locus CUFF.653_From_kn_0_3751597_ [******* ] 30% > Processing Locus CUFF.663_From_kn_0_3613403_ [******* ] 31% > Processing Locus CUFF.665_From_hi_0_2939638_ [******** ] 32% > Processing Locus CUFF.671_From_edi_0_2859720 [******** ] 33% > Processing Locus CUFF.677_From_ct_1_3133995_ [******** ] 34% > Processing Locus CUFF.679_From_ler_0_3998410 [******** ] 35% > Processing Locus CUFF.685_From_mt_0_4231054_ [********* ] 36% > Processing Locus CUFF.687_From_mt_0_4230874_ [********* ] 37% > Processing Locus CUFF.689_From_ler_0_4018856 [********* ] 38% > Processing Locus CUFF.691_From_hi_0_2961678_ [********* ] 39% > Processing Locus CUFF.695_From_mt_0_4217716_ [********** ] 40% > Processing Locus CUFF.699_From_no_0_2905273_ [********** ] 41% > Processing Locus CUFF.703_From_no_0_2885444_ [********** ] 42% > Processing Locus CUFF.721_From_no_0_3120392_ [********** ] 43% > Processing Locus CUFF.725_From_no_0_3116640_ [*********** ] 44% > Processing Locus CUFF.729_From_oy_0_3001818_ [*********** ] 45% > Processing Locus CUFF.731_From_po_0_3324652_ [*********** ] 46% > Processing Locus CUFF.733_From_no_0_2956652_ [*********** ] 47% > Processing Locus CUFF.737_From_ct_1_3132277_ [************ ] 48% > Processing Locus CUFF.741_From_po_0_3382155_ [************ ] 49% > Processing Locus CUFF.753_From_oy_0_3121110_ [************ ] 50% > Processing Locus CUFF.755_From_mt_0_4193196_ [************ ] 50% > Processing Locus CUFF.759_From_no_0_2936769_ [************ ] 51% > Processing Locus CUFF.761_From_po_0_3606391_ [************* ] 52% > Processing Locus CUFF.763_From_rsch_4_403203 [************* ] 53% > Processing Locus CUFF.773_From_po_0_3606391_ [************* ] 54% > Processing Locus CUFF.783_From_oy_0_2965192_ [************* ] 55% > Processing Locus CUFF.785_From_no_0_3128142_ [************** ] 56% > Processing Locus CUFF.785_From_no_0_3128142_ [************** ] 57% > Processing Locus CUFF.789_From_rsch_4_427544 [************** ] 58% > Processing Locus CUFF.799_From_sf_2_2662232_ [************** ] 59% > Processing Locus CUFF.803_From_po_0_3573778_ [*************** ] 60% > Processing Locus CUFF.811_From_sf_2_2459023_ [*************** ] 61% > Processing Locus CUFF.817_From_sf_2_2524453_ [*************** ] 62% > Processing Locus CUFF.825_From_sf_2_2700286_ [*************** ] 63% > Processing Locus CUFF.825_From_sf_2_2700286_ [**************** ] 64% > Processing Locus CUFF.839_From_sf_2_2680171_ [**************** ] 65% > Processing Locus CUFF.847_From_tsu_0_3242833 [**************** ] 66% > Processing Locus CUFF.861_From_mt_0_4528444_ [**************** ] 67% > Processing Locus CUFF.873_From_wil_2_3050523 [***************** ] 68% > Processing Locus CUFF.877_From_sf_2_2687786_ [***************** ] 69% > Processing Locus CUFF.879_From_rsch_4_405516 [***************** ] 70% > Processing Locus CUFF.881_From_wil_2_2925323 [***************** ] 71% > Processing Locus CUFF.895_From_tsu_0_3215821 [****************** ] 72% > Processing Locus CUFF.907_From_ws_0_3182508_ [****************** ] 73% > Processing Locus CUFF.913_From_wil_2_2834553 [****************** ] 74% > Processing Locus CUFF.919_From_ws_0_3347582_ [****************** ] 75% > Processing Locus CUFF.925_From_ws_0_3371988_ [******************* ] 76% > Processing Locus CUFF.945_From_wu_0_2678387_ [******************* ] 77% > Processing Locus CUFF.947_From_wu_0_2654219_ [******************* ] 78% > Processing Locus CUFF.953_From_ws_0_3382500_ [******************* ] 79% > Processing Locus CUFF.953_From_ws_0_3382500_ [******************** ] 80% > Processing Locus CUFF.953_From_ws_0_3382500_ [******************** ] 81% > Processing Locus CUFF.953_From_ws_0_3382500_ [******************** ] 82% > Processing Locus CUFF.953_From_ws_0_3382500_ [******************** ] 83% > Processing Locus CUFF.953_From_ws_0_3382500_ [********************* ] 84% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************* ] 85% > Processing Locus CUFF.957_From_ws_0_3381390_ [********************* ] 86% > Processing Locus CUFF.963_From_zu_0_3092045_ [********************* ] 87% > Processing Locus CUFF.965_From_zu_0_3238769_ [********************** ] 88% > Processing Locus CUFF.967_From_zu_0_3022629_ [********************** ] 89% > Processing Locus CUFF.975_From_zu_0_3259399_ [********************** ] 90% > Processing Locus CUFF.983_From_zu_0_3243571_ [********************** ] 91% > Processing Locus CUFF.983_From_zu_0_3243571_ [*********************** ] 92% > Processing Locus CUFF.985_From_zu_0_3280213_ [*********************** ] 93% > Processing Locus CUFF.985_From_zu_0_3280213_ [*********************** ] 94% > Processing Locus CUFF.985_From_zu_0_3280213_ [*********************** ] 95% > Processing Locus CUFF.985_From_zu_0_3280213_ [************************ ] 96% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 97% > Processing Locus CUFF.989_From_zu_0_3289907_ [************************ ] 98% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 99% > Processed 102 loci. [*************************] 100% [16:20:06] Loading reference annotation and sequence [16:20:06] Learning bias parameters. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.527_From_bur_0_1967596 [ ] 1% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 2% > Processing Locus CUFF.531_From_bur_0_1868430 [ ] 3% > Processing Locus CUFF.535_From_bur_0_1969548 [* ] 4% > Processing Locus CUFF.537_From_bur_0_1999718 [* ] 5% > Processing Locus CUFF.539_From_bur_0_2021834 [* ] 6% > Processing Locus CUFF.545_From_bur_0_1856286 [* ] 7% > Processing Locus CUFF.557_From_can_0_3234869 [** ] 8% > Processing Locus CUFF.563_From_bur_0_2020452 [** ] 9% > Processing Locus CUFF.569_From_can_0_3263637 [** ] 10% > Processing Locus CUFF.571_From_can_0_3076940 [** ] 11% > Processing Locus CUFF.575_From_ct_1_3082021_ [*** ] 12% > Processing Locus CUFF.577_From_ct_1_3125173_ [*** ] 13% > Processing Locus CUFF.587_From_ct_1_3277323_ [*** ] 14% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 15% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 16% > Processing Locus CUFF.603_From_bur_0_2025286 [**** ] 17% > Processing Locus CUFF.607_From_edi_0_2891226 [**** ] 18% > Processing Locus CUFF.611_From_edi_0_2921730 [**** ] 19% > Processing Locus CUFF.613_From_hi_0_2773206_ [***** ] 20% > Processing Locus CUFF.615_From_edi_0_2932438 [***** ] 21% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 22% > Processing Locus CUFF.641_From_kn_0_3605300_ [***** ] 23% > Processing Locus CUFF.653_From_kn_0_3751597_ [****** ] 24% > Processing Locus CUFF.663_From_kn_0_3613403_ [****** ] 25% > Processing Locus CUFF.665_From_hi_0_2939638_ [****** ] 26% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 27% > Processing Locus CUFF.677_From_ct_1_3133995_ [******* ] 28% > Processing Locus CUFF.679_From_ler_0_3998410 [******* ] 29% > Processing Locus CUFF.685_From_mt_0_4231054_ [******* ] 30% > Processing Locus CUFF.687_From_mt_0_4230874_ [******* ] 31% > Processing Locus CUFF.689_From_ler_0_4018856 [******** ] 32% > Processing Locus CUFF.691_From_hi_0_2961678_ [******** ] 33% > Processing Locus CUFF.695_From_mt_0_4217716_ [******** ] 34% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 35% > Processing Locus CUFF.703_From_no_0_2885444_ [********* ] 36% > Processing Locus CUFF.721_From_no_0_3120392_ [********* ] 37% > Processing Locus CUFF.725_From_no_0_3116640_ [********* ] 38% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 39% > Processing Locus CUFF.731_From_po_0_3324652_ [********** ] 40% > Processing Locus CUFF.733_From_no_0_2956652_ [********** ] 41% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 42% > Processing Locus CUFF.753_From_oy_0_3121110_ [********** ] 43% > Processing Locus CUFF.755_From_mt_0_4193196_ [*********** ] 44% > Processing Locus CUFF.759_From_no_0_2936769_ [*********** ] 45% > Processing Locus CUFF.761_From_po_0_3606391_ [*********** ] 46% > Processing Locus CUFF.763_From_rsch_4_403203 [*********** ] 47% > Processing Locus CUFF.773_From_po_0_3606391_ [************ ] 48% > Processing Locus CUFF.785_From_no_0_3128142_ [************ ] 49% > Processing Locus CUFF.785_From_no_0_3128142_ [************ ] 50% > Processing Locus CUFF.789_From_rsch_4_427544 [************ ] 50% > Processing Locus CUFF.799_From_sf_2_2662232_ [************ ] 51% > Processing Locus CUFF.803_From_po_0_3573778_ [************* ] 52% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 53% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 54% > Processing Locus CUFF.825_From_sf_2_2700286_ [************* ] 55% > Processing Locus CUFF.873_From_wil_2_3050523 [************** ] 56% > Processing Locus CUFF.879_From_rsch_4_405516 [************** ] 57% > Processing Locus CUFF.881_From_wil_2_2925323 [************** ] 58% > Processing Locus CUFF.895_From_tsu_0_3215821 [************** ] 59% > Processing Locus CUFF.919_From_ws_0_3347582_ [*************** ] 60% > Processing Locus CUFF.925_From_ws_0_3371988_ [*************** ] 61% > Processing Locus CUFF.945_From_wu_0_2678387_ [*************** ] 62% > Processing Locus CUFF.947_From_wu_0_2654219_ [*************** ] 63% > Processing Locus CUFF.957_From_ws_0_3381390_ [**************** ] 64% > Processing Locus CUFF.963_From_zu_0_3092045_ [**************** ] 65% > Processing Locus CUFF.965_From_zu_0_3238769_ [**************** ] 66% > Processing Locus CUFF.967_From_zu_0_3022629_ [**************** ] 67% > Processing Locus CUFF.975_From_zu_0_3259399_ [***************** ] 68% > Processing Locus CUFF.983_From_zu_0_3243571_ [***************** ] 69% > Processing Locus CUFF.987_From_zu_0_3118546_ [***************** ] 70% > Processing Locus CUFF.993_From_zu_0_3082201_ [***************** ] 71% > Processed 74 loci. [*************************] 100% [16:20:07] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.527_From_bur_0_1967596 [ ] 1% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 2% > Processing Locus CUFF.531_From_bur_0_1868430 [ ] 3% > Processing Locus CUFF.535_From_bur_0_1969548 [* ] 4% > Processing Locus CUFF.537_From_bur_0_1999718 [* ] 5% > Processing Locus CUFF.539_From_bur_0_2021834 [* ] 6% > Processing Locus CUFF.545_From_bur_0_1856286 [* ] 7% > Processing Locus CUFF.557_From_can_0_3234869 [** ] 8% > Processing Locus CUFF.563_From_bur_0_2020452 [** ] 9% > Processing Locus CUFF.569_From_can_0_3263637 [** ] 10% > Processing Locus CUFF.571_From_can_0_3076940 [** ] 11% > Processing Locus CUFF.575_From_ct_1_3082021_ [*** ] 12% > Processing Locus CUFF.577_From_ct_1_3125173_ [*** ] 13% > Processing Locus CUFF.587_From_ct_1_3277323_ [*** ] 14% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 15% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 16% > Processing Locus CUFF.603_From_bur_0_2025286 [**** ] 17% > Processing Locus CUFF.607_From_edi_0_2891226 [**** ] 18% > Processing Locus CUFF.611_From_edi_0_2921730 [**** ] 19% > Processing Locus CUFF.613_From_hi_0_2773206_ [***** ] 20% > Processing Locus CUFF.615_From_edi_0_2932438 [***** ] 21% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 22% > Processing Locus CUFF.641_From_kn_0_3605300_ [***** ] 23% > Processing Locus CUFF.653_From_kn_0_3751597_ [****** ] 24% > Processing Locus CUFF.663_From_kn_0_3613403_ [****** ] 25% > Processing Locus CUFF.665_From_hi_0_2939638_ [****** ] 26% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 27% > Processing Locus CUFF.677_From_ct_1_3133995_ [******* ] 28% > Processing Locus CUFF.679_From_ler_0_3998410 [******* ] 29% > Processing Locus CUFF.685_From_mt_0_4231054_ [******* ] 30% > Processing Locus CUFF.687_From_mt_0_4230874_ [******* ] 31% > Processing Locus CUFF.689_From_ler_0_4018856 [******** ] 32% > Processing Locus CUFF.691_From_hi_0_2961678_ [******** ] 33% > Processing Locus CUFF.695_From_mt_0_4217716_ [******** ] 34% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 35% > Processing Locus CUFF.703_From_no_0_2885444_ [********* ] 36% > Processing Locus CUFF.721_From_no_0_3120392_ [********* ] 37% > Processing Locus CUFF.725_From_no_0_3116640_ [********* ] 38% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 39% > Processing Locus CUFF.731_From_po_0_3324652_ [********** ] 40% > Processing Locus CUFF.733_From_no_0_2956652_ [********** ] 41% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 42% > Processing Locus CUFF.753_From_oy_0_3121110_ [********** ] 43% > Processing Locus CUFF.755_From_mt_0_4193196_ [*********** ] 44% > Processing Locus CUFF.759_From_no_0_2936769_ [*********** ] 45% > Processing Locus CUFF.761_From_po_0_3606391_ [*********** ] 46% > Processing Locus CUFF.763_From_rsch_4_403203 [*********** ] 47% > Processing Locus CUFF.773_From_po_0_3606391_ [************ ] 48% > Processing Locus CUFF.785_From_no_0_3128142_ [************ ] 49% > Processing Locus CUFF.785_From_no_0_3128142_ [************ ] 50% > Processing Locus CUFF.789_From_rsch_4_427544 [************ ] 50% > Processing Locus CUFF.799_From_sf_2_2662232_ [************ ] 51% > Processing Locus CUFF.803_From_po_0_3573778_ [************* ] 52% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 53% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 54% > Processing Locus CUFF.825_From_sf_2_2700286_ [************* ] 55% > Processing Locus CUFF.873_From_wil_2_3050523 [************** ] 56% > Processing Locus CUFF.879_From_rsch_4_405516 [************** ] 57% > Processing Locus CUFF.881_From_wil_2_2925323 [************** ] 58% > Processing Locus CUFF.895_From_tsu_0_3215821 [************** ] 59% > Processing Locus CUFF.919_From_ws_0_3347582_ [*************** ] 60% > Processing Locus CUFF.925_From_ws_0_3371988_ [*************** ] 61% > Processing Locus CUFF.945_From_wu_0_2678387_ [*************** ] 62% > Processing Locus CUFF.947_From_wu_0_2654219_ [*************** ] 63% > Processing Locus CUFF.957_From_ws_0_3381390_ [**************** ] 64% > Processing Locus CUFF.963_From_zu_0_3092045_ [**************** ] 65% > Processing Locus CUFF.965_From_zu_0_3238769_ [**************** ] 66% > Processing Locus CUFF.967_From_zu_0_3022629_ [**************** ] 67% > Processing Locus CUFF.975_From_zu_0_3259399_ [***************** ] 68% > Processing Locus CUFF.983_From_zu_0_3243571_ [***************** ] 69% > Processing Locus CUFF.987_From_zu_0_3118546_ [***************** ] 70% > Processing Locus CUFF.993_From_zu_0_3082201_ [***************** ] 71% > Processed 74 loci. [*************************] 100% file: /data/arabidopsis/xiang/magic_founder/Hi_0_R1/R38_L3_Hi_0_sdlg_R1_nss_barcode_CAT.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Hi_0_R2/R38_L4_Hi_0_sdlg_R2_nss_barcode_CAT.unmap_1.fq file: /data/arabidopsis/xiang/magic_founder/Kn_0_R1/R38_L3_Kn_0_sdlg_R1_nss_barcode_GTA.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Kn_0_R2/R38_L4_Kn_0_sdlg_R2_nss_barcode_GTA.unmap_1.fq $RNAGI/rnagi.sh -o ./Hi_0 -n ngene.fa Hi_0.Tongene.merge.fq reference: ngene.fa $RNAGI/rnagi.sh -o ./Kn_0 -n ngene.fa Kn_0.Tongene.merge.fq reference: ngene.fa file: /data/arabidopsis/xiang/magic_founder/Ler_0_R1/R38_L3_Ler_0_sdlg_R1_nss_barcode_TGC.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Ler_0_R2/R38_L4_Ler_0_sdlg_R2_nss_barcode_TGC.unmap_1.fq $RNAGI/rnagi.sh -o ./Ler_0 -n ngene.fa Ler_0.Tongene.merge.fq reference: ngene.fa tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Hi_0 ngene.fa ./Hi_0/Hi_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:20:52 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:20:52 2011] Preparing output location ./Hi_0// [Mon Apr 4 16:20:52 2011] Checking for Bowtie index files [Mon Apr 4 16:20:52 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:20:52 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:20:53 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:20:53 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:20:53 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Kn_0 ngene.fa ./Kn_0/Kn_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:20:57 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:20:57 2011] Preparing output location ./Kn_0// [Mon Apr 4 16:20:57 2011] Checking for Bowtie index files [Mon Apr 4 16:20:57 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:20:57 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:20:57 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:20:57 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:20:57 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Ler_0 ngene.fa ./Ler_0/Ler_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:21:00 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:21:00 2011] Preparing output location ./Ler_0// [Mon Apr 4 16:21:00 2011] Checking for Bowtie index files [Mon Apr 4 16:21:00 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:21:00 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:21:00 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:21:00 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:21:00 2011] Checking reads min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:21:13 2011] Mapping reads against ngene.fa with Bowtie min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:21:19 2011] Joining segment hits [Mon Apr 4 16:21:20 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:21:22 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:21:28 2011] Joining segment hits [Mon Apr 4 16:21:30 2011] Joining segment hits [Mon Apr 4 16:21:39 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:21:43 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:21:45 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:21:46 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:21:50 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:21:52 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:21:52 2011] Searching for junctions via segment mapping [Mon Apr 4 16:21:55 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:21:58 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:22:02 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:22:04 2011] Searching for junctions via segment mapping [Mon Apr 4 16:22:08 2011] Searching for junctions via segment mapping [Mon Apr 4 16:22:20 2011] Retrieving sequences for splices [Mon Apr 4 16:22:20 2011] Indexing splices [Mon Apr 4 16:22:20 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:22:22 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:22:24 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:22:27 2011] Joining segment hits [Mon Apr 4 16:22:29 2011] Reporting output tracks [Mon Apr 4 16:22:30 2011] Retrieving sequences for splices [Mon Apr 4 16:22:30 2011] Indexing splices [Mon Apr 4 16:22:30 2011] Mapping reads against segment_juncs with Bowtie ----------------------------------------------- Run complete [00:01:39 elapsed] [Mon Apr 4 16:22:33 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:22:36 2011] Retrieving sequences for splices [Mon Apr 4 16:22:36 2011] Indexing splices [Mon Apr 4 16:22:36 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:22:37 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:22:40 2011] Joining segment hits [Mon Apr 4 16:22:40 2011] Mapping reads against segment_juncs with Bowtie cufflinks -p 4 -o ./Hi_0 -r ngene.fa ./Hi_0/accepted_hits.bam [16:22:41] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399f [ ] > Processing Locus CUFF.525_From_bur_0_1863298f [ ] > Processing Locus CUFF.529_From_bur_0_1873494f [ ] > Processing Locus CUFF.551_From_can_0_3122480f [ ] > Processing Locus CUFF.553_From_can_0_3223655f [ ] > Processing Locus CUFF.561_From_can_0_3189753f [ ] > Processing Locus CUFF.571_From_can_0_3076940f [ ] > Processing Locus CUFF.575_From_ct_1_3082021_f [ ] > Processing Locus CUFF.581_From_can_0_3218459f [ ] > Processing Locus CUFF.583_From_ct_1_3302721_f [ ] > Processing Locus CUFF.593_From_can_0_3270131f [* ] > Processing Locus CUFF.593_From_can_0_3270131f [* ] > Processing Locus CUFF.593_From_can_0_3270131f [* ] > Processing Locus CUFF.593_From_can_0_3270131f [* ] > Processing Locus CUFF.595_From_ct_1_3302721_f [* ] > Processing Locus CUFF.599_From_edi_0_2744702f [* ] > Processing Locus CUFF.603_From_bur_0_2025286f [* ] > Processing Locus CUFF.609_From_hi_0_2755116_f [* ] > Processing Locus CUFF.613_From_hi_0_2773206_f [* ] > Processing Locus CUFF.623_From_hi_0_2778596_f [* ] > Processing Locus CUFF.631_From_hi_0_2959094_f [* ] > Processing Locus CUFF.633_From_hi_0_2959094_f [* ] > Processing Locus CUFF.639_From_hi_0_2916184_f [** ] > Processing Locus CUFF.641_From_kn_0_3605300_f [** ] > Processing Locus CUFF.643_From_kn_0_3799876_f [** ] > Processing Locus CUFF.653_From_kn_0_3751597_f [** ] > Processing Locus CUFF.655_From_hi_0_2795398_f [** ] > Processing Locus CUFF.663_From_kn_0_3613403_f [** ] > Processing Locus CUFF.665_From_hi_0_2939638_f [** ] > Processing Locus CUFF.666_From_ler_0_4004770f [** ] > Processing Locus CUFF.671_From_edi_0_2859720f [** ] > Processing Locus CUFF.675_From_mt_0_4213448_f [** ] > Processing Locus CUFF.679_From_ler_0_3998410f [*** ] > Processing Locus CUFF.681_From_mt_0_4399784_f [*** ] > Processing Locus CUFF.685_From_mt_0_4231054_f [*** ] > Processing Locus CUFF.687_From_mt_0_4230874_f [*** ] > Processing Locus CUFF.689_From_ler_0_4018856f [*** ] > Processing Locus CUFF.691_From_hi_0_2961678_f [*** ] > Processing Locus CUFF.693_From_no_0_2934639_f [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_f [*** ] > Processing Locus CUFF.697_From_mt_0_4229662_f [*** ] > Processing Locus CUFF.699_From_no_0_2905273_f [**** ] > Processing Locus CUFF.703_From_no_0_2885444_f [**** ] > Processing Locus CUFF.711_From_no_0_3088052_f [**** ] > Processing Locus CUFF.725_From_no_0_3116640_f [**** ] > Processing Locus CUFF.727_From_hi_0_2953648_f [**** ] > Processing Locus CUFF.733_From_no_0_2956652_f [**** ] > Processing Locus CUFF.737_From_ct_1_3132277_f [**** ] > Processing Locus CUFF.743_From_po_0_3330421_f [**** ] > Processing Locus CUFF.755_From_mt_0_4193196_f [**** ] > Processing Locus CUFF.759_From_no_0_2936769_f [**** ] > Processing Locus CUFF.763_From_rsch_4_403203f [***** ] > Processing Locus CUFF.765_From_rsch_4_411079f [***** ] > Processing Locus CUFF.785_From_no_0_3128142_f [***** ] > Processing Locus CUFF.785_From_no_0_3128142_f [***** ] > Processing Locus CUFF.785_From_no_0_3128142_f [***** ] > Processing Locus CUFF.789_From_rsch_4_427544f [***** ] > Processing Locus CUFF.793_From_sf_2_2504999_f [***** ] > Processing Locus CUFF.795_From_rsch_4_429714f [***** ] > Processing Locus CUFF.807_From_sf_2_2488391_f [***** ] > Processing Locus CUFF.809_From_sf_2_2682779_f [***** ] > Processing Locus CUFF.817_From_sf_2_2524453_f [***** ] > Processing Locus CUFF.831_From_sf_2_2687774_f [****** ] > Processing Locus CUFF.839_From_sf_2_2680171_f [****** ] > Processing Locus CUFF.851_From_wil_2_2906137f [****** ] > Processing Locus CUFF.857_From_sf_2_2653966_f [****** ] > Processing Locus CUFF.861_From_mt_0_4528444_f [****** ] > Processing Locus CUFF.867_From_wil_2_2945095f [****** ] > Processing Locus CUFF.871_From_rsch_4_426655f [****** ] > Processing Locus CUFF.877_From_sf_2_2687786_f [****** ] > Processing Locus CUFF.877_From_sf_2_2687786_f [****** ] > Processing Locus CUFF.879_From_rsch_4_405516f [****** ] > Processing Locus CUFF.881_From_wil_2_2925323f [****** ] > Processing Locus CUFF.893_From_ws_0_3190679_f [******* ] > Processing Locus CUFF.897_From_ws_0_3298283_f [******* ] > Processing Locus CUFF.899_From_ws_0_3190963_f [******* ] > Processing Locus CUFF.907_From_ws_0_3182508_f [******* ] > Processing Locus CUFF.909_From_wil_2_3052273f [******* ] > Processing Locus CUFF.913_From_wil_2_2834553f [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_f [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_f [******* ] > Processing Locus CUFF.921_From_wil_2_3077447f [******* ] > Processing Locus CUFF.925_From_ws_0_3371988_f [******* ] > Processing Locus CUFF.927_From_wu_0_2655481_f [******** ] > Processing Locus CUFF.935_From_ws_0_3380934_f [******** ] > Processing Locus CUFF.939_From_ws_0_3365892_f [******** ] > Processing Locus CUFF.945_From_wu_0_2678387_f [******** ] > Processing Locus CUFF.947_From_wu_0_2654219_f [******** ] > Processing Locus CUFF.955_From_ws_0_3340488_f [******** ] > Processing Locus CUFF.963_From_zu_0_3092045_f [******** ] > Processing Locus CUFF.969_From_zu_0_3190435_f [******** ] > Processing Locus CUFF.979_From_zu_0_3278243_f [******** ] > Processing Locus CUFF.983_From_zu_0_3243571_f [********* ] > Processing Locus CUFF.983_From_zu_0_3243571_f [********* ] > Processing Locus CUFF.987_From_zu_0_3118546_f [********* ] > Processed 95 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5957.65 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:22:41] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 1% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 2% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 3% > Processing Locus CUFF.553_From_can_0_3223655 [* ] 4% > Processing Locus CUFF.561_From_can_0_3189753 [* ] 5% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 6% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 7% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 8% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 10% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 11% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 12% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 13% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 14% > Processing Locus CUFF.599_From_edi_0_2744702 [*** ] 15% > Processing Locus CUFF.603_From_bur_0_2025286 [**** ] 16% > Processing Locus CUFF.609_From_hi_0_2755116_ [**** ] 17% > Processing Locus CUFF.613_From_hi_0_2773206_ [**** ] 18% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 20% > Processing Locus CUFF.631_From_hi_0_2959094_ [***** ] 21% > Processing Locus CUFF.633_From_hi_0_2959094_ [***** ] 22% > Processing Locus CUFF.639_From_hi_0_2916184_ [***** ] 23% > Processing Locus CUFF.641_From_kn_0_3605300_ [****** ] 24% > Processing Locus CUFF.643_From_kn_0_3799876_ [****** ] 25% > Processing Locus CUFF.653_From_kn_0_3751597_ [****** ] 26% > Processing Locus CUFF.655_From_hi_0_2795398_ [****** ] 27% > Processing Locus CUFF.663_From_kn_0_3613403_ [******* ] 28% > Processing Locus CUFF.665_From_hi_0_2939638_ [******* ] 29% > Processing Locus CUFF.666_From_ler_0_4004770 [******* ] 30% > Processing Locus CUFF.671_From_edi_0_2859720 [******* ] 31% > Processing Locus CUFF.675_From_mt_0_4213448_ [******** ] 32% > Processing Locus CUFF.679_From_ler_0_3998410 [******** ] 33% > Processing Locus CUFF.681_From_mt_0_4399784_ [******** ] 34% > Processing Locus CUFF.685_From_mt_0_4231054_ [******** ] 35% > Processing Locus CUFF.687_From_mt_0_4230874_ [********* ] 36% > Processing Locus CUFF.689_From_ler_0_4018856 [********* ] 37% > Processing Locus CUFF.691_From_hi_0_2961678_ [********* ] 38% > Processing Locus CUFF.693_From_no_0_2934639_ [********** ] 40% > Processing Locus CUFF.695_From_mt_0_4217716_ [********** ] 41% > Processing Locus CUFF.697_From_mt_0_4229662_ [********** ] 42% > Processing Locus CUFF.699_From_no_0_2905273_ [********** ] 43% > Processing Locus CUFF.703_From_no_0_2885444_ [*********** ] 44% > Processing Locus CUFF.711_From_no_0_3088052_ [*********** ] 45% > Processing Locus CUFF.725_From_no_0_3116640_ [*********** ] 46% > Processing Locus CUFF.727_From_hi_0_2953648_ [*********** ] 47% > Processing Locus CUFF.733_From_no_0_2956652_ [************ ] 48% > Processing Locus CUFF.737_From_ct_1_3132277_ [************ ] 49% > Processing Locus CUFF.743_From_po_0_3330421_ [************ ] 50% > Processing Locus CUFF.755_From_mt_0_4193196_ [************ ] 51% > Processing Locus CUFF.759_From_no_0_2936769_ [************* ] 52% > Processing Locus CUFF.763_From_rsch_4_403203 [************* ] 53% > Processing Locus CUFF.765_From_rsch_4_411079 [************* ] 54% > Processing Locus CUFF.785_From_no_0_3128142_ [************* ] 55% > Processing Locus CUFF.785_From_no_0_3128142_ [************** ] 56% > Processing Locus CUFF.785_From_no_0_3128142_ [************** ] 57% > Processing Locus CUFF.789_From_rsch_4_427544 [************** ] 58% > Processing Locus CUFF.793_From_sf_2_2504999_ [*************** ] 60% > Processing Locus CUFF.795_From_rsch_4_429714 [*************** ] 61% > Processing Locus CUFF.807_From_sf_2_2488391_ [*************** ] 62% > Processing Locus CUFF.809_From_sf_2_2682779_ [*************** ] 63% > Processing Locus CUFF.817_From_sf_2_2524453_ [**************** ] 64% > Processing Locus CUFF.831_From_sf_2_2687774_ [**************** ] 65% > Processing Locus CUFF.839_From_sf_2_2680171_ [**************** ] 66% > Processing Locus CUFF.851_From_wil_2_2906137 [**************** ] 67% > Processing Locus CUFF.857_From_sf_2_2653966_ [***************** ] 68% > Processing Locus CUFF.861_From_mt_0_4528444_ [***************** ] 69% > Processing Locus CUFF.867_From_wil_2_2945095 [***************** ] 70% > Processing Locus CUFF.871_From_rsch_4_426655 [***************** ] 71% > Processing Locus CUFF.877_From_sf_2_2687786_ [****************** ] 72% > Processing Locus CUFF.877_From_sf_2_2687786_ [****************** ] 73% > Processing Locus CUFF.879_From_rsch_4_405516 [****************** ] 74% > Processing Locus CUFF.881_From_wil_2_2925323 [****************** ] 75% > Processing Locus CUFF.893_From_ws_0_3190679_ [******************* ] 76% > Processing Locus CUFF.897_From_ws_0_3298283_ [******************* ] 77% > Processing Locus CUFF.899_From_ws_0_3190963_ [******************* ] 78% > Processing Locus CUFF.907_From_ws_0_3182508_ [******************** ] 80% > Processing Locus CUFF.909_From_wil_2_3052273 [******************** ] 81% > Processing Locus CUFF.913_From_wil_2_2834553 [******************** ] 82% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 83% > Processing Locus CUFF.919_From_ws_0_3347582_ [********************* ] 84% > Processing Locus CUFF.921_From_wil_2_3077447 [********************* ] 85% > Processing Locus CUFF.925_From_ws_0_3371988_ [********************* ] 86% > Processing Locus CUFF.927_From_wu_0_2655481_ [********************* ] 87% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************** ] 88% > Processing Locus CUFF.939_From_ws_0_3365892_ [********************** ] 89% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************** ] 90% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************** ] 91% > Processing Locus CUFF.955_From_ws_0_3340488_ [*********************** ] 92% > Processing Locus CUFF.963_From_zu_0_3092045_ [*********************** ] 93% > Processing Locus CUFF.969_From_zu_0_3190435_ [*********************** ] 94% > Processing Locus CUFF.979_From_zu_0_3278243_ [*********************** ] 95% > Processing Locus CUFF.983_From_zu_0_3243571_ [************************ ] 96% > Processing Locus CUFF.983_From_zu_0_3243571_ [************************ ] 97% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 98% > Processed 95 loci. [*************************] 100% [16:22:42] Loading reference annotation and sequence [16:22:42] Learning bias parameters. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 2% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 4% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 5% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 6% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 7% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 8% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 9% > Processing Locus CUFF.639_From_hi_0_2916184_ [** ] 10% > Processing Locus CUFF.641_From_kn_0_3605300_ [** ] 11% > Processing Locus CUFF.643_From_kn_0_3799876_ [*** ] 12% > Processing Locus CUFF.655_From_hi_0_2795398_ [*** ] 13% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 14% > Processing Locus CUFF.671_From_edi_0_2859720 [*** ] 15% > Processing Locus CUFF.675_From_mt_0_4213448_ [**** ] 16% > Processing Locus CUFF.679_From_ler_0_3998410 [**** ] 17% > Processing Locus CUFF.681_From_mt_0_4399784_ [**** ] 18% > Processing Locus CUFF.685_From_mt_0_4231054_ [***** ] 20% > Processing Locus CUFF.689_From_ler_0_4018856 [***** ] 21% > Processing Locus CUFF.691_From_hi_0_2961678_ [***** ] 22% > Processing Locus CUFF.695_From_mt_0_4217716_ [***** ] 23% > Processing Locus CUFF.697_From_mt_0_4229662_ [****** ] 24% > Processing Locus CUFF.699_From_no_0_2905273_ [****** ] 25% > Processing Locus CUFF.703_From_no_0_2885444_ [****** ] 26% > Processing Locus CUFF.725_From_no_0_3116640_ [****** ] 27% > Processing Locus CUFF.727_From_hi_0_2953648_ [******* ] 28% > Processing Locus CUFF.733_From_no_0_2956652_ [******* ] 29% > Processing Locus CUFF.743_From_po_0_3330421_ [******* ] 30% > Processing Locus CUFF.755_From_mt_0_4193196_ [******* ] 31% > Processing Locus CUFF.759_From_no_0_2936769_ [******** ] 32% > Processing Locus CUFF.763_From_rsch_4_403203 [******** ] 33% > Processing Locus CUFF.765_From_rsch_4_411079 [******** ] 34% > Processing Locus CUFF.785_From_no_0_3128142_ [******** ] 35% > Processing Locus CUFF.785_From_no_0_3128142_ [********* ] 36% > Processing Locus CUFF.789_From_rsch_4_427544 [********* ] 37% > Processing Locus CUFF.793_From_sf_2_2504999_ [********* ] 38% > Processing Locus CUFF.795_From_rsch_4_429714 [********** ] 40% > Processing Locus CUFF.807_From_sf_2_2488391_ [********** ] 41% > Processing Locus CUFF.817_From_sf_2_2524453_ [********** ] 42% > Processing Locus CUFF.831_From_sf_2_2687774_ [********** ] 43% > Processing Locus CUFF.839_From_sf_2_2680171_ [*********** ] 44% > Processing Locus CUFF.851_From_wil_2_2906137 [*********** ] 45% > Processing Locus CUFF.857_From_sf_2_2653966_ [*********** ] 46% > Processing Locus CUFF.861_From_mt_0_4528444_ [*********** ] 47% > Processing Locus CUFF.867_From_wil_2_2945095 [************ ] 48% > Processing Locus CUFF.871_From_rsch_4_426655 [************ ] 49% > Processing Locus CUFF.877_From_sf_2_2687786_ [************ ] 50% > Processing Locus CUFF.877_From_sf_2_2687786_ [************ ] 51% > Processing Locus CUFF.879_From_rsch_4_405516 [************* ] 52% > Processing Locus CUFF.881_From_wil_2_2925323 [************* ] 53% > Processing Locus CUFF.897_From_ws_0_3298283_ [************* ] 54% > Processing Locus CUFF.899_From_ws_0_3190963_ [************* ] 55% > Processing Locus CUFF.907_From_ws_0_3182508_ [************** ] 56% > Processing Locus CUFF.909_From_wil_2_3052273 [************** ] 57% > Processing Locus CUFF.913_From_wil_2_2834553 [************** ] 58% > Processing Locus CUFF.919_From_ws_0_3347582_ [*************** ] 60% > Processing Locus CUFF.921_From_wil_2_3077447 [*************** ] 61% > Processing Locus CUFF.925_From_ws_0_3371988_ [*************** ] 62% > Processing Locus CUFF.927_From_wu_0_2655481_ [*************** ] 63% > Processing Locus CUFF.935_From_ws_0_3380934_ [**************** ] 64% > Processing Locus CUFF.939_From_ws_0_3365892_ [**************** ] 65% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 66% > Processing Locus CUFF.947_From_wu_0_2654219_ [**************** ] 67% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 68% > Processing Locus CUFF.983_From_zu_0_3243571_ [***************** ] 69% > Processing Locus CUFF.987_From_zu_0_3118546_ [***************** ] 70% > Processed 68 loci. [*************************] 100% [16:22:42] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 2% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 4% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 5% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 6% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 7% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 8% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 9% > Processing Locus CUFF.639_From_hi_0_2916184_ [** ] 10% > Processing Locus CUFF.641_From_kn_0_3605300_ [** ] 11% > Processing Locus CUFF.643_From_kn_0_3799876_ [*** ] 12% > Processing Locus CUFF.655_From_hi_0_2795398_ [*** ] 13% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 14% > Processing Locus CUFF.671_From_edi_0_2859720 [*** ] 15% > Processing Locus CUFF.675_From_mt_0_4213448_ [**** ] 16% > Processing Locus CUFF.679_From_ler_0_3998410 [**** ] 17% > Processing Locus CUFF.681_From_mt_0_4399784_ [**** ] 18% > Processing Locus CUFF.685_From_mt_0_4231054_ [***** ] 20% > Processing Locus CUFF.689_From_ler_0_4018856 [***** ] 21% > Processing Locus CUFF.691_From_hi_0_2961678_ [***** ] 22% > Processing Locus CUFF.695_From_mt_0_4217716_ [***** ] 23% > Processing Locus CUFF.697_From_mt_0_4229662_ [****** ] 24% > Processing Locus CUFF.699_From_no_0_2905273_ [****** ] 25% > Processing Locus CUFF.703_From_no_0_2885444_ [****** ] 26% > Processing Locus CUFF.725_From_no_0_3116640_ [****** ] 27% > Processing Locus CUFF.727_From_hi_0_2953648_ [******* ] 28% > Processing Locus CUFF.733_From_no_0_2956652_ [******* ] 29% > Processing Locus CUFF.743_From_po_0_3330421_ [******* ] 30% > Processing Locus CUFF.755_From_mt_0_4193196_ [******* ] 31% > Processing Locus CUFF.759_From_no_0_2936769_ [******** ] 32% > Processing Locus CUFF.763_From_rsch_4_403203 [******** ] 33% > Processing Locus CUFF.765_From_rsch_4_411079 [******** ] 34% > Processing Locus CUFF.785_From_no_0_3128142_ [******** ] 35% > Processing Locus CUFF.785_From_no_0_3128142_ [********* ] 36% > Processing Locus CUFF.789_From_rsch_4_427544 [********* ] 37% > Processing Locus CUFF.793_From_sf_2_2504999_ [********* ] 38% > Processing Locus CUFF.795_From_rsch_4_429714 [********** ] 40% > Processing Locus CUFF.807_From_sf_2_2488391_ [********** ] 41% > Processing Locus CUFF.817_From_sf_2_2524453_ [********** ] 42% > Processing Locus CUFF.831_From_sf_2_2687774_ [********** ] 43% > Processing Locus CUFF.839_From_sf_2_2680171_ [*********** ] 44% > Processing Locus CUFF.851_From_wil_2_2906137 [*********** ] 45% > Processing Locus CUFF.857_From_sf_2_2653966_ [*********** ] 46% > Processing Locus CUFF.861_From_mt_0_4528444_ [*********** ] 47% > Processing Locus CUFF.867_From_wil_2_2945095 [************ ] 48% > Processing Locus CUFF.871_From_rsch_4_426655 [************ ] 49% > Processing Locus CUFF.877_From_sf_2_2687786_ [************ ] 50% > Processing Locus CUFF.877_From_sf_2_2687786_ [************ ] 51% > Processing Locus CUFF.879_From_rsch_4_405516 [************* ] 52% > Processing Locus CUFF.881_From_wil_2_2925323 [************* ] 53% > Processing Locus CUFF.897_From_ws_0_3298283_ [************* ] 54% > Processing Locus CUFF.899_From_ws_0_3190963_ [************* ] 55% > Processing Locus CUFF.907_From_ws_0_3182508_ [************** ] 56% > Processing Locus CUFF.909_From_wil_2_3052273 [************** ] 57% > Processing Locus CUFF.913_From_wil_2_2834553 [************** ] 58% > Processing Locus CUFF.919_From_ws_0_3347582_ [*************** ] 60% > Processing Locus CUFF.921_From_wil_2_3077447 [*************** ] 61% > Processing Locus CUFF.925_From_ws_0_3371988_ [*************** ] 62% > Processing Locus CUFF.927_From_wu_0_2655481_ [*************** ] 63% > Processing Locus CUFF.935_From_ws_0_3380934_ [**************** ] 64% > Processing Locus CUFF.939_From_ws_0_3365892_ [**************** ] 65% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 66% > Processing Locus CUFF.947_From_wu_0_2654219_ [**************** ] 67% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 68% > Processing Locus CUFF.983_From_zu_0_3243571_ [***************** ] 69% > Processing Locus CUFF.987_From_zu_0_3118546_ [***************** ] 70% > Processed 68 loci. [*************************] 100% [Mon Apr 4 16:22:43 2011] Reporting output tracks [Mon Apr 4 16:22:44 2011] Mapping reads against segment_juncs with Bowtie ----------------------------------------------- Run complete [00:01:46 elapsed] [Mon Apr 4 16:22:47 2011] Joining segment hits [Mon Apr 4 16:22:49 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:54 elapsed] cufflinks -p 4 -o ./Ler_0 -r ngene.fa ./Ler_0/accepted_hits.bam [16:22:51] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399Æ [ ] > Processing Locus CUFF.525_From_bur_0_1863298Æ [ ] > Processing Locus CUFF.529_From_bur_0_1873494Æ [ ] > Processing Locus CUFF.553_From_can_0_3223655Æ [ ] > Processing Locus CUFF.561_From_can_0_3189753Æ [ ] > Processing Locus CUFF.571_From_can_0_3076940Æ [ ] > Processing Locus CUFF.573_From_can_0_3233581Æ [ ] > Processing Locus CUFF.575_From_ct_1_3082021_Æ [ ] > Processing Locus CUFF.583_From_ct_1_3302721_Æ [ ] > Processing Locus CUFF.585_From_ct_1_3247037_Æ [ ] > Processing Locus CUFF.585_From_ct_1_3247037_Æ [ ] > Processing Locus CUFF.593_From_can_0_3270131Æ [* ] > Processing Locus CUFF.593_From_can_0_3270131Æ [* ] > Processing Locus CUFF.593_From_can_0_3270131Æ [* ] > Processing Locus CUFF.595_From_ct_1_3302721_Æ [* ] > Processing Locus CUFF.609_From_hi_0_2755116_Æ [* ] > Processing Locus CUFF.617_From_edi_0_2918156Æ [* ] > Processing Locus CUFF.623_From_hi_0_2778596_Æ [* ] > Processing Locus CUFF.635_From_ct_1_3241157_Æ [* ] > Processing Locus CUFF.639_From_hi_0_2916184_Æ [* ] > Processing Locus CUFF.651_From_ler_0_3967940Æ [* ] > Processing Locus CUFF.653_From_kn_0_3751597_Æ [* ] > Processing Locus CUFF.657_From_ler_0_3998132Æ [** ] > Processing Locus CUFF.663_From_kn_0_3613403_Æ [** ] > Processing Locus CUFF.665_From_hi_0_2939638_Æ [** ] > Processing Locus CUFF.666_From_ler_0_4004770Æ [** ] > Processing Locus CUFF.669_From_ler_0_4225073Æ [** ] > Processing Locus CUFF.671_From_edi_0_2859720Æ [** ] > Processing Locus CUFF.673_From_ler_0_4224097Æ [** ] > Processing Locus CUFF.679_From_ler_0_3998410Æ [** ] > Processing Locus CUFF.683_From_ler_0_4165287Æ [** ] > Processing Locus CUFF.685_From_mt_0_4231054_Æ [** ] > Processing Locus CUFF.687_From_mt_0_4230874_Æ [*** ] > Processing Locus CUFF.689_From_ler_0_4018856Æ [*** ] > Processing Locus CUFF.691_From_hi_0_2961678_Æ [*** ] > Processing Locus CUFF.693_From_no_0_2934639_Æ [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_Æ [*** ] > Processing Locus CUFF.697_From_mt_0_4229662_Æ [*** ] > Processing Locus CUFF.699_From_no_0_2905273_Æ [*** ] > Processing Locus CUFF.703_From_no_0_2885444_Æ [*** ] > Processing Locus CUFF.709_From_no_0_3101262_Æ [*** ] > Processing Locus CUFF.719_From_oy_0_2936927_Æ [**** ] > Processing Locus CUFF.727_From_hi_0_2953648_Æ [**** ] > Processing Locus CUFF.729_From_oy_0_3001818_Æ [**** ] > Processing Locus CUFF.731_From_po_0_3324652_Æ [**** ] > Processing Locus CUFF.733_From_no_0_2956652_Æ [**** ] > Processing Locus CUFF.737_From_ct_1_3132277_Æ [**** ] > Processing Locus CUFF.747_From_po_0_3299272_Æ [**** ] > Processing Locus CUFF.749_From_oy_0_3162092_Æ [**** ] > Processing Locus CUFF.749_From_oy_0_3162092_Æ [**** ] > Processing Locus CUFF.755_From_mt_0_4193196_Æ [**** ] > Processing Locus CUFF.763_From_rsch_4_403203Æ [**** ] > Processing Locus CUFF.779_From_rsch_4_421454Æ [***** ] > Processing Locus CUFF.783_From_oy_0_2965192_Æ [***** ] > Processing Locus CUFF.785_From_no_0_3128142_Æ [***** ] > Processing Locus CUFF.789_From_rsch_4_427544Æ [***** ] > Processing Locus CUFF.791_From_rsch_4_425553Æ [***** ] > Processing Locus CUFF.795_From_rsch_4_429714Æ [***** ] > Processing Locus CUFF.801_From_sf_2_2532172_Æ [***** ] > Processing Locus CUFF.805_From_sf_2_2486157_Æ [***** ] > Processing Locus CUFF.817_From_sf_2_2524453_Æ [***** ] > Processing Locus CUFF.819_From_tsu_0_3036945Æ [****** ] > Processing Locus CUFF.823_From_tsu_0_3175121Æ [****** ] > Processing Locus CUFF.825_From_sf_2_2700286_Æ [****** ] > Processing Locus CUFF.831_From_sf_2_2687774_Æ [****** ] > Processing Locus CUFF.835_From_tsu_0_3211741Æ [****** ] > Processing Locus CUFF.843_From_rsch_4_429219Æ [****** ] > Processing Locus CUFF.861_From_mt_0_4528444_Æ [****** ] > Processing Locus CUFF.877_From_sf_2_2687786_Æ [****** ] > Processing Locus CUFF.879_From_rsch_4_405516Æ [****** ] > Processing Locus CUFF.881_From_wil_2_2925323Æ [****** ] > Processing Locus CUFF.883_From_wil_2_3066229Æ [******* ] > Processing Locus CUFF.887_From_wil_2_3054893Æ [******* ] > Processing Locus CUFF.893_From_ws_0_3190679_Æ [******* ] > Processing Locus CUFF.907_From_ws_0_3182508_Æ [******* ] > Processing Locus CUFF.909_From_wil_2_3052273Æ [******* ] > Processing Locus CUFF.909_From_wil_2_3052273Æ [******* ] > Processing Locus CUFF.911_From_wil_2_3068737Æ [******* ] > Processing Locus CUFF.913_From_wil_2_2834553Æ [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_Æ [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_Æ [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_Æ [******* ] > Processing Locus CUFF.925_From_ws_0_3371988_Æ [******* ] > Processing Locus CUFF.935_From_ws_0_3380934_Æ [******** ] > Processing Locus CUFF.945_From_wu_0_2678387_Æ [******** ] > Processing Locus CUFF.947_From_wu_0_2654219_Æ [******** ] > Processing Locus CUFF.949_From_wu_0_2687576_Æ [******** ] > Processing Locus CUFF.955_From_ws_0_3340488_Æ [******** ] > Processing Locus CUFF.959_From_ws_0_3344070_Æ [******** ] > Processing Locus CUFF.965_From_zu_0_3238769_Æ [******** ] > Processing Locus CUFF.965_From_zu_0_3238769_Æ [******** ] > Processing Locus CUFF.969_From_zu_0_3190435_Æ [******** ] > Processing Locus CUFF.973_From_zu_0_3242889_Æ [******** ] > Processing Locus CUFF.977_From_zu_0_3255503_Æ [********* ] > Processing Locus CUFF.979_From_zu_0_3278243_Æ [********* ] > Processing Locus CUFF.987_From_zu_0_3118546_Æ [********* ] > Processing Locus CUFF.991_From_zu_0_3277661_Æ [********* ] > Processed 97 loci. [*************************] 100% > Map Properties: > Total Map Mass: 7616.81 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:22:51] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 1% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 2% > Processing Locus CUFF.553_From_can_0_3223655 [ ] 3% > Processing Locus CUFF.561_From_can_0_3189753 [* ] 4% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.573_From_can_0_3233581 [* ] 6% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 7% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 8% > Processing Locus CUFF.585_From_ct_1_3247037_ [** ] 9% > Processing Locus CUFF.585_From_ct_1_3247037_ [** ] 10% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 11% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 12% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 13% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 14% > Processing Locus CUFF.609_From_hi_0_2755116_ [*** ] 15% > Processing Locus CUFF.617_From_edi_0_2918156 [**** ] 16% > Processing Locus CUFF.623_From_hi_0_2778596_ [**** ] 17% > Processing Locus CUFF.635_From_ct_1_3241157_ [**** ] 18% > Processing Locus CUFF.639_From_hi_0_2916184_ [**** ] 19% > Processing Locus CUFF.651_From_ler_0_3967940 [***** ] 20% > Processing Locus CUFF.653_From_kn_0_3751597_ [***** ] 21% > Processing Locus CUFF.657_From_ler_0_3998132 [***** ] 22% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 23% > Processing Locus CUFF.665_From_hi_0_2939638_ [****** ] 24% > Processing Locus CUFF.666_From_ler_0_4004770 [****** ] 25% > Processing Locus CUFF.669_From_ler_0_4225073 [****** ] 26% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 27% > Processing Locus CUFF.673_From_ler_0_4224097 [******* ] 28% > Processing Locus CUFF.679_From_ler_0_3998410 [******* ] 29% > Processing Locus CUFF.683_From_ler_0_4165287 [******* ] 30% > Processing Locus CUFF.685_From_mt_0_4231054_ [******* ] 31% > Processing Locus CUFF.687_From_mt_0_4230874_ [******** ] 32% > Processing Locus CUFF.689_From_ler_0_4018856 [******** ] 34% > Processing Locus CUFF.691_From_hi_0_2961678_ [******** ] 35% > Processing Locus CUFF.693_From_no_0_2934639_ [********* ] 36% > Processing Locus CUFF.695_From_mt_0_4217716_ [********* ] 37% > Processing Locus CUFF.697_From_mt_0_4229662_ [********* ] 38% > Processing Locus CUFF.699_From_no_0_2905273_ [********* ] 39% > Processing Locus CUFF.703_From_no_0_2885444_ [********** ] 40% > Processing Locus CUFF.709_From_no_0_3101262_ [********** ] 41% > Processing Locus CUFF.719_From_oy_0_2936927_ [********** ] 42% > Processing Locus CUFF.727_From_hi_0_2953648_ [********** ] 43% > Processing Locus CUFF.729_From_oy_0_3001818_ [*********** ] 44% > Processing Locus CUFF.731_From_po_0_3324652_ [*********** ] 45% > Processing Locus CUFF.733_From_no_0_2956652_ [*********** ] 46% > Processing Locus CUFF.737_From_ct_1_3132277_ [*********** ] 47% > Processing Locus CUFF.747_From_po_0_3299272_ [************ ] 48% > Processing Locus CUFF.749_From_oy_0_3162092_ [************ ] 49% > Processing Locus CUFF.749_From_oy_0_3162092_ [************ ] 50% > Processing Locus CUFF.755_From_mt_0_4193196_ [************ ] 51% > Processing Locus CUFF.763_From_rsch_4_403203 [************* ] 52% > Processing Locus CUFF.779_From_rsch_4_421454 [************* ] 53% > Processing Locus CUFF.783_From_oy_0_2965192_ [************* ] 54% > Processing Locus CUFF.785_From_no_0_3128142_ [************* ] 55% > Processing Locus CUFF.789_From_rsch_4_427544 [************** ] 56% > Processing Locus CUFF.791_From_rsch_4_425553 [************** ] 57% > Processing Locus CUFF.795_From_rsch_4_429714 [************** ] 58% > Processing Locus CUFF.801_From_sf_2_2532172_ [************** ] 59% > Processing Locus CUFF.805_From_sf_2_2486157_ [*************** ] 60% > Processing Locus CUFF.817_From_sf_2_2524453_ [*************** ] 61% > Processing Locus CUFF.819_From_tsu_0_3036945 [*************** ] 62% > Processing Locus CUFF.823_From_tsu_0_3175121 [*************** ] 63% > Processing Locus CUFF.825_From_sf_2_2700286_ [**************** ] 64% > Processing Locus CUFF.831_From_sf_2_2687774_ [**************** ] 65% > Processing Locus CUFF.835_From_tsu_0_3211741 [**************** ] 67% > Processing Locus CUFF.843_From_rsch_4_429219 [***************** ] 68% > Processing Locus CUFF.861_From_mt_0_4528444_ [***************** ] 69% > Processing Locus CUFF.877_From_sf_2_2687786_ [***************** ] 70% > Processing Locus CUFF.879_From_rsch_4_405516 [***************** ] 71% > Processing Locus CUFF.881_From_wil_2_2925323 [****************** ] 72% > Processing Locus CUFF.883_From_wil_2_3066229 [****************** ] 73% > Processing Locus CUFF.887_From_wil_2_3054893 [****************** ] 74% > Processing Locus CUFF.893_From_ws_0_3190679_ [****************** ] 75% > Processing Locus CUFF.907_From_ws_0_3182508_ [******************* ] 76% > Processing Locus CUFF.909_From_wil_2_3052273 [******************* ] 77% > Processing Locus CUFF.909_From_wil_2_3052273 [******************* ] 78% > Processing Locus CUFF.911_From_wil_2_3068737 [******************* ] 79% > Processing Locus CUFF.913_From_wil_2_2834553 [******************** ] 80% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 81% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 82% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 83% > Processing Locus CUFF.925_From_ws_0_3371988_ [********************* ] 84% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************* ] 85% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************* ] 86% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************* ] 87% > Processing Locus CUFF.949_From_wu_0_2687576_ [********************** ] 88% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************** ] 89% > Processing Locus CUFF.959_From_ws_0_3344070_ [********************** ] 90% > Processing Locus CUFF.965_From_zu_0_3238769_ [********************** ] 91% > Processing Locus CUFF.965_From_zu_0_3238769_ [*********************** ] 92% > Processing Locus CUFF.969_From_zu_0_3190435_ [*********************** ] 93% > Processing Locus CUFF.973_From_zu_0_3242889_ [*********************** ] 94% > Processing Locus CUFF.977_From_zu_0_3255503_ [*********************** ] 95% > Processing Locus CUFF.979_From_zu_0_3278243_ [************************ ] 96% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 97% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 98% > Processed 97 loci. [*************************] 100% [16:22:51] Loading reference annotation and sequence [16:22:52] Learning bias parameters. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 1% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 2% > Processing Locus CUFF.553_From_can_0_3223655 [ ] 3% > Processing Locus CUFF.561_From_can_0_3189753 [* ] 4% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.573_From_can_0_3233581 [* ] 6% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 7% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 8% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.617_From_edi_0_2918156 [** ] 10% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 11% > Processing Locus CUFF.635_From_ct_1_3241157_ [*** ] 12% > Processing Locus CUFF.639_From_hi_0_2916184_ [*** ] 13% > Processing Locus CUFF.651_From_ler_0_3967940 [*** ] 14% > Processing Locus CUFF.657_From_ler_0_3998132 [*** ] 15% > Processing Locus CUFF.663_From_kn_0_3613403_ [**** ] 16% > Processing Locus CUFF.665_From_hi_0_2939638_ [**** ] 17% > Processing Locus CUFF.669_From_ler_0_4225073 [**** ] 18% > Processing Locus CUFF.671_From_edi_0_2859720 [**** ] 19% > Processing Locus CUFF.673_From_ler_0_4224097 [***** ] 20% > Processing Locus CUFF.679_From_ler_0_3998410 [***** ] 21% > Processing Locus CUFF.683_From_ler_0_4165287 [***** ] 22% > Processing Locus CUFF.687_From_mt_0_4230874_ [***** ] 23% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 24% > Processing Locus CUFF.691_From_hi_0_2961678_ [****** ] 25% > Processing Locus CUFF.693_From_no_0_2934639_ [****** ] 26% > Processing Locus CUFF.695_From_mt_0_4217716_ [****** ] 27% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 28% > Processing Locus CUFF.699_From_no_0_2905273_ [******* ] 29% > Processing Locus CUFF.703_From_no_0_2885444_ [******* ] 30% > Processing Locus CUFF.709_From_no_0_3101262_ [******* ] 31% > Processing Locus CUFF.719_From_oy_0_2936927_ [******** ] 32% > Processing Locus CUFF.727_From_hi_0_2953648_ [******** ] 34% > Processing Locus CUFF.729_From_oy_0_3001818_ [******** ] 35% > Processing Locus CUFF.731_From_po_0_3324652_ [********* ] 36% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 37% > Processing Locus CUFF.737_From_ct_1_3132277_ [********* ] 38% > Processing Locus CUFF.747_From_po_0_3299272_ [********* ] 39% > Processing Locus CUFF.755_From_mt_0_4193196_ [********** ] 40% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 41% > Processing Locus CUFF.779_From_rsch_4_421454 [********** ] 42% > Processing Locus CUFF.785_From_no_0_3128142_ [********** ] 43% > Processing Locus CUFF.789_From_rsch_4_427544 [*********** ] 44% > Processing Locus CUFF.791_From_rsch_4_425553 [*********** ] 45% > Processing Locus CUFF.795_From_rsch_4_429714 [*********** ] 46% > Processing Locus CUFF.801_From_sf_2_2532172_ [*********** ] 47% > Processing Locus CUFF.805_From_sf_2_2486157_ [************ ] 48% > Processing Locus CUFF.817_From_sf_2_2524453_ [************ ] 49% > Processing Locus CUFF.823_From_tsu_0_3175121 [************ ] 50% > Processing Locus CUFF.825_From_sf_2_2700286_ [************ ] 51% > Processing Locus CUFF.831_From_sf_2_2687774_ [************* ] 52% > Processing Locus CUFF.835_From_tsu_0_3211741 [************* ] 53% > Processing Locus CUFF.843_From_rsch_4_429219 [************* ] 54% > Processing Locus CUFF.861_From_mt_0_4528444_ [************* ] 55% > Processing Locus CUFF.877_From_sf_2_2687786_ [************** ] 56% > Processing Locus CUFF.879_From_rsch_4_405516 [************** ] 57% > Processing Locus CUFF.881_From_wil_2_2925323 [************** ] 58% > Processing Locus CUFF.883_From_wil_2_3066229 [************** ] 59% > Processing Locus CUFF.887_From_wil_2_3054893 [*************** ] 60% > Processing Locus CUFF.907_From_ws_0_3182508_ [*************** ] 61% > Processing Locus CUFF.909_From_wil_2_3052273 [*************** ] 62% > Processing Locus CUFF.911_From_wil_2_3068737 [*************** ] 63% > Processing Locus CUFF.913_From_wil_2_2834553 [**************** ] 64% > Processing Locus CUFF.919_From_ws_0_3347582_ [**************** ] 65% > Processing Locus CUFF.925_From_ws_0_3371988_ [**************** ] 67% > Processing Locus CUFF.935_From_ws_0_3380934_ [***************** ] 68% > Processing Locus CUFF.945_From_wu_0_2678387_ [***************** ] 69% > Processing Locus CUFF.947_From_wu_0_2654219_ [***************** ] 70% > Processing Locus CUFF.949_From_wu_0_2687576_ [***************** ] 71% > Processing Locus CUFF.955_From_ws_0_3340488_ [****************** ] 72% > Processing Locus CUFF.959_From_ws_0_3344070_ [****************** ] 73% > Processing Locus CUFF.969_From_zu_0_3190435_ [****************** ] 74% > Processing Locus CUFF.973_From_zu_0_3242889_ [****************** ] 75% > Processing Locus CUFF.977_From_zu_0_3255503_ [******************* ] 76% > Processing Locus CUFF.979_From_zu_0_3278243_ [******************* ] 77% > Processing Locus CUFF.987_From_zu_0_3118546_ [******************* ] 78% > Processing Locus CUFF.991_From_zu_0_3277661_ [******************* ] 79% > Processed 78 loci. [*************************] 100% [16:22:52] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 1% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 2% > Processing Locus CUFF.553_From_can_0_3223655 [ ] 3% > Processing Locus CUFF.561_From_can_0_3189753 [* ] 4% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.573_From_can_0_3233581 [* ] 6% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 7% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 8% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.617_From_edi_0_2918156 [** ] 10% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 11% > Processing Locus CUFF.635_From_ct_1_3241157_ [*** ] 12% > Processing Locus CUFF.639_From_hi_0_2916184_ [*** ] 13% > Processing Locus CUFF.651_From_ler_0_3967940 [*** ] 14% > Processing Locus CUFF.657_From_ler_0_3998132 [*** ] 15% > Processing Locus CUFF.663_From_kn_0_3613403_ [**** ] 16% > Processing Locus CUFF.665_From_hi_0_2939638_ [**** ] 17% > Processing Locus CUFF.669_From_ler_0_4225073 [**** ] 18% > Processing Locus CUFF.671_From_edi_0_2859720 [**** ] 19% > Processing Locus CUFF.673_From_ler_0_4224097 [***** ] 20% > Processing Locus CUFF.679_From_ler_0_3998410 [***** ] 21% > Processing Locus CUFF.683_From_ler_0_4165287 [***** ] 22% > Processing Locus CUFF.687_From_mt_0_4230874_ [***** ] 23% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 24% > Processing Locus CUFF.691_From_hi_0_2961678_ [****** ] 25% > Processing Locus CUFF.693_From_no_0_2934639_ [****** ] 26% > Processing Locus CUFF.695_From_mt_0_4217716_ [****** ] 27% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 28% > Processing Locus CUFF.699_From_no_0_2905273_ [******* ] 29% > Processing Locus CUFF.703_From_no_0_2885444_ [******* ] 30% > Processing Locus CUFF.709_From_no_0_3101262_ [******* ] 31% > Processing Locus CUFF.719_From_oy_0_2936927_ [******** ] 32% > Processing Locus CUFF.727_From_hi_0_2953648_ [******** ] 34% > Processing Locus CUFF.729_From_oy_0_3001818_ [******** ] 35% > Processing Locus CUFF.731_From_po_0_3324652_ [********* ] 36% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 37% > Processing Locus CUFF.737_From_ct_1_3132277_ [********* ] 38% > Processing Locus CUFF.747_From_po_0_3299272_ [********* ] 39% > Processing Locus CUFF.755_From_mt_0_4193196_ [********** ] 40% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 41% > Processing Locus CUFF.779_From_rsch_4_421454 [********** ] 42% > Processing Locus CUFF.785_From_no_0_3128142_ [********** ] 43% > Processing Locus CUFF.789_From_rsch_4_427544 [*********** ] 44% > Processing Locus CUFF.791_From_rsch_4_425553 [*********** ] 45% > Processing Locus CUFF.795_From_rsch_4_429714 [*********** ] 46% > Processing Locus CUFF.801_From_sf_2_2532172_ [*********** ] 47% > Processing Locus CUFF.805_From_sf_2_2486157_ [************ ] 48% > Processing Locus CUFF.817_From_sf_2_2524453_ [************ ] 49% > Processing Locus CUFF.823_From_tsu_0_3175121 [************ ] 50% > Processing Locus CUFF.825_From_sf_2_2700286_ [************ ] 51% > Processing Locus CUFF.831_From_sf_2_2687774_ [************* ] 52% > Processing Locus CUFF.835_From_tsu_0_3211741 [************* ] 53% > Processing Locus CUFF.843_From_rsch_4_429219 [************* ] 54% > Processing Locus CUFF.861_From_mt_0_4528444_ [************* ] 55% > Processing Locus CUFF.877_From_sf_2_2687786_ [************** ] 56% > Processing Locus CUFF.879_From_rsch_4_405516 [************** ] 57% > Processing Locus CUFF.881_From_wil_2_2925323 [************** ] 58% > Processing Locus CUFF.883_From_wil_2_3066229 [************** ] 59% > Processing Locus CUFF.887_From_wil_2_3054893 [*************** ] 60% > Processing Locus CUFF.907_From_ws_0_3182508_ [*************** ] 61% > Processing Locus CUFF.909_From_wil_2_3052273 [*************** ] 62% > Processing Locus CUFF.911_From_wil_2_3068737 [*************** ] 63% > Processing Locus CUFF.913_From_wil_2_2834553 [**************** ] 64% > Processing Locus CUFF.919_From_ws_0_3347582_ [**************** ] 65% > Processing Locus CUFF.925_From_ws_0_3371988_ [**************** ] 67% > Processing Locus CUFF.935_From_ws_0_3380934_ [***************** ] 68% > Processing Locus CUFF.945_From_wu_0_2678387_ [***************** ] 69% > Processing Locus CUFF.947_From_wu_0_2654219_ [***************** ] 70% > Processing Locus CUFF.949_From_wu_0_2687576_ [***************** ] 71% > Processing Locus CUFF.955_From_ws_0_3340488_ [****************** ] 72% > Processing Locus CUFF.959_From_ws_0_3344070_ [****************** ] 73% > Processing Locus CUFF.969_From_zu_0_3190435_ [****************** ] 74% > Processing Locus CUFF.973_From_zu_0_3242889_ [****************** ] 75% > Processing Locus CUFF.977_From_zu_0_3255503_ [******************* ] 76% > Processing Locus CUFF.979_From_zu_0_3278243_ [******************* ] 77% > Processing Locus CUFF.987_From_zu_0_3118546_ [******************* ] 78% > Processing Locus CUFF.991_From_zu_0_3277661_ [******************* ] 79% > Processed 78 loci. [*************************] 100% cufflinks -p 4 -o ./Kn_0 -r ngene.fa ./Kn_0/accepted_hits.bam [16:22:56] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.525_From_bur_0_1863298ƒ [ ] > Processing Locus CUFF.553_From_can_0_3223655ƒ [ ] > Processing Locus CUFF.561_From_can_0_3189753ƒ [ ] > Processing Locus CUFF.571_From_can_0_3076940ƒ [ ] > Processing Locus CUFF.573_From_can_0_3233581ƒ [ ] > Processing Locus CUFF.575_From_ct_1_3082021_ƒ [ ] > Processing Locus CUFF.583_From_ct_1_3302721_ƒ [ ] > Processing Locus CUFF.585_From_ct_1_3247037_ƒ [ ] > Processing Locus CUFF.589_From_edi_0_2723255ƒ [ ] > Processing Locus CUFF.593_From_can_0_3270131ƒ [ ] > Processing Locus CUFF.593_From_can_0_3270131ƒ [ ] > Processing Locus CUFF.595_From_ct_1_3302721_ƒ [* ] > Processing Locus CUFF.597_From_edi_0_2759827ƒ [* ] > Processing Locus CUFF.601_From_edi_0_2934714ƒ [* ] > Processing Locus CUFF.604_From_edi_0_2934714ƒ [* ] > Processing Locus CUFF.604_From_edi_0_2934714ƒ [* ] > Processing Locus CUFF.609_From_hi_0_2755116_ƒ [* ] > Processing Locus CUFF.615_From_edi_0_2932438ƒ [* ] > Processing Locus CUFF.619_From_edi_0_2871668ƒ [* ] > Processing Locus CUFF.621_From_edi_0_2934714ƒ [* ] > Processing Locus CUFF.621_From_edi_0_2934714ƒ [* ] > Processing Locus CUFF.621_From_edi_0_2934714ƒ [* ] > Processing Locus CUFF.621_From_edi_0_2934714ƒ [* ] > Processing Locus CUFF.621_From_edi_0_2934714ƒ [* ] > Processing Locus CUFF.621_From_edi_0_2934714ƒ [* ] > Processing Locus CUFF.625_From_hi_0_2964064_ƒ [* ] > Processing Locus CUFF.629_From_kn_0_3594465_ƒ [** ] > Processing Locus CUFF.637_From_kn_0_3626969_ƒ [** ] > Processing Locus CUFF.641_From_kn_0_3605300_ƒ [** ] > Processing Locus CUFF.643_From_kn_0_3799876_ƒ [** ] > Processing Locus CUFF.643_From_kn_0_3799876_ƒ [** ] > Processing Locus CUFF.643_From_kn_0_3799876_ƒ [** ] > Processing Locus CUFF.647_From_kn_0_3802200_ƒ [** ] > Processing Locus CUFF.649_From_kn_0_3617271_ƒ [** ] > Processing Locus CUFF.655_From_hi_0_2795398_ƒ [** ] > Processing Locus CUFF.661_From_kn_0_3819922_ƒ [** ] > Processing Locus CUFF.661_From_kn_0_3819922_ƒ [** ] > Processing Locus CUFF.661_From_kn_0_3819922_ƒ [** ] > Processing Locus CUFF.663_From_kn_0_3613403_ƒ [** ] > Processing Locus CUFF.665_From_hi_0_2939638_ƒ [** ] > Processing Locus CUFF.666_From_ler_0_4004770ƒ [*** ] > Processing Locus CUFF.671_From_edi_0_2859720ƒ [*** ] > Processing Locus CUFF.673_From_ler_0_4224097ƒ [*** ] > Processing Locus CUFF.679_From_ler_0_3998410ƒ [*** ] > Processing Locus CUFF.683_From_ler_0_4165287ƒ [*** ] > Processing Locus CUFF.685_From_mt_0_4231054_ƒ [*** ] > Processing Locus CUFF.687_From_mt_0_4230874_ƒ [*** ] > Processing Locus CUFF.689_From_ler_0_4018856ƒ [*** ] > Processing Locus CUFF.693_From_no_0_2934639_ƒ [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_ƒ [**** ] > Processing Locus CUFF.697_From_mt_0_4229662_ƒ [**** ] > Processing Locus CUFF.699_From_no_0_2905273_ƒ [**** ] > Processing Locus CUFF.701_From_no_0_2951521_ƒ [**** ] > Processing Locus CUFF.703_From_no_0_2885444_ƒ [**** ] > Processing Locus CUFF.705_From_no_0_3113578_ƒ [**** ] > Processing Locus CUFF.707_From_no_0_2959683_ƒ [**** ] > Processing Locus CUFF.723_From_po_0_3306688_ƒ [**** ] > Processing Locus CUFF.729_From_oy_0_3001818_ƒ [**** ] > Processing Locus CUFF.733_From_no_0_2956652_ƒ [**** ] > Processing Locus CUFF.737_From_ct_1_3132277_ƒ [***** ] > Processing Locus CUFF.741_From_po_0_3382155_ƒ [***** ] > Processing Locus CUFF.747_From_po_0_3299272_ƒ [***** ] > Processing Locus CUFF.749_From_oy_0_3162092_ƒ [***** ] > Processing Locus CUFF.753_From_oy_0_3121110_ƒ [***** ] > Processing Locus CUFF.755_From_mt_0_4193196_ƒ [***** ] > Processing Locus CUFF.757_From_po_0_3372769_ƒ [***** ] > Processing Locus CUFF.759_From_no_0_2936769_ƒ [***** ] > Processing Locus CUFF.763_From_rsch_4_403203ƒ [***** ] > Processing Locus CUFF.767_From_rsch_4_411814ƒ [****** ] > Processing Locus CUFF.771_From_po_0_3332479_ƒ [****** ] > Processing Locus CUFF.775_From_rsch_4_409124ƒ [****** ] > Processing Locus CUFF.779_From_rsch_4_421454ƒ [****** ] > Processing Locus CUFF.791_From_rsch_4_425553ƒ [****** ] > Processing Locus CUFF.795_From_rsch_4_429714ƒ [****** ] > Processing Locus CUFF.803_From_po_0_3573778_ƒ [****** ] > Processing Locus CUFF.817_From_sf_2_2524453_ƒ [****** ] > Processing Locus CUFF.843_From_rsch_4_429219ƒ [****** ] > Processing Locus CUFF.861_From_mt_0_4528444_ƒ [****** ] > Processing Locus CUFF.867_From_wil_2_2945095ƒ [******* ] > Processing Locus CUFF.871_From_rsch_4_426655ƒ [******* ] > Processing Locus CUFF.879_From_rsch_4_405516ƒ [******* ] > Processing Locus CUFF.883_From_wil_2_3066229ƒ [******* ] > Processing Locus CUFF.887_From_wil_2_3054893ƒ [******* ] > Processing Locus CUFF.893_From_ws_0_3190679_ƒ [******* ] > Processing Locus CUFF.895_From_tsu_0_3215821ƒ [******* ] > Processing Locus CUFF.897_From_ws_0_3298283_ƒ [******* ] > Processing Locus CUFF.901_From_wil_2_3088151ƒ [******* ] > Processing Locus CUFF.901_From_wil_2_3088151ƒ [******* ] > Processing Locus CUFF.901_From_wil_2_3088151ƒ [******* ] > Processing Locus CUFF.907_From_ws_0_3182508_ƒ [******** ] > Processing Locus CUFF.911_From_wil_2_3068737ƒ [******** ] > Processing Locus CUFF.913_From_wil_2_2834553ƒ [******** ] > Processing Locus CUFF.925_From_ws_0_3371988_ƒ [******** ] > Processing Locus CUFF.935_From_ws_0_3380934_ƒ [******** ] > Processing Locus CUFF.945_From_wu_0_2678387_ƒ [******** ] > Processing Locus CUFF.955_From_ws_0_3340488_ƒ [******** ] > Processing Locus CUFF.957_From_ws_0_3381390_ƒ [******** ] > Processing Locus CUFF.965_From_zu_0_3238769_ƒ [******** ] > Processing Locus CUFF.973_From_zu_0_3242889_ƒ [********* ] > Processing Locus CUFF.975_From_zu_0_3259399_ƒ [********* ] > Processing Locus CUFF.977_From_zu_0_3255503_ƒ [********* ] > Processing Locus CUFF.979_From_zu_0_3278243_ƒ [********* ] > Processing Locus CUFF.987_From_zu_0_3118546_ƒ [********* ] > Processing Locus CUFF.991_From_zu_0_3277661_ƒ [********* ] > Processed 104 loci. [*************************] 100% > Map Properties: > Total Map Mass: 7219.98 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:22:56] Assembling transcripts and estimating abundances. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.553_From_can_0_3223655 [ ] 0% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 1% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 2% > Processing Locus CUFF.573_From_can_0_3233581 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.583_From_ct_1_3302721_ [* ] 5% > Processing Locus CUFF.585_From_ct_1_3247037_ [* ] 6% > Processing Locus CUFF.589_From_edi_0_2723255 [* ] 7% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 8% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 9% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 10% > Processing Locus CUFF.597_From_edi_0_2759827 [** ] 11% > Processing Locus CUFF.601_From_edi_0_2934714 [*** ] 12% > Processing Locus CUFF.604_From_edi_0_2934714 [*** ] 13% > Processing Locus CUFF.604_From_edi_0_2934714 [*** ] 14% > Processing Locus CUFF.609_From_hi_0_2755116_ [*** ] 15% > Processing Locus CUFF.615_From_edi_0_2932438 [**** ] 16% > Processing Locus CUFF.619_From_edi_0_2871668 [**** ] 17% > Processing Locus CUFF.621_From_edi_0_2934714 [**** ] 18% > Processing Locus CUFF.621_From_edi_0_2934714 [**** ] 19% > Processing Locus CUFF.621_From_edi_0_2934714 [***** ] 20% > Processing Locus CUFF.621_From_edi_0_2934714 [***** ] 21% > Processing Locus CUFF.621_From_edi_0_2934714 [***** ] 22% > Processing Locus CUFF.621_From_edi_0_2934714 [***** ] 23% > Processing Locus CUFF.625_From_hi_0_2964064_ [****** ] 24% > Processing Locus CUFF.629_From_kn_0_3594465_ [****** ] 25% > Processing Locus CUFF.637_From_kn_0_3626969_ [****** ] 25% > Processing Locus CUFF.641_From_kn_0_3605300_ [****** ] 26% > Processing Locus CUFF.643_From_kn_0_3799876_ [****** ] 27% > Processing Locus CUFF.643_From_kn_0_3799876_ [******* ] 28% > Processing Locus CUFF.643_From_kn_0_3799876_ [******* ] 29% > Processing Locus CUFF.647_From_kn_0_3802200_ [******* ] 30% > Processing Locus CUFF.649_From_kn_0_3617271_ [******* ] 31% > Processing Locus CUFF.655_From_hi_0_2795398_ [******** ] 32% > Processing Locus CUFF.661_From_kn_0_3819922_ [******** ] 33% > Processing Locus CUFF.661_From_kn_0_3819922_ [******** ] 34% > Processing Locus CUFF.661_From_kn_0_3819922_ [******** ] 35% > Processing Locus CUFF.663_From_kn_0_3613403_ [********* ] 36% > Processing Locus CUFF.665_From_hi_0_2939638_ [********* ] 37% > Processing Locus CUFF.666_From_ler_0_4004770 [********* ] 38% > Processing Locus CUFF.671_From_edi_0_2859720 [********* ] 39% > Processing Locus CUFF.673_From_ler_0_4224097 [********** ] 40% > Processing Locus CUFF.679_From_ler_0_3998410 [********** ] 41% > Processing Locus CUFF.683_From_ler_0_4165287 [********** ] 42% > Processing Locus CUFF.685_From_mt_0_4231054_ [********** ] 43% > Processing Locus CUFF.687_From_mt_0_4230874_ [*********** ] 44% > Processing Locus CUFF.689_From_ler_0_4018856 [*********** ] 45% > Processing Locus CUFF.693_From_no_0_2934639_ [*********** ] 46% > Processing Locus CUFF.695_From_mt_0_4217716_ [*********** ] 47% > Processing Locus CUFF.697_From_mt_0_4229662_ [************ ] 48% > Processing Locus CUFF.699_From_no_0_2905273_ [************ ] 49% > Processing Locus CUFF.701_From_no_0_2951521_ [************ ] 50% > Processing Locus CUFF.703_From_no_0_2885444_ [************ ] 50% > Processing Locus CUFF.705_From_no_0_3113578_ [************ ] 51% > Processing Locus CUFF.707_From_no_0_2959683_ [************* ] 52% > Processing Locus CUFF.723_From_po_0_3306688_ [************* ] 53% > Processing Locus CUFF.729_From_oy_0_3001818_ [************* ] 54% > Processing Locus CUFF.733_From_no_0_2956652_ [************* ] 55% > Processing Locus CUFF.737_From_ct_1_3132277_ [************** ] 56% > Processing Locus CUFF.741_From_po_0_3382155_ [************** ] 57% > Processing Locus CUFF.747_From_po_0_3299272_ [************** ] 58% > Processing Locus CUFF.749_From_oy_0_3162092_ [************** ] 59% > Processing Locus CUFF.753_From_oy_0_3121110_ [*************** ] 60% > Processing Locus CUFF.755_From_mt_0_4193196_ [*************** ] 61% > Processing Locus CUFF.757_From_po_0_3372769_ [*************** ] 62% > Processing Locus CUFF.759_From_no_0_2936769_ [*************** ] 63% > Processing Locus CUFF.763_From_rsch_4_403203 [**************** ] 64% > Processing Locus CUFF.767_From_rsch_4_411814 [**************** ] 65% > Processing Locus CUFF.771_From_po_0_3332479_ [**************** ] 66% > Processing Locus CUFF.775_From_rsch_4_409124 [**************** ] 67% > Processing Locus CUFF.779_From_rsch_4_421454 [***************** ] 68% > Processing Locus CUFF.791_From_rsch_4_425553 [***************** ] 69% > Processing Locus CUFF.795_From_rsch_4_429714 [***************** ] 70% > Processing Locus CUFF.803_From_po_0_3573778_ [***************** ] 71% > Processing Locus CUFF.817_From_sf_2_2524453_ [****************** ] 72% > Processing Locus CUFF.843_From_rsch_4_429219 [****************** ] 73% > Processing Locus CUFF.861_From_mt_0_4528444_ [****************** ] 74% > Processing Locus CUFF.867_From_wil_2_2945095 [****************** ] 75% > Processing Locus CUFF.871_From_rsch_4_426655 [****************** ] 75% > Processing Locus CUFF.879_From_rsch_4_405516 [******************* ] 76% > Processing Locus CUFF.883_From_wil_2_3066229 [******************* ] 77% > Processing Locus CUFF.887_From_wil_2_3054893 [******************* ] 78% > Processing Locus CUFF.893_From_ws_0_3190679_ [******************* ] 79% > Processing Locus CUFF.895_From_tsu_0_3215821 [******************** ] 80% > Processing Locus CUFF.897_From_ws_0_3298283_ [******************** ] 81% > Processing Locus CUFF.901_From_wil_2_3088151 [******************** ] 82% > Processing Locus CUFF.901_From_wil_2_3088151 [******************** ] 83% > Processing Locus CUFF.901_From_wil_2_3088151 [********************* ] 84% > Processing Locus CUFF.907_From_ws_0_3182508_ [********************* ] 85% > Processing Locus CUFF.911_From_wil_2_3068737 [********************* ] 86% > Processing Locus CUFF.913_From_wil_2_2834553 [********************* ] 87% > Processing Locus CUFF.925_From_ws_0_3371988_ [********************** ] 88% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************** ] 89% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************** ] 90% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************** ] 91% > Processing Locus CUFF.957_From_ws_0_3381390_ [*********************** ] 92% > Processing Locus CUFF.965_From_zu_0_3238769_ [*********************** ] 93% > Processing Locus CUFF.973_From_zu_0_3242889_ [*********************** ] 94% > Processing Locus CUFF.975_From_zu_0_3259399_ [*********************** ] 95% > Processing Locus CUFF.977_From_zu_0_3255503_ [************************ ] 96% > Processing Locus CUFF.979_From_zu_0_3278243_ [************************ ] 97% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 98% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 99% > Processed 104 loci. [*************************] 100% [16:22:56] Loading reference annotation and sequence [16:22:56] Learning bias parameters. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 0% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 1% > Processing Locus CUFF.573_From_can_0_3233581 [ ] 2% > Processing Locus CUFF.575_From_ct_1_3082021_ [ ] 3% > Processing Locus CUFF.585_From_ct_1_3247037_ [* ] 4% > Processing Locus CUFF.589_From_edi_0_2723255 [* ] 5% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 6% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 7% > Processing Locus CUFF.597_From_edi_0_2759827 [** ] 8% > Processing Locus CUFF.615_From_edi_0_2932438 [** ] 9% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 10% > Processing Locus CUFF.625_From_hi_0_2964064_ [** ] 11% > Processing Locus CUFF.629_From_kn_0_3594465_ [*** ] 12% > Processing Locus CUFF.637_From_kn_0_3626969_ [*** ] 13% > Processing Locus CUFF.641_From_kn_0_3605300_ [*** ] 14% > Processing Locus CUFF.643_From_kn_0_3799876_ [*** ] 15% > Processing Locus CUFF.643_From_kn_0_3799876_ [**** ] 16% > Processing Locus CUFF.647_From_kn_0_3802200_ [**** ] 17% > Processing Locus CUFF.649_From_kn_0_3617271_ [**** ] 18% > Processing Locus CUFF.655_From_hi_0_2795398_ [**** ] 19% > Processing Locus CUFF.661_From_kn_0_3819922_ [***** ] 20% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 21% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 22% > Processing Locus CUFF.666_From_ler_0_4004770 [***** ] 23% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 24% > Processing Locus CUFF.673_From_ler_0_4224097 [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 25% > Processing Locus CUFF.683_From_ler_0_4165287 [****** ] 26% > Processing Locus CUFF.685_From_mt_0_4231054_ [****** ] 27% > Processing Locus CUFF.687_From_mt_0_4230874_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.693_From_no_0_2934639_ [******* ] 30% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 31% > Processing Locus CUFF.697_From_mt_0_4229662_ [******** ] 32% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 33% > Processing Locus CUFF.701_From_no_0_2951521_ [******** ] 34% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 35% > Processing Locus CUFF.707_From_no_0_2959683_ [********* ] 36% > Processing Locus CUFF.723_From_po_0_3306688_ [********* ] 37% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 38% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 39% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 40% > Processing Locus CUFF.741_From_po_0_3382155_ [********** ] 41% > Processing Locus CUFF.747_From_po_0_3299272_ [********** ] 42% > Processing Locus CUFF.749_From_oy_0_3162092_ [********** ] 43% > Processing Locus CUFF.753_From_oy_0_3121110_ [*********** ] 44% > Processing Locus CUFF.755_From_mt_0_4193196_ [*********** ] 45% > Processing Locus CUFF.757_From_po_0_3372769_ [*********** ] 46% > Processing Locus CUFF.759_From_no_0_2936769_ [*********** ] 47% > Processing Locus CUFF.763_From_rsch_4_403203 [************ ] 48% > Processing Locus CUFF.767_From_rsch_4_411814 [************ ] 49% > Processing Locus CUFF.771_From_po_0_3332479_ [************ ] 50% > Processing Locus CUFF.775_From_rsch_4_409124 [************ ] 50% > Processing Locus CUFF.779_From_rsch_4_421454 [************ ] 51% > Processing Locus CUFF.791_From_rsch_4_425553 [************* ] 52% > Processing Locus CUFF.795_From_rsch_4_429714 [************* ] 53% > Processing Locus CUFF.803_From_po_0_3573778_ [************* ] 54% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 55% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 56% > Processing Locus CUFF.861_From_mt_0_4528444_ [************** ] 57% > Processing Locus CUFF.867_From_wil_2_2945095 [************** ] 58% > Processing Locus CUFF.871_From_rsch_4_426655 [************** ] 59% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 60% > Processing Locus CUFF.883_From_wil_2_3066229 [*************** ] 61% > Processing Locus CUFF.887_From_wil_2_3054893 [*************** ] 62% > Processing Locus CUFF.897_From_ws_0_3298283_ [*************** ] 63% > Processing Locus CUFF.911_From_wil_2_3068737 [**************** ] 64% > Processing Locus CUFF.925_From_ws_0_3371988_ [**************** ] 65% > Processing Locus CUFF.935_From_ws_0_3380934_ [**************** ] 66% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 67% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 68% > Processing Locus CUFF.957_From_ws_0_3381390_ [***************** ] 69% > Processing Locus CUFF.973_From_zu_0_3242889_ [***************** ] 70% > Processing Locus CUFF.975_From_zu_0_3259399_ [***************** ] 71% > Processing Locus CUFF.977_From_zu_0_3255503_ [****************** ] 72% > Processing Locus CUFF.979_From_zu_0_3278243_ [****************** ] 73% > Processing Locus CUFF.987_From_zu_0_3118546_ [****************** ] 74% > Processing Locus CUFF.991_From_zu_0_3277661_ [****************** ] 75% > Processed 79 loci. [*************************] 100% [16:22:56] Assembling transcripts and estimating abundances. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 0% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 1% > Processing Locus CUFF.573_From_can_0_3233581 [ ] 2% > Processing Locus CUFF.575_From_ct_1_3082021_ [ ] 3% > Processing Locus CUFF.585_From_ct_1_3247037_ [* ] 4% > Processing Locus CUFF.589_From_edi_0_2723255 [* ] 5% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 6% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 7% > Processing Locus CUFF.597_From_edi_0_2759827 [** ] 8% > Processing Locus CUFF.615_From_edi_0_2932438 [** ] 9% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 10% > Processing Locus CUFF.625_From_hi_0_2964064_ [** ] 11% > Processing Locus CUFF.629_From_kn_0_3594465_ [*** ] 12% > Processing Locus CUFF.637_From_kn_0_3626969_ [*** ] 13% > Processing Locus CUFF.641_From_kn_0_3605300_ [*** ] 14% > Processing Locus CUFF.643_From_kn_0_3799876_ [*** ] 15% > Processing Locus CUFF.643_From_kn_0_3799876_ [**** ] 16% > Processing Locus CUFF.647_From_kn_0_3802200_ [**** ] 17% > Processing Locus CUFF.649_From_kn_0_3617271_ [**** ] 18% > Processing Locus CUFF.655_From_hi_0_2795398_ [**** ] 19% > Processing Locus CUFF.661_From_kn_0_3819922_ [***** ] 20% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 21% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 22% > Processing Locus CUFF.666_From_ler_0_4004770 [***** ] 23% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 24% > Processing Locus CUFF.673_From_ler_0_4224097 [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 25% > Processing Locus CUFF.683_From_ler_0_4165287 [****** ] 26% > Processing Locus CUFF.685_From_mt_0_4231054_ [****** ] 27% > Processing Locus CUFF.687_From_mt_0_4230874_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.693_From_no_0_2934639_ [******* ] 30% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 31% > Processing Locus CUFF.697_From_mt_0_4229662_ [******** ] 32% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 33% > Processing Locus CUFF.701_From_no_0_2951521_ [******** ] 34% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 35% > Processing Locus CUFF.707_From_no_0_2959683_ [********* ] 36% > Processing Locus CUFF.723_From_po_0_3306688_ [********* ] 37% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 38% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 39% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 40% > Processing Locus CUFF.741_From_po_0_3382155_ [********** ] 41% > Processing Locus CUFF.747_From_po_0_3299272_ [********** ] 42% > Processing Locus CUFF.749_From_oy_0_3162092_ [********** ] 43% > Processing Locus CUFF.753_From_oy_0_3121110_ [*********** ] 44% > Processing Locus CUFF.755_From_mt_0_4193196_ [*********** ] 45% > Processing Locus CUFF.757_From_po_0_3372769_ [*********** ] 46% > Processing Locus CUFF.759_From_no_0_2936769_ [*********** ] 47% > Processing Locus CUFF.763_From_rsch_4_403203 [************ ] 48% > Processing Locus CUFF.767_From_rsch_4_411814 [************ ] 49% > Processing Locus CUFF.771_From_po_0_3332479_ [************ ] 50% > Processing Locus CUFF.775_From_rsch_4_409124 [************ ] 50% > Processing Locus CUFF.779_From_rsch_4_421454 [************ ] 51% > Processing Locus CUFF.791_From_rsch_4_425553 [************* ] 52% > Processing Locus CUFF.795_From_rsch_4_429714 [************* ] 53% > Processing Locus CUFF.803_From_po_0_3573778_ [************* ] 54% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 55% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 56% > Processing Locus CUFF.861_From_mt_0_4528444_ [************** ] 57% > Processing Locus CUFF.867_From_wil_2_2945095 [************** ] 58% > Processing Locus CUFF.871_From_rsch_4_426655 [************** ] 59% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 60% > Processing Locus CUFF.883_From_wil_2_3066229 [*************** ] 61% > Processing Locus CUFF.887_From_wil_2_3054893 [*************** ] 62% > Processing Locus CUFF.897_From_ws_0_3298283_ [*************** ] 63% > Processing Locus CUFF.911_From_wil_2_3068737 [**************** ] 64% > Processing Locus CUFF.925_From_ws_0_3371988_ [**************** ] 65% > Processing Locus CUFF.935_From_ws_0_3380934_ [**************** ] 66% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 67% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 68% > Processing Locus CUFF.957_From_ws_0_3381390_ [***************** ] 69% > Processing Locus CUFF.973_From_zu_0_3242889_ [***************** ] 70% > Processing Locus CUFF.975_From_zu_0_3259399_ [***************** ] 71% > Processing Locus CUFF.977_From_zu_0_3255503_ [****************** ] 72% > Processing Locus CUFF.979_From_zu_0_3278243_ [****************** ] 73% > Processing Locus CUFF.987_From_zu_0_3118546_ [****************** ] 74% > Processing Locus CUFF.991_From_zu_0_3277661_ [****************** ] 75% > Processed 79 loci. [*************************] 100% file: /data/arabidopsis/xiang/magic_founder/Mt_0_R1/R38_L5_Mt_0_sdlg_R1_nss_barcode_ACG.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Mt_0_R2/R38_L6_Mt_0_sdlg_R2_nss_barcode_ACG.unmap_1.fq file: /data/arabidopsis/xiang/magic_founder/No_0_R1/R38_L5_No_0_sdlg_R1_nss_barcode_CAT.unmap_1.fq /data/arabidopsis/xiang/magic_founder/No_0_R2/R38_L6_No_0_sdlg_R2_nss_barcode_CAT.unmap_1.fq file: /data/arabidopsis/xiang/magic_founder/Oy_0_R1/R38_L5_Oy_0_sdlg_R1_nss_barcode_GTA.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Oy_0_R2/R38_L6_Oy_0_sdlg_R2_nss_barcode_GTA.unmap_1.fq file: /data/arabidopsis/xiang/magic_founder/Po_0_R1/R38_L5_Po_0_sdlg_R1_nss_barcode_TGC.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Po_0_R2/R38_L6_Po_0_sdlg_R2_nss_barcode_TGC.unmap_1.fq $RNAGI/rnagi.sh -o ./No_0 -n ngene.fa No_0.Tongene.merge.fq reference: ngene.fa $RNAGI/rnagi.sh -o ./Mt_0 -n ngene.fa Mt_0.Tongene.merge.fq reference: ngene.fa $RNAGI/rnagi.sh -o ./Oy_0 -n ngene.fa Oy_0.Tongene.merge.fq reference: ngene.fa $RNAGI/rnagi.sh -o ./Po_0 -n ngene.fa Po_0.Tongene.merge.fq reference: ngene.fa tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Po_0 ngene.fa ./Po_0/Po_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:23:22 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:23:22 2011] Preparing output location ./Po_0// [Mon Apr 4 16:23:22 2011] Checking for Bowtie index files [Mon Apr 4 16:23:22 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:23:22 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:23:22 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:23:22 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:23:22 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./No_0 ngene.fa ./No_0/No_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:23:23 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:23:23 2011] Preparing output location ./No_0// [Mon Apr 4 16:23:23 2011] Checking for Bowtie index files [Mon Apr 4 16:23:23 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:23:23 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:23:23 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:23:23 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:23:23 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Oy_0 ngene.fa ./Oy_0/Oy_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:23:24 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:23:24 2011] Preparing output location ./Oy_0// [Mon Apr 4 16:23:24 2011] Checking for Bowtie index files [Mon Apr 4 16:23:24 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:23:24 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:23:24 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:23:24 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:23:24 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Mt_0 ngene.fa ./Mt_0/Mt_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:23:26 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:23:26 2011] Preparing output location ./Mt_0// [Mon Apr 4 16:23:26 2011] Checking for Bowtie index files [Mon Apr 4 16:23:26 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:23:26 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:23:26 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:23:26 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:23:26 2011] Checking reads file: /data/arabidopsis/xiang/magic_founder/Rsch_4_R1/R38_L7_Rsch_4_sdlg_R1_nss_barcode_ACG.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Rsch_4_R2/R38_L8_Rsch_4_sdlg_R2_nss_barcode_ACG.unmap_1.fq $RNAGI/rnagi.sh -o ./Rsch_4 -n ngene.fa Rsch_4.Tongene.merge.fq reference: ngene.fa min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:23:40 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:23:41 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:23:45 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:23:50 2011] Joining segment hits [Mon Apr 4 16:23:50 2011] Joining segment hits min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:23:52 2011] Joining segment hits [Mon Apr 4 16:23:54 2011] Mapping reads against ngene.fa with Bowtie tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Rsch_4 ngene.fa ./Rsch_4/Rsch_4.Tongene.merge.flt_1.fq [Mon Apr 4 16:23:55 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:23:55 2011] Preparing output location ./Rsch_4// [Mon Apr 4 16:23:55 2011] Checking for Bowtie index files [Mon Apr 4 16:23:55 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:23:55 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:23:55 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:23:55 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:23:56 2011] Checking reads [Mon Apr 4 16:23:59 2011] Joining segment hits [Mon Apr 4 16:24:02 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:24:05 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:24:06 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:24:06 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:24:10 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:24:12 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:24:12 2011] Mapping reads against ngene.fa with Bowtie(2/3) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:24:16 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:24:17 2011] Searching for junctions via segment mapping [Mon Apr 4 16:24:18 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:24:19 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:24:21 2011] Searching for junctions via segment mapping [Mon Apr 4 16:24:23 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:24:24 2011] Searching for junctions via segment mapping [Mon Apr 4 16:24:28 2011] Joining segment hits [Mon Apr 4 16:24:29 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:24:34 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:24:39 2011] Searching for junctions via segment mapping [Mon Apr 4 16:24:42 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:24:42 2011] Retrieving sequences for splices [Mon Apr 4 16:24:42 2011] Indexing splices [Mon Apr 4 16:24:43 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:24:45 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:24:46 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:24:47 2011] Retrieving sequences for splices [Mon Apr 4 16:24:47 2011] Indexing splices [Mon Apr 4 16:24:47 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:24:48 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:24:49 2011] Retrieving sequences for splices [Mon Apr 4 16:24:49 2011] Indexing splices [Mon Apr 4 16:24:50 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:24:51 2011] Joining segment hits [Mon Apr 4 16:24:51 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:24:52 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:24:53 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:24:54 2011] Reporting output tracks [Mon Apr 4 16:24:55 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:24:56 2011] Mapping reads against segment_juncs with Bowtie ----------------------------------------------- Run complete [00:01:34 elapsed] [Mon Apr 4 16:24:57 2011] Searching for junctions via segment mapping [Mon Apr 4 16:24:58 2011] Joining segment hits [Mon Apr 4 16:24:59 2011] Joining segment hits [Mon Apr 4 16:25:00 2011] Reporting output tracks [Mon Apr 4 16:25:01 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:39 elapsed] ----------------------------------------------- Run complete [00:01:39 elapsed] cufflinks -p 4 -o ./No_0 -r ngene.fa ./No_0/accepted_hits.bam [16:25:03] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399‘+ [ ] > Processing Locus CUFF.525_From_bur_0_1863298‘+ [ ] > Processing Locus CUFF.529_From_bur_0_1873494‘+ [ ] > Processing Locus CUFF.547_From_bur_0_2032354‘+ [ ] > Processing Locus CUFF.553_From_can_0_3223655‘+ [ ] > Processing Locus CUFF.553_From_can_0_3223655‘+ [ ] > Processing Locus CUFF.559_From_can_0_3231205‘+ [ ] > Processing Locus CUFF.561_From_can_0_3189753‘+ [ ] > Processing Locus CUFF.571_From_can_0_3076940‘+ [ ] > Processing Locus CUFF.573_From_can_0_3233581‘+ [ ] > Processing Locus CUFF.575_From_ct_1_3082021_‘+ [ ] > Processing Locus CUFF.579_From_ct_1_3133451_‘+ [* ] > Processing Locus CUFF.581_From_can_0_3218459‘+ [* ] > Processing Locus CUFF.581_From_can_0_3218459‘+ [* ] > Processing Locus CUFF.583_From_ct_1_3302721_‘+ [* ] > Processing Locus CUFF.585_From_ct_1_3247037_‘+ [* ] > Processing Locus CUFF.593_From_can_0_3270131‘+ [* ] > Processing Locus CUFF.593_From_can_0_3270131‘+ [* ] > Processing Locus CUFF.593_From_can_0_3270131‘+ [* ] > Processing Locus CUFF.595_From_ct_1_3302721_‘+ [* ] > Processing Locus CUFF.601_From_edi_0_2934714‘+ [* ] > Processing Locus CUFF.603_From_bur_0_2025286‘+ [* ] > Processing Locus CUFF.609_From_hi_0_2755116_‘+ [* ] > Processing Locus CUFF.619_From_edi_0_2871668‘+ [** ] > Processing Locus CUFF.621_From_edi_0_2934714‘+ [** ] > Processing Locus CUFF.623_From_hi_0_2778596_‘+ [** ] > Processing Locus CUFF.637_From_kn_0_3626969_‘+ [** ] > Processing Locus CUFF.641_From_kn_0_3605300_‘+ [** ] > Processing Locus CUFF.649_From_kn_0_3617271_‘+ [** ] > Processing Locus CUFF.655_From_hi_0_2795398_‘+ [** ] > Processing Locus CUFF.657_From_ler_0_3998132‘+ [** ] > Processing Locus CUFF.661_From_kn_0_3819922_‘+ [** ] > Processing Locus CUFF.663_From_kn_0_3613403_‘+ [** ] > Processing Locus CUFF.666_From_ler_0_4004770‘+ [*** ] > Processing Locus CUFF.671_From_edi_0_2859720‘+ [*** ] > Processing Locus CUFF.673_From_ler_0_4224097‘+ [*** ] > Processing Locus CUFF.673_From_ler_0_4224097‘+ [*** ] > Processing Locus CUFF.677_From_ct_1_3133995_‘+ [*** ] > Processing Locus CUFF.679_From_ler_0_3998410‘+ [*** ] > Processing Locus CUFF.685_From_mt_0_4231054_‘+ [*** ] > Processing Locus CUFF.687_From_mt_0_4230874_‘+ [*** ] > Processing Locus CUFF.689_From_ler_0_4018856‘+ [*** ] > Processing Locus CUFF.693_From_no_0_2934639_‘+ [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_‘+ [**** ] > Processing Locus CUFF.697_From_mt_0_4229662_‘+ [**** ] > Processing Locus CUFF.699_From_no_0_2905273_‘+ [**** ] > Processing Locus CUFF.703_From_no_0_2885444_‘+ [**** ] > Processing Locus CUFF.705_From_no_0_3113578_‘+ [**** ] > Processing Locus CUFF.713_From_no_0_3116320_‘+ [**** ] > Processing Locus CUFF.721_From_no_0_3120392_‘+ [**** ] > Processing Locus CUFF.721_From_no_0_3120392_‘+ [**** ] > Processing Locus CUFF.721_From_no_0_3120392_‘+ [**** ] > Processing Locus CUFF.721_From_no_0_3120392_‘+ [**** ] > Processing Locus CUFF.721_From_no_0_3120392_‘+ [**** ] > Processing Locus CUFF.721_From_no_0_3120392_‘+ [**** ] > Processing Locus CUFF.723_From_po_0_3306688_‘+ [**** ] > Processing Locus CUFF.725_From_no_0_3116640_‘+ [**** ] > Processing Locus CUFF.729_From_oy_0_3001818_‘+ [**** ] > Processing Locus CUFF.733_From_no_0_2956652_‘+ [***** ] > Processing Locus CUFF.737_From_ct_1_3132277_‘+ [***** ] > Processing Locus CUFF.741_From_po_0_3382155_‘+ [***** ] > Processing Locus CUFF.743_From_po_0_3330421_‘+ [***** ] > Processing Locus CUFF.753_From_oy_0_3121110_‘+ [***** ] > Processing Locus CUFF.757_From_po_0_3372769_‘+ [***** ] > Processing Locus CUFF.759_From_no_0_2936769_‘+ [***** ] > Processing Locus CUFF.763_From_rsch_4_403203‘+ [***** ] > Processing Locus CUFF.771_From_po_0_3332479_‘+ [***** ] > Processing Locus CUFF.783_From_oy_0_2965192_‘+ [****** ] > Processing Locus CUFF.785_From_no_0_3128142_‘+ [****** ] > Processing Locus CUFF.785_From_no_0_3128142_‘+ [****** ] > Processing Locus CUFF.785_From_no_0_3128142_‘+ [****** ] > Processing Locus CUFF.795_From_rsch_4_429714‘+ [****** ] > Processing Locus CUFF.801_From_sf_2_2532172_‘+ [****** ] > Processing Locus CUFF.803_From_po_0_3573778_‘+ [****** ] > Processing Locus CUFF.805_From_sf_2_2486157_‘+ [****** ] > Processing Locus CUFF.809_From_sf_2_2682779_‘+ [****** ] > Processing Locus CUFF.809_From_sf_2_2682779_‘+ [****** ] > Processing Locus CUFF.811_From_sf_2_2459023_‘+ [****** ] > Processing Locus CUFF.817_From_sf_2_2524453_‘+ [****** ] > Processing Locus CUFF.841_From_tsu_0_3243273‘+ [****** ] > Processing Locus CUFF.849_From_tsu_0_3222297‘+ [******* ] > Processing Locus CUFF.861_From_mt_0_4528444_‘+ [******* ] > Processing Locus CUFF.871_From_rsch_4_426655‘+ [******* ] > Processing Locus CUFF.873_From_wil_2_3050523‘+ [******* ] > Processing Locus CUFF.879_From_rsch_4_405516‘+ [******* ] > Processing Locus CUFF.881_From_wil_2_2925323‘+ [******* ] > Processing Locus CUFF.891_From_wil_2_3079625‘+ [******* ] > Processing Locus CUFF.893_From_ws_0_3190679_‘+ [******* ] > Processing Locus CUFF.907_From_ws_0_3182508_‘+ [******* ] > Processing Locus CUFF.915_From_ws_0_3349444_‘+ [******** ] > Processing Locus CUFF.917_From_ws_0_3371988_‘+ [******** ] > Processing Locus CUFF.917_From_ws_0_3371988_‘+ [******** ] > Processing Locus CUFF.925_From_ws_0_3371988_‘+ [******** ] > Processing Locus CUFF.935_From_ws_0_3380934_‘+ [******** ] > Processing Locus CUFF.945_From_wu_0_2678387_‘+ [******** ] > Processing Locus CUFF.947_From_wu_0_2654219_‘+ [******** ] > Processing Locus CUFF.957_From_ws_0_3381390_‘+ [******** ] > Processing Locus CUFF.967_From_zu_0_3022629_‘+ [******** ] > Processing Locus CUFF.969_From_zu_0_3190435_‘+ [******** ] > Processing Locus CUFF.973_From_zu_0_3242889_‘+ [********* ] > Processing Locus CUFF.975_From_zu_0_3259399_‘+ [********* ] > Processing Locus CUFF.979_From_zu_0_3278243_‘+ [********* ] > Processing Locus CUFF.987_From_zu_0_3118546_‘+ [********* ] > Processing Locus CUFF.993_From_zu_0_3082201_‘+ [********* ] > Processed 104 loci. [*************************] 100% > Map Properties: > Total Map Mass: 4571.00 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:25:03] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.547_From_bur_0_2032354 [ ] 2% > Processing Locus CUFF.553_From_can_0_3223655 [ ] 3% > Processing Locus CUFF.553_From_can_0_3223655 [* ] 4% > Processing Locus CUFF.559_From_can_0_3231205 [* ] 5% > Processing Locus CUFF.561_From_can_0_3189753 [* ] 6% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 7% > Processing Locus CUFF.573_From_can_0_3233581 [** ] 8% > Processing Locus CUFF.575_From_ct_1_3082021_ [** ] 9% > Processing Locus CUFF.579_From_ct_1_3133451_ [** ] 10% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 11% > Processing Locus CUFF.581_From_can_0_3218459 [*** ] 12% > Processing Locus CUFF.583_From_ct_1_3302721_ [*** ] 13% > Processing Locus CUFF.585_From_ct_1_3247037_ [*** ] 14% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 15% > Processing Locus CUFF.593_From_can_0_3270131 [**** ] 16% > Processing Locus CUFF.593_From_can_0_3270131 [**** ] 17% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 18% > Processing Locus CUFF.601_From_edi_0_2934714 [**** ] 19% > Processing Locus CUFF.603_From_bur_0_2025286 [***** ] 20% > Processing Locus CUFF.609_From_hi_0_2755116_ [***** ] 21% > Processing Locus CUFF.619_From_edi_0_2871668 [***** ] 22% > Processing Locus CUFF.621_From_edi_0_2934714 [***** ] 23% > Processing Locus CUFF.623_From_hi_0_2778596_ [****** ] 24% > Processing Locus CUFF.637_From_kn_0_3626969_ [****** ] 25% > Processing Locus CUFF.641_From_kn_0_3605300_ [****** ] 25% > Processing Locus CUFF.649_From_kn_0_3617271_ [****** ] 26% > Processing Locus CUFF.655_From_hi_0_2795398_ [****** ] 27% > Processing Locus CUFF.657_From_ler_0_3998132 [******* ] 28% > Processing Locus CUFF.661_From_kn_0_3819922_ [******* ] 29% > Processing Locus CUFF.663_From_kn_0_3613403_ [******* ] 30% > Processing Locus CUFF.666_From_ler_0_4004770 [******* ] 31% > Processing Locus CUFF.671_From_edi_0_2859720 [******** ] 32% > Processing Locus CUFF.673_From_ler_0_4224097 [******** ] 33% > Processing Locus CUFF.673_From_ler_0_4224097 [******** ] 34% > Processing Locus CUFF.677_From_ct_1_3133995_ [******** ] 35% > Processing Locus CUFF.679_From_ler_0_3998410 [********* ] 36% > Processing Locus CUFF.685_From_mt_0_4231054_ [********* ] 37% > Processing Locus CUFF.687_From_mt_0_4230874_ [********* ] 38% > Processing Locus CUFF.689_From_ler_0_4018856 [********* ] 39% > Processing Locus CUFF.693_From_no_0_2934639_ [********** ] 40% > Processing Locus CUFF.695_From_mt_0_4217716_ [********** ] 41% > Processing Locus CUFF.697_From_mt_0_4229662_ [********** ] 42% > Processing Locus CUFF.699_From_no_0_2905273_ [********** ] 43% > Processing Locus CUFF.703_From_no_0_2885444_ [*********** ] 44% > Processing Locus CUFF.705_From_no_0_3113578_ [*********** ] 45% > Processing Locus CUFF.713_From_no_0_3116320_ [*********** ] 46% > Processing Locus CUFF.721_From_no_0_3120392_ [*********** ] 47% > Processing Locus CUFF.721_From_no_0_3120392_ [************ ] 48% > Processing Locus CUFF.721_From_no_0_3120392_ [************ ] 49% > Processing Locus CUFF.721_From_no_0_3120392_ [************ ] 50% > Processing Locus CUFF.721_From_no_0_3120392_ [************ ] 50% > Processing Locus CUFF.721_From_no_0_3120392_ [************ ] 51% > Processing Locus CUFF.723_From_po_0_3306688_ [************* ] 52% > Processing Locus CUFF.725_From_no_0_3116640_ [************* ] 53% > Processing Locus CUFF.729_From_oy_0_3001818_ [************* ] 54% > Processing Locus CUFF.733_From_no_0_2956652_ [************* ] 55% > Processing Locus CUFF.737_From_ct_1_3132277_ [************** ] 56% > Processing Locus CUFF.741_From_po_0_3382155_ [************** ] 57% > Processing Locus CUFF.743_From_po_0_3330421_ [************** ] 58% > Processing Locus CUFF.753_From_oy_0_3121110_ [************** ] 59% > Processing Locus CUFF.757_From_po_0_3372769_ [*************** ] 60% > Processing Locus CUFF.759_From_no_0_2936769_ [*************** ] 61% > Processing Locus CUFF.763_From_rsch_4_403203 [*************** ] 62% > Processing Locus CUFF.771_From_po_0_3332479_ [*************** ] 63% > Processing Locus CUFF.783_From_oy_0_2965192_ [**************** ] 64% > Processing Locus CUFF.785_From_no_0_3128142_ [**************** ] 65% > Processing Locus CUFF.785_From_no_0_3128142_ [**************** ] 66% > Processing Locus CUFF.785_From_no_0_3128142_ [**************** ] 67% > Processing Locus CUFF.795_From_rsch_4_429714 [***************** ] 68% > Processing Locus CUFF.801_From_sf_2_2532172_ [***************** ] 69% > Processing Locus CUFF.803_From_po_0_3573778_ [***************** ] 70% > Processing Locus CUFF.805_From_sf_2_2486157_ [***************** ] 71% > Processing Locus CUFF.809_From_sf_2_2682779_ [****************** ] 72% > Processing Locus CUFF.809_From_sf_2_2682779_ [****************** ] 73% > Processing Locus CUFF.811_From_sf_2_2459023_ [****************** ] 74% > Processing Locus CUFF.817_From_sf_2_2524453_ [****************** ] 75% > Processing Locus CUFF.841_From_tsu_0_3243273 [****************** ] 75% > Processing Locus CUFF.849_From_tsu_0_3222297 [******************* ] 76% > Processing Locus CUFF.861_From_mt_0_4528444_ [******************* ] 77% > Processing Locus CUFF.871_From_rsch_4_426655 [******************* ] 78% > Processing Locus CUFF.873_From_wil_2_3050523 [******************* ] 79% > Processing Locus CUFF.879_From_rsch_4_405516 [******************** ] 80% > Processing Locus CUFF.881_From_wil_2_2925323 [******************** ] 81% > Processing Locus CUFF.891_From_wil_2_3079625 [******************** ] 82% > Processing Locus CUFF.893_From_ws_0_3190679_ [******************** ] 83% > Processing Locus CUFF.907_From_ws_0_3182508_ [********************* ] 84% > Processing Locus CUFF.915_From_ws_0_3349444_ [********************* ] 85% > Processing Locus CUFF.917_From_ws_0_3371988_ [********************* ] 86% > Processing Locus CUFF.917_From_ws_0_3371988_ [********************* ] 87% > Processing Locus CUFF.925_From_ws_0_3371988_ [********************** ] 88% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************** ] 89% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************** ] 90% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************** ] 91% > Processing Locus CUFF.957_From_ws_0_3381390_ [*********************** ] 92% > Processing Locus CUFF.967_From_zu_0_3022629_ [*********************** ] 93% > Processing Locus CUFF.969_From_zu_0_3190435_ [*********************** ] 94% > Processing Locus CUFF.973_From_zu_0_3242889_ [*********************** ] 95% > Processing Locus CUFF.975_From_zu_0_3259399_ [************************ ] 96% > Processing Locus CUFF.979_From_zu_0_3278243_ [************************ ] 97% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 98% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 99% > Processed 104 loci. [*************************] 100% [16:25:03] Loading reference annotation and sequence [16:25:03] Learning bias parameters. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.559_From_can_0_3231205 [ ] 2% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 4% > Processing Locus CUFF.573_From_can_0_3233581 [* ] 5% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 6% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 7% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 8% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 9% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 10% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 11% > Processing Locus CUFF.603_From_bur_0_2025286 [*** ] 12% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 13% > Processing Locus CUFF.623_From_hi_0_2778596_ [*** ] 14% > Processing Locus CUFF.641_From_kn_0_3605300_ [*** ] 15% > Processing Locus CUFF.655_From_hi_0_2795398_ [**** ] 16% > Processing Locus CUFF.657_From_ler_0_3998132 [**** ] 17% > Processing Locus CUFF.663_From_kn_0_3613403_ [**** ] 18% > Processing Locus CUFF.666_From_ler_0_4004770 [**** ] 19% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 20% > Processing Locus CUFF.673_From_ler_0_4224097 [***** ] 21% > Processing Locus CUFF.685_From_mt_0_4231054_ [***** ] 22% > Processing Locus CUFF.687_From_mt_0_4230874_ [***** ] 23% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 24% > Processing Locus CUFF.695_From_mt_0_4217716_ [****** ] 25% > Processing Locus CUFF.697_From_mt_0_4229662_ [****** ] 25% > Processing Locus CUFF.699_From_no_0_2905273_ [****** ] 26% > Processing Locus CUFF.703_From_no_0_2885444_ [****** ] 27% > Processing Locus CUFF.713_From_no_0_3116320_ [******* ] 28% > Processing Locus CUFF.723_From_po_0_3306688_ [******* ] 29% > Processing Locus CUFF.725_From_no_0_3116640_ [******* ] 30% > Processing Locus CUFF.729_From_oy_0_3001818_ [******* ] 31% > Processing Locus CUFF.733_From_no_0_2956652_ [******** ] 32% > Processing Locus CUFF.737_From_ct_1_3132277_ [******** ] 33% > Processing Locus CUFF.741_From_po_0_3382155_ [******** ] 34% > Processing Locus CUFF.743_From_po_0_3330421_ [******** ] 35% > Processing Locus CUFF.753_From_oy_0_3121110_ [********* ] 36% > Processing Locus CUFF.757_From_po_0_3372769_ [********* ] 37% > Processing Locus CUFF.759_From_no_0_2936769_ [********* ] 38% > Processing Locus CUFF.771_From_po_0_3332479_ [********* ] 39% > Processing Locus CUFF.785_From_no_0_3128142_ [********** ] 40% > Processing Locus CUFF.785_From_no_0_3128142_ [********** ] 41% > Processing Locus CUFF.795_From_rsch_4_429714 [********** ] 42% > Processing Locus CUFF.801_From_sf_2_2532172_ [********** ] 43% > Processing Locus CUFF.803_From_po_0_3573778_ [*********** ] 44% > Processing Locus CUFF.805_From_sf_2_2486157_ [*********** ] 45% > Processing Locus CUFF.809_From_sf_2_2682779_ [*********** ] 46% > Processing Locus CUFF.811_From_sf_2_2459023_ [*********** ] 47% > Processing Locus CUFF.817_From_sf_2_2524453_ [************ ] 48% > Processing Locus CUFF.849_From_tsu_0_3222297 [************ ] 49% > Processing Locus CUFF.871_From_rsch_4_426655 [************ ] 50% > Processing Locus CUFF.873_From_wil_2_3050523 [************ ] 50% > Processing Locus CUFF.879_From_rsch_4_405516 [************ ] 51% > Processing Locus CUFF.881_From_wil_2_2925323 [************* ] 52% > Processing Locus CUFF.893_From_ws_0_3190679_ [************* ] 53% > Processing Locus CUFF.907_From_ws_0_3182508_ [************* ] 54% > Processing Locus CUFF.925_From_ws_0_3371988_ [************* ] 55% > Processing Locus CUFF.935_From_ws_0_3380934_ [************** ] 56% > Processing Locus CUFF.947_From_wu_0_2654219_ [************** ] 57% > Processing Locus CUFF.957_From_ws_0_3381390_ [************** ] 58% > Processing Locus CUFF.967_From_zu_0_3022629_ [************** ] 59% > Processing Locus CUFF.969_From_zu_0_3190435_ [*************** ] 60% > Processing Locus CUFF.975_From_zu_0_3259399_ [*************** ] 61% > Processing Locus CUFF.979_From_zu_0_3278243_ [*************** ] 62% > Processing Locus CUFF.987_From_zu_0_3118546_ [*************** ] 63% > Processing Locus CUFF.993_From_zu_0_3082201_ [**************** ] 64% > Processed 68 loci. [*************************] 100% [16:25:04] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.559_From_can_0_3231205 [ ] 2% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 4% > Processing Locus CUFF.573_From_can_0_3233581 [* ] 5% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 6% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 7% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 8% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 9% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 10% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 11% > Processing Locus CUFF.603_From_bur_0_2025286 [*** ] 12% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 13% > Processing Locus CUFF.623_From_hi_0_2778596_ [*** ] 14% > Processing Locus CUFF.641_From_kn_0_3605300_ [*** ] 15% > Processing Locus CUFF.655_From_hi_0_2795398_ [**** ] 16% > Processing Locus CUFF.657_From_ler_0_3998132 [**** ] 17% > Processing Locus CUFF.663_From_kn_0_3613403_ [**** ] 18% > Processing Locus CUFF.666_From_ler_0_4004770 [**** ] 19% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 20% > Processing Locus CUFF.673_From_ler_0_4224097 [***** ] 21% > Processing Locus CUFF.685_From_mt_0_4231054_ [***** ] 22% > Processing Locus CUFF.687_From_mt_0_4230874_ [***** ] 23% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 24% > Processing Locus CUFF.695_From_mt_0_4217716_ [****** ] 25% > Processing Locus CUFF.697_From_mt_0_4229662_ [****** ] 25% > Processing Locus CUFF.699_From_no_0_2905273_ [****** ] 26% > Processing Locus CUFF.703_From_no_0_2885444_ [****** ] 27% > Processing Locus CUFF.713_From_no_0_3116320_ [******* ] 28% > Processing Locus CUFF.723_From_po_0_3306688_ [******* ] 29% > Processing Locus CUFF.725_From_no_0_3116640_ [******* ] 30% > Processing Locus CUFF.729_From_oy_0_3001818_ [******* ] 31% > Processing Locus CUFF.733_From_no_0_2956652_ [******** ] 32% > Processing Locus CUFF.737_From_ct_1_3132277_ [******** ] 33% > Processing Locus CUFF.741_From_po_0_3382155_ [******** ] 34% > Processing Locus CUFF.743_From_po_0_3330421_ [******** ] 35% > Processing Locus CUFF.753_From_oy_0_3121110_ [********* ] 36% > Processing Locus CUFF.757_From_po_0_3372769_ [********* ] 37% > Processing Locus CUFF.759_From_no_0_2936769_ [********* ] 38% > Processing Locus CUFF.771_From_po_0_3332479_ [********* ] 39% > Processing Locus CUFF.785_From_no_0_3128142_ [********** ] 40% > Processing Locus CUFF.785_From_no_0_3128142_ [********** ] 41% > Processing Locus CUFF.795_From_rsch_4_429714 [********** ] 42% > Processing Locus CUFF.801_From_sf_2_2532172_ [********** ] 43% > Processing Locus CUFF.803_From_po_0_3573778_ [*********** ] 44% > Processing Locus CUFF.805_From_sf_2_2486157_ [*********** ] 45% > Processing Locus CUFF.809_From_sf_2_2682779_ [*********** ] 46% > Processing Locus CUFF.811_From_sf_2_2459023_ [*********** ] 47% > Processing Locus CUFF.817_From_sf_2_2524453_ [************ ] 48% > Processing Locus CUFF.849_From_tsu_0_3222297 [************ ] 49% > Processing Locus CUFF.871_From_rsch_4_426655 [************ ] 50% > Processing Locus CUFF.873_From_wil_2_3050523 [************ ] 50% > Processing Locus CUFF.879_From_rsch_4_405516 [************ ] 51% > Processing Locus CUFF.881_From_wil_2_2925323 [************* ] 52% > Processing Locus CUFF.893_From_ws_0_3190679_ [************* ] 53% > Processing Locus CUFF.907_From_ws_0_3182508_ [************* ] 54% > Processing Locus CUFF.925_From_ws_0_3371988_ [************* ] 55% > Processing Locus CUFF.935_From_ws_0_3380934_ [************** ] 56% > Processing Locus CUFF.947_From_wu_0_2654219_ [************** ] 57% > Processing Locus CUFF.957_From_ws_0_3381390_ [************** ] 58% > Processing Locus CUFF.967_From_zu_0_3022629_ [************** ] 59% > Processing Locus CUFF.969_From_zu_0_3190435_ [*************** ] 60% > Processing Locus CUFF.975_From_zu_0_3259399_ [*************** ] 61% > Processing Locus CUFF.979_From_zu_0_3278243_ [*************** ] 62% > Processing Locus CUFF.987_From_zu_0_3118546_ [*************** ] 63% > Processing Locus CUFF.993_From_zu_0_3082201_ [**************** ] 64% > Processed 68 loci. [*************************] 100% [Mon Apr 4 16:25:05 2011] Retrieving sequences for splices [Mon Apr 4 16:25:05 2011] Indexing splices [Mon Apr 4 16:25:05 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:25:08 2011] Mapping reads against segment_juncs with Bowtie cufflinks -p 4 -o ./Po_0 -r ngene.fa ./Po_0/accepted_hits.bam [16:25:10] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399óG [ ] > Processing Locus CUFF.533_From_bur_0_2020452óG [ ] > Processing Locus CUFF.547_From_bur_0_2032354óG [ ] > Processing Locus CUFF.555_From_can_0_3217045óG [ ] > Processing Locus CUFF.561_From_can_0_3189753óG [ ] > Processing Locus CUFF.563_From_bur_0_2020452óG [ ] > Processing Locus CUFF.571_From_can_0_3076940óG [ ] > Processing Locus CUFF.575_From_ct_1_3082021_óG [ ] > Processing Locus CUFF.579_From_ct_1_3133451_óG [ ] > Processing Locus CUFF.581_From_can_0_3218459óG [ ] > Processing Locus CUFF.583_From_ct_1_3302721_óG [* ] > Processing Locus CUFF.585_From_ct_1_3247037_óG [* ] > Processing Locus CUFF.593_From_can_0_3270131óG [* ] > Processing Locus CUFF.593_From_can_0_3270131óG [* ] > Processing Locus CUFF.593_From_can_0_3270131óG [* ] > Processing Locus CUFF.595_From_ct_1_3302721_óG [* ] > Processing Locus CUFF.599_From_edi_0_2744702óG [* ] > Processing Locus CUFF.603_From_bur_0_2025286óG [* ] > Processing Locus CUFF.603_From_bur_0_2025286óG [* ] > Processing Locus CUFF.603_From_bur_0_2025286óG [* ] > Processing Locus CUFF.603_From_bur_0_2025286óG [* ] > Processing Locus CUFF.603_From_bur_0_2025286óG [* ] > Processing Locus CUFF.613_From_hi_0_2773206_óG [* ] > Processing Locus CUFF.615_From_edi_0_2932438óG [* ] > Processing Locus CUFF.617_From_edi_0_2918156óG [* ] > Processing Locus CUFF.619_From_edi_0_2871668óG [** ] > Processing Locus CUFF.623_From_hi_0_2778596_óG [** ] > Processing Locus CUFF.627_From_edi_0_2889434óG [** ] > Processing Locus CUFF.627_From_edi_0_2889434óG [** ] > Processing Locus CUFF.635_From_ct_1_3241157_óG [** ] > Processing Locus CUFF.661_From_kn_0_3819922_óG [** ] > Processing Locus CUFF.661_From_kn_0_3819922_óG [** ] > Processing Locus CUFF.663_From_kn_0_3613403_óG [** ] > Processing Locus CUFF.665_From_hi_0_2939638_óG [** ] > Processing Locus CUFF.677_From_ct_1_3133995_óG [** ] > Processing Locus CUFF.679_From_ler_0_3998410óG [** ] > Processing Locus CUFF.685_From_mt_0_4231054_óG [** ] > Processing Locus CUFF.689_From_ler_0_4018856óG [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_óG [*** ] > Processing Locus CUFF.697_From_mt_0_4229662_óG [*** ] > Processing Locus CUFF.699_From_no_0_2905273_óG [*** ] > Processing Locus CUFF.703_From_no_0_2885444_óG [*** ] > Processing Locus CUFF.705_From_no_0_3113578_óG [*** ] > Processing Locus CUFF.715_From_oy_0_3098144_óG [*** ] > Processing Locus CUFF.717_From_oy_0_2966542_óG [*** ] > Processing Locus CUFF.725_From_no_0_3116640_óG [*** ] > Processing Locus CUFF.725_From_no_0_3116640_óG [*** ] > Processing Locus CUFF.729_From_oy_0_3001818_óG [**** ] > Processing Locus CUFF.731_From_po_0_3324652_óG [**** ] > Processing Locus CUFF.733_From_no_0_2956652_óG [**** ] > Processing Locus CUFF.735_From_po_0_3293868_óG [**** ] > Processing Locus CUFF.737_From_ct_1_3132277_óG [**** ] > Processing Locus CUFF.739_From_po_0_3340213_óG [**** ] > Processing Locus CUFF.741_From_po_0_3382155_óG [**** ] > Processing Locus CUFF.743_From_po_0_3330421_óG [**** ] > Processing Locus CUFF.745_From_po_0_3507160_óG [**** ] > Processing Locus CUFF.747_From_po_0_3299272_óG [**** ] > Processing Locus CUFF.749_From_oy_0_3162092_óG [***** ] > Processing Locus CUFF.753_From_oy_0_3121110_óG [***** ] > Processing Locus CUFF.757_From_po_0_3372769_óG [***** ] > Processing Locus CUFF.759_From_no_0_2936769_óG [***** ] > Processing Locus CUFF.761_From_po_0_3606391_óG [***** ] > Processing Locus CUFF.761_From_po_0_3606391_óG [***** ] > Processing Locus CUFF.761_From_po_0_3606391_óG [***** ] > Processing Locus CUFF.763_From_rsch_4_403203óG [***** ] > Processing Locus CUFF.765_From_rsch_4_411079óG [***** ] > Processing Locus CUFF.771_From_po_0_3332479_óG [***** ] > Processing Locus CUFF.773_From_po_0_3606391_óG [***** ] > Processing Locus CUFF.773_From_po_0_3606391_óG [***** ] > Processing Locus CUFF.773_From_po_0_3606391_óG [***** ] > Processing Locus CUFF.773_From_po_0_3606391_óG [***** ] > Processing Locus CUFF.773_From_po_0_3606391_óG [***** ] > Processing Locus CUFF.773_From_po_0_3606391_óG [***** ] > Processing Locus CUFF.779_From_rsch_4_421454óG [****** ] > Processing Locus CUFF.785_From_no_0_3128142_óG [****** ] > Processing Locus CUFF.785_From_no_0_3128142_óG [****** ] > Processing Locus CUFF.785_From_no_0_3128142_óG [****** ] > Processing Locus CUFF.791_From_rsch_4_425553óG [****** ] > Processing Locus CUFF.795_From_rsch_4_429714óG [****** ] > Processing Locus CUFF.803_From_po_0_3573778_óG [****** ] > Processing Locus CUFF.805_From_sf_2_2486157_óG [****** ] > Processing Locus CUFF.809_From_sf_2_2682779_óG [****** ] > Processing Locus CUFF.811_From_sf_2_2459023_óG [****** ] > Processing Locus CUFF.817_From_sf_2_2524453_óG [****** ] > Processing Locus CUFF.819_From_tsu_0_3036945óG [****** ] > Processing Locus CUFF.835_From_tsu_0_3211741óG [******* ] > Processing Locus CUFF.837_From_tsu_0_3215671óG [******* ] > Processing Locus CUFF.837_From_tsu_0_3215671óG [******* ] > Processing Locus CUFF.839_From_sf_2_2680171_óG [******* ] > Processing Locus CUFF.843_From_rsch_4_429219óG [******* ] > Processing Locus CUFF.855_From_wil_2_2915899óG [******* ] > Processing Locus CUFF.861_From_mt_0_4528444_óG [******* ] > Processing Locus CUFF.869_From_sf_2_2701328_óG [******* ] > Processing Locus CUFF.871_From_rsch_4_426655óG [******* ] > Processing Locus CUFF.879_From_rsch_4_405516óG [******* ] > Processing Locus CUFF.881_From_wil_2_2925323óG [******** ] > Processing Locus CUFF.891_From_wil_2_3079625óG [******** ] > Processing Locus CUFF.899_From_ws_0_3190963_óG [******** ] > Processing Locus CUFF.907_From_ws_0_3182508_óG [******** ] > Processing Locus CUFF.913_From_wil_2_2834553óG [******** ] > Processing Locus CUFF.919_From_ws_0_3347582_óG [******** ] > Processing Locus CUFF.919_From_ws_0_3347582_óG [******** ] > Processing Locus CUFF.941_From_wu_0_2824308_óG [******** ] > Processing Locus CUFF.941_From_wu_0_2824308_óG [******** ] > Processing Locus CUFF.945_From_wu_0_2678387_óG [******** ] > Processing Locus CUFF.947_From_wu_0_2654219_óG [******** ] > Processing Locus CUFF.949_From_wu_0_2687576_óG [********* ] > Processing Locus CUFF.955_From_ws_0_3340488_óG [********* ] > Processing Locus CUFF.957_From_ws_0_3381390_óG [********* ] > Processing Locus CUFF.957_From_ws_0_3381390_óG [********* ] > Processing Locus CUFF.965_From_zu_0_3238769_óG [********* ] > Processing Locus CUFF.969_From_zu_0_3190435_óG [********* ] > Processing Locus CUFF.971_From_zu_0_3255169_óG [********* ] > Processing Locus CUFF.971_From_zu_0_3255169_óG [********* ] > Processing Locus CUFF.973_From_zu_0_3242889_óG [********* ] > Processing Locus CUFF.975_From_zu_0_3259399_óG [********* ] > Processing Locus CUFF.977_From_zu_0_3255503_óG [********* ] > Processing Locus CUFF.979_From_zu_0_3278243_óG [********* ] > Processing Locus CUFF.981_From_zu_0_3289907_óG [********** ] > Processing Locus CUFF.985_From_zu_0_3280213_óG [********** ] > Processing Locus CUFF.985_From_zu_0_3280213_óG [********** ] > Processing Locus CUFF.987_From_zu_0_3118546_óG [********** ] > Processing Locus CUFF.989_From_zu_0_3289907_óG [********** ] > Processing Locus CUFF.989_From_zu_0_3289907_óG [********** ] > Processing Locus CUFF.991_From_zu_0_3277661_óG [********** ] > Processed 125 loci. [*************************] 100% > Map Properties: > Total Map Mass: 4809.92 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:25:10] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.533_From_bur_0_2020452 [ ] 0% > Processing Locus CUFF.547_From_bur_0_2032354 [ ] 1% > Processing Locus CUFF.555_From_can_0_3217045 [ ] 2% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 3% > Processing Locus CUFF.563_From_bur_0_2020452 [* ] 4% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 4% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 5% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 6% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 7% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 8% > Processing Locus CUFF.585_From_ct_1_3247037_ [** ] 8% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 9% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 10% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 11% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 12% > Processing Locus CUFF.599_From_edi_0_2744702 [*** ] 12% > Processing Locus CUFF.603_From_bur_0_2025286 [*** ] 13% > Processing Locus CUFF.603_From_bur_0_2025286 [*** ] 14% > Processing Locus CUFF.603_From_bur_0_2025286 [*** ] 15% > Processing Locus CUFF.603_From_bur_0_2025286 [**** ] 16% > Processing Locus CUFF.603_From_bur_0_2025286 [**** ] 16% > Processing Locus CUFF.613_From_hi_0_2773206_ [**** ] 17% > Processing Locus CUFF.615_From_edi_0_2932438 [**** ] 18% > Processing Locus CUFF.617_From_edi_0_2918156 [**** ] 19% > Processing Locus CUFF.619_From_edi_0_2871668 [***** ] 20% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 20% > Processing Locus CUFF.627_From_edi_0_2889434 [***** ] 21% > Processing Locus CUFF.627_From_edi_0_2889434 [***** ] 22% > Processing Locus CUFF.635_From_ct_1_3241157_ [***** ] 23% > Processing Locus CUFF.661_From_kn_0_3819922_ [****** ] 24% > Processing Locus CUFF.661_From_kn_0_3819922_ [****** ] 24% > Processing Locus CUFF.663_From_kn_0_3613403_ [****** ] 25% > Processing Locus CUFF.665_From_hi_0_2939638_ [****** ] 26% > Processing Locus CUFF.677_From_ct_1_3133995_ [****** ] 27% > Processing Locus CUFF.679_From_ler_0_3998410 [******* ] 28% > Processing Locus CUFF.685_From_mt_0_4231054_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 30% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 31% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 32% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 32% > Processing Locus CUFF.705_From_no_0_3113578_ [******** ] 33% > Processing Locus CUFF.715_From_oy_0_3098144_ [******** ] 34% > Processing Locus CUFF.717_From_oy_0_2966542_ [******** ] 35% > Processing Locus CUFF.725_From_no_0_3116640_ [********* ] 36% > Processing Locus CUFF.725_From_no_0_3116640_ [********* ] 36% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 37% > Processing Locus CUFF.731_From_po_0_3324652_ [********* ] 38% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 39% > Processing Locus CUFF.735_From_po_0_3293868_ [********** ] 40% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 40% > Processing Locus CUFF.739_From_po_0_3340213_ [********** ] 41% > Processing Locus CUFF.741_From_po_0_3382155_ [********** ] 42% > Processing Locus CUFF.743_From_po_0_3330421_ [********** ] 43% > Processing Locus CUFF.745_From_po_0_3507160_ [*********** ] 44% > Processing Locus CUFF.747_From_po_0_3299272_ [*********** ] 44% > Processing Locus CUFF.749_From_oy_0_3162092_ [*********** ] 45% > Processing Locus CUFF.753_From_oy_0_3121110_ [*********** ] 46% > Processing Locus CUFF.757_From_po_0_3372769_ [*********** ] 47% > Processing Locus CUFF.759_From_no_0_2936769_ [************ ] 48% > Processing Locus CUFF.761_From_po_0_3606391_ [************ ] 48% > Processing Locus CUFF.761_From_po_0_3606391_ [************ ] 49% > Processing Locus CUFF.761_From_po_0_3606391_ [************ ] 50% > Processing Locus CUFF.763_From_rsch_4_403203 [************ ] 51% > Processing Locus CUFF.765_From_rsch_4_411079 [************* ] 52% > Processing Locus CUFF.771_From_po_0_3332479_ [************* ] 52% > Processing Locus CUFF.773_From_po_0_3606391_ [************* ] 53% > Processing Locus CUFF.773_From_po_0_3606391_ [************* ] 54% > Processing Locus CUFF.773_From_po_0_3606391_ [************* ] 55% > Processing Locus CUFF.773_From_po_0_3606391_ [************** ] 56% > Processing Locus CUFF.773_From_po_0_3606391_ [************** ] 56% > Processing Locus CUFF.773_From_po_0_3606391_ [************** ] 57% > Processing Locus CUFF.779_From_rsch_4_421454 [************** ] 58% > Processing Locus CUFF.785_From_no_0_3128142_ [************** ] 59% > Processing Locus CUFF.785_From_no_0_3128142_ [*************** ] 60% > Processing Locus CUFF.785_From_no_0_3128142_ [*************** ] 60% > Processing Locus CUFF.791_From_rsch_4_425553 [*************** ] 61% > Processing Locus CUFF.795_From_rsch_4_429714 [*************** ] 62% > Processing Locus CUFF.803_From_po_0_3573778_ [*************** ] 63% > Processing Locus CUFF.805_From_sf_2_2486157_ [**************** ] 64% > Processing Locus CUFF.809_From_sf_2_2682779_ [**************** ] 64% > Processing Locus CUFF.811_From_sf_2_2459023_ [**************** ] 65% > Processing Locus CUFF.817_From_sf_2_2524453_ [**************** ] 66% > Processing Locus CUFF.819_From_tsu_0_3036945 [**************** ] 67% > Processing Locus CUFF.835_From_tsu_0_3211741 [***************** ] 68% > Processing Locus CUFF.837_From_tsu_0_3215671 [***************** ] 68% > Processing Locus CUFF.837_From_tsu_0_3215671 [***************** ] 69% > Processing Locus CUFF.839_From_sf_2_2680171_ [***************** ] 70% > Processing Locus CUFF.843_From_rsch_4_429219 [***************** ] 71% > Processing Locus CUFF.855_From_wil_2_2915899 [****************** ] 72% > Processing Locus CUFF.861_From_mt_0_4528444_ [****************** ] 72% > Processing Locus CUFF.869_From_sf_2_2701328_ [****************** ] 73% > Processing Locus CUFF.871_From_rsch_4_426655 [****************** ] 74% > Processing Locus CUFF.879_From_rsch_4_405516 [****************** ] 75% > Processing Locus CUFF.881_From_wil_2_2925323 [******************* ] 76% > Processing Locus CUFF.891_From_wil_2_3079625 [******************* ] 76% > Processing Locus CUFF.899_From_ws_0_3190963_ [******************* ] 77% > Processing Locus CUFF.907_From_ws_0_3182508_ [******************* ] 78% > Processing Locus CUFF.913_From_wil_2_2834553 [******************* ] 79% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 80% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 80% > Processing Locus CUFF.941_From_wu_0_2824308_ [******************** ] 81% > Processing Locus CUFF.941_From_wu_0_2824308_ [******************** ] 82% > Processing Locus CUFF.945_From_wu_0_2678387_ [******************** ] 83% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************* ] 84% > Processing Locus CUFF.949_From_wu_0_2687576_ [********************* ] 84% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************* ] 85% > Processing Locus CUFF.957_From_ws_0_3381390_ [********************* ] 86% > Processing Locus CUFF.957_From_ws_0_3381390_ [********************* ] 87% > Processing Locus CUFF.965_From_zu_0_3238769_ [********************** ] 88% > Processing Locus CUFF.969_From_zu_0_3190435_ [********************** ] 88% > Processing Locus CUFF.971_From_zu_0_3255169_ [********************** ] 89% > Processing Locus CUFF.971_From_zu_0_3255169_ [********************** ] 90% > Processing Locus CUFF.973_From_zu_0_3242889_ [********************** ] 91% > Processing Locus CUFF.975_From_zu_0_3259399_ [*********************** ] 92% > Processing Locus CUFF.977_From_zu_0_3255503_ [*********************** ] 92% > Processing Locus CUFF.979_From_zu_0_3278243_ [*********************** ] 93% > Processing Locus CUFF.981_From_zu_0_3289907_ [*********************** ] 94% > Processing Locus CUFF.985_From_zu_0_3280213_ [*********************** ] 95% > Processing Locus CUFF.985_From_zu_0_3280213_ [************************ ] 96% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 96% > Processing Locus CUFF.989_From_zu_0_3289907_ [************************ ] 97% > Processing Locus CUFF.989_From_zu_0_3289907_ [************************ ] 98% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 99% > Processed 125 loci. [*************************] 100% [16:25:11] Loading reference annotation and sequence [16:25:11] Learning bias parameters. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.547_From_bur_0_2032354 [ ] 0% > Processing Locus CUFF.555_From_can_0_3217045 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.563_From_bur_0_2020452 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 4% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 5% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 6% > Processing Locus CUFF.599_From_edi_0_2744702 [* ] 7% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 8% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 8% > Processing Locus CUFF.615_From_edi_0_2932438 [** ] 9% > Processing Locus CUFF.617_From_edi_0_2918156 [** ] 10% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 11% > Processing Locus CUFF.623_From_hi_0_2778596_ [*** ] 12% > Processing Locus CUFF.635_From_ct_1_3241157_ [*** ] 12% > Processing Locus CUFF.661_From_kn_0_3819922_ [*** ] 13% > Processing Locus CUFF.665_From_hi_0_2939638_ [*** ] 14% > Processing Locus CUFF.677_From_ct_1_3133995_ [*** ] 15% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 16% > Processing Locus CUFF.695_From_mt_0_4217716_ [**** ] 16% > Processing Locus CUFF.697_From_mt_0_4229662_ [**** ] 17% > Processing Locus CUFF.699_From_no_0_2905273_ [**** ] 18% > Processing Locus CUFF.705_From_no_0_3113578_ [**** ] 19% > Processing Locus CUFF.715_From_oy_0_3098144_ [***** ] 20% > Processing Locus CUFF.717_From_oy_0_2966542_ [***** ] 20% > Processing Locus CUFF.729_From_oy_0_3001818_ [***** ] 21% > Processing Locus CUFF.731_From_po_0_3324652_ [***** ] 22% > Processing Locus CUFF.733_From_no_0_2956652_ [***** ] 23% > Processing Locus CUFF.735_From_po_0_3293868_ [****** ] 24% > Processing Locus CUFF.737_From_ct_1_3132277_ [****** ] 24% > Processing Locus CUFF.741_From_po_0_3382155_ [****** ] 25% > Processing Locus CUFF.743_From_po_0_3330421_ [****** ] 26% > Processing Locus CUFF.745_From_po_0_3507160_ [****** ] 27% > Processing Locus CUFF.747_From_po_0_3299272_ [******* ] 28% > Processing Locus CUFF.749_From_oy_0_3162092_ [******* ] 28% > Processing Locus CUFF.753_From_oy_0_3121110_ [******* ] 29% > Processing Locus CUFF.757_From_po_0_3372769_ [******* ] 30% > Processing Locus CUFF.759_From_no_0_2936769_ [******* ] 31% > Processing Locus CUFF.765_From_rsch_4_411079 [******** ] 32% > Processing Locus CUFF.771_From_po_0_3332479_ [******** ] 32% > Processing Locus CUFF.779_From_rsch_4_421454 [******** ] 33% > Processing Locus CUFF.791_From_rsch_4_425553 [******** ] 34% > Processing Locus CUFF.795_From_rsch_4_429714 [******** ] 35% > Processing Locus CUFF.803_From_po_0_3573778_ [********* ] 36% > Processing Locus CUFF.805_From_sf_2_2486157_ [********* ] 36% > Processing Locus CUFF.811_From_sf_2_2459023_ [********* ] 37% > Processing Locus CUFF.817_From_sf_2_2524453_ [********* ] 38% > Processing Locus CUFF.835_From_tsu_0_3211741 [********* ] 39% > Processing Locus CUFF.837_From_tsu_0_3215671 [********** ] 40% > Processing Locus CUFF.837_From_tsu_0_3215671 [********** ] 40% > Processing Locus CUFF.839_From_sf_2_2680171_ [********** ] 41% > Processing Locus CUFF.843_From_rsch_4_429219 [********** ] 42% > Processing Locus CUFF.861_From_mt_0_4528444_ [********** ] 43% > Processing Locus CUFF.871_From_rsch_4_426655 [*********** ] 44% > Processing Locus CUFF.879_From_rsch_4_405516 [*********** ] 44% > Processing Locus CUFF.881_From_wil_2_2925323 [*********** ] 45% > Processing Locus CUFF.891_From_wil_2_3079625 [*********** ] 46% > Processing Locus CUFF.907_From_ws_0_3182508_ [*********** ] 47% > Processing Locus CUFF.919_From_ws_0_3347582_ [************ ] 48% > Processing Locus CUFF.919_From_ws_0_3347582_ [************ ] 48% > Processing Locus CUFF.941_From_wu_0_2824308_ [************ ] 49% > Processing Locus CUFF.947_From_wu_0_2654219_ [************ ] 50% > Processing Locus CUFF.949_From_wu_0_2687576_ [************ ] 51% > Processing Locus CUFF.955_From_ws_0_3340488_ [************* ] 52% > Processing Locus CUFF.957_From_ws_0_3381390_ [************* ] 52% > Processing Locus CUFF.969_From_zu_0_3190435_ [************* ] 53% > Processing Locus CUFF.971_From_zu_0_3255169_ [************* ] 54% > Processing Locus CUFF.973_From_zu_0_3242889_ [************* ] 55% > Processing Locus CUFF.975_From_zu_0_3259399_ [************** ] 56% > Processing Locus CUFF.977_From_zu_0_3255503_ [************** ] 56% > Processing Locus CUFF.981_From_zu_0_3289907_ [************** ] 57% > Processing Locus CUFF.987_From_zu_0_3118546_ [************** ] 58% > Processing Locus CUFF.989_From_zu_0_3289907_ [************** ] 59% > Processing Locus CUFF.989_From_zu_0_3289907_ [*************** ] 60% > Processing Locus CUFF.991_From_zu_0_3277661_ [*************** ] 60% > Processed 77 loci. [*************************] 100% [16:25:11] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.547_From_bur_0_2032354 [ ] 0% > Processing Locus CUFF.555_From_can_0_3217045 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.563_From_bur_0_2020452 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 4% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 5% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 6% > Processing Locus CUFF.599_From_edi_0_2744702 [* ] 7% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 8% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 8% > Processing Locus CUFF.615_From_edi_0_2932438 [** ] 9% > Processing Locus CUFF.617_From_edi_0_2918156 [** ] 10% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 11% > Processing Locus CUFF.623_From_hi_0_2778596_ [*** ] 12% > Processing Locus CUFF.635_From_ct_1_3241157_ [*** ] 12% > Processing Locus CUFF.661_From_kn_0_3819922_ [*** ] 13% > Processing Locus CUFF.665_From_hi_0_2939638_ [*** ] 14% > Processing Locus CUFF.677_From_ct_1_3133995_ [*** ] 15% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 16% > Processing Locus CUFF.695_From_mt_0_4217716_ [**** ] 16% > Processing Locus CUFF.697_From_mt_0_4229662_ [**** ] 17% > Processing Locus CUFF.699_From_no_0_2905273_ [**** ] 18% > Processing Locus CUFF.705_From_no_0_3113578_ [**** ] 19% > Processing Locus CUFF.715_From_oy_0_3098144_ [***** ] 20% > Processing Locus CUFF.717_From_oy_0_2966542_ [***** ] 20% > Processing Locus CUFF.729_From_oy_0_3001818_ [***** ] 21% > Processing Locus CUFF.731_From_po_0_3324652_ [***** ] 22% > Processing Locus CUFF.733_From_no_0_2956652_ [***** ] 23% > Processing Locus CUFF.735_From_po_0_3293868_ [****** ] 24% > Processing Locus CUFF.737_From_ct_1_3132277_ [****** ] 24% > Processing Locus CUFF.741_From_po_0_3382155_ [****** ] 25% > Processing Locus CUFF.743_From_po_0_3330421_ [****** ] 26% > Processing Locus CUFF.745_From_po_0_3507160_ [****** ] 27% > Processing Locus CUFF.747_From_po_0_3299272_ [******* ] 28% > Processing Locus CUFF.749_From_oy_0_3162092_ [******* ] 28% > Processing Locus CUFF.753_From_oy_0_3121110_ [******* ] 29% > Processing Locus CUFF.757_From_po_0_3372769_ [******* ] 30% > Processing Locus CUFF.759_From_no_0_2936769_ [******* ] 31% > Processing Locus CUFF.765_From_rsch_4_411079 [******** ] 32% > Processing Locus CUFF.771_From_po_0_3332479_ [******** ] 32% > Processing Locus CUFF.779_From_rsch_4_421454 [******** ] 33% > Processing Locus CUFF.791_From_rsch_4_425553 [******** ] 34% > Processing Locus CUFF.795_From_rsch_4_429714 [******** ] 35% > Processing Locus CUFF.803_From_po_0_3573778_ [********* ] 36% > Processing Locus CUFF.805_From_sf_2_2486157_ [********* ] 36% > Processing Locus CUFF.811_From_sf_2_2459023_ [********* ] 37% > Processing Locus CUFF.817_From_sf_2_2524453_ [********* ] 38%[Mon Apr 4 16:25:11 2011] Mapping reads against segment_juncs with Bowtie > Processing Locus CUFF.835_From_tsu_0_3211741 [********* ] 39% > Processing Locus CUFF.837_From_tsu_0_3215671 [********** ] 40% > Processing Locus CUFF.837_From_tsu_0_3215671 [********** ] 40% > Processing Locus CUFF.839_From_sf_2_2680171_ [********** ] 41% > Processing Locus CUFF.843_From_rsch_4_429219 [********** ] 42% > Processing Locus CUFF.861_From_mt_0_4528444_ [********** ] 43% > Processing Locus CUFF.871_From_rsch_4_426655 [*********** ] 44% > Processing Locus CUFF.879_From_rsch_4_405516 [*********** ] 44% > Processing Locus CUFF.881_From_wil_2_2925323 [*********** ] 45% > Processing Locus CUFF.891_From_wil_2_3079625 [*********** ] 46% > Processing Locus CUFF.907_From_ws_0_3182508_ [*********** ] 47% > Processing Locus CUFF.919_From_ws_0_3347582_ [************ ] 48% > Processing Locus CUFF.919_From_ws_0_3347582_ [************ ] 48% > Processing Locus CUFF.941_From_wu_0_2824308_ [************ ] 49% > Processing Locus CUFF.947_From_wu_0_2654219_ [************ ] 50% > Processing Locus CUFF.949_From_wu_0_2687576_ [************ ] 51% > Processing Locus CUFF.955_From_ws_0_3340488_ [************* ] 52% > Processing Locus CUFF.957_From_ws_0_3381390_ [************* ] 52% > Processing Locus CUFF.969_From_zu_0_3190435_ [************* ] 53% > Processing Locus CUFF.971_From_zu_0_3255169_ [************* ] 54% > Processing Locus CUFF.973_From_zu_0_3242889_ [************* ] 55% > Processing Locus CUFF.975_From_zu_0_3259399_ [************** ] 56% > Processing Locus CUFF.977_From_zu_0_3255503_ [************** ] 56% > Processing Locus CUFF.981_From_zu_0_3289907_ [************** ] 57% > Processing Locus CUFF.987_From_zu_0_3118546_ [************** ] 58% > Processing Locus CUFF.989_From_zu_0_3289907_ [************** ] 59% > Processing Locus CUFF.989_From_zu_0_3289907_ [*************** ] 60% > Processing Locus CUFF.991_From_zu_0_3277661_ [*************** ] 60% > Processed 77 loci. [*************************] 100% cufflinks -p 4 -o ./Oy_0 -r ngene.fa ./Oy_0/accepted_hits.bam [16:25:11] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399ð6 [ ] > Processing Locus CUFF.547_From_bur_0_2032354ð6 [ ] > Processing Locus CUFF.555_From_can_0_3217045ð6 [ ] > Processing Locus CUFF.561_From_can_0_3189753ð6 [ ] > Processing Locus CUFF.571_From_can_0_3076940ð6 [ ] > Processing Locus CUFF.575_From_ct_1_3082021_ð6 [ ] > Processing Locus CUFF.579_From_ct_1_3133451_ð6 [ ] > Processing Locus CUFF.581_From_can_0_3218459ð6 [ ] > Processing Locus CUFF.583_From_ct_1_3302721_ð6 [ ] > Processing Locus CUFF.585_From_ct_1_3247037_ð6 [ ] > Processing Locus CUFF.593_From_can_0_3270131ð6 [* ] > Processing Locus CUFF.593_From_can_0_3270131ð6 [* ] > Processing Locus CUFF.593_From_can_0_3270131ð6 [* ] > Processing Locus CUFF.595_From_ct_1_3302721_ð6 [* ] > Processing Locus CUFF.613_From_hi_0_2773206_ð6 [* ] > Processing Locus CUFF.615_From_edi_0_2932438ð6 [* ] > Processing Locus CUFF.617_From_edi_0_2918156ð6 [* ] > Processing Locus CUFF.619_From_edi_0_2871668ð6 [* ] > Processing Locus CUFF.623_From_hi_0_2778596_ð6 [* ] > Processing Locus CUFF.627_From_edi_0_2889434ð6 [* ] > Processing Locus CUFF.635_From_ct_1_3241157_ð6 [* ] > Processing Locus CUFF.661_From_kn_0_3819922_ð6 [** ] > Processing Locus CUFF.663_From_kn_0_3613403_ð6 [** ] > Processing Locus CUFF.665_From_hi_0_2939638_ð6 [** ] > Processing Locus CUFF.671_From_edi_0_2859720ð6 [** ] > Processing Locus CUFF.677_From_ct_1_3133995_ð6 [** ] > Processing Locus CUFF.679_From_ler_0_3998410ð6 [** ] > Processing Locus CUFF.685_From_mt_0_4231054_ð6 [** ] > Processing Locus CUFF.689_From_ler_0_4018856ð6 [** ] > Processing Locus CUFF.695_From_mt_0_4217716_ð6 [** ] > Processing Locus CUFF.697_From_mt_0_4229662_ð6 [** ] > Processing Locus CUFF.699_From_no_0_2905273_ð6 [*** ] > Processing Locus CUFF.703_From_no_0_2885444_ð6 [*** ] > Processing Locus CUFF.715_From_oy_0_3098144_ð6 [*** ] > Processing Locus CUFF.717_From_oy_0_2966542_ð6 [*** ] > Processing Locus CUFF.719_From_oy_0_2936927_ð6 [*** ] > Processing Locus CUFF.729_From_oy_0_3001818_ð6 [*** ] > Processing Locus CUFF.733_From_no_0_2956652_ð6 [*** ] > Processing Locus CUFF.735_From_po_0_3293868_ð6 [*** ] > Processing Locus CUFF.737_From_ct_1_3132277_ð6 [*** ] > Processing Locus CUFF.749_From_oy_0_3162092_ð6 [**** ] > Processing Locus CUFF.749_From_oy_0_3162092_ð6 [**** ] > Processing Locus CUFF.763_From_rsch_4_403203ð6 [**** ] > Processing Locus CUFF.771_From_po_0_3332479_ð6 [**** ] > Processing Locus CUFF.779_From_rsch_4_421454ð6 [**** ] > Processing Locus CUFF.783_From_oy_0_2965192_ð6 [**** ] > Processing Locus CUFF.791_From_rsch_4_425553ð6 [**** ] > Processing Locus CUFF.805_From_sf_2_2486157_ð6 [**** ] > Processing Locus CUFF.809_From_sf_2_2682779_ð6 [**** ] > Processing Locus CUFF.811_From_sf_2_2459023_ð6 [**** ] > Processing Locus CUFF.817_From_sf_2_2524453_ð6 [**** ] > Processing Locus CUFF.835_From_tsu_0_3211741ð6 [***** ] > Processing Locus CUFF.839_From_sf_2_2680171_ð6 [***** ] > Processing Locus CUFF.839_From_sf_2_2680171_ð6 [***** ] > Processing Locus CUFF.843_From_rsch_4_429219ð6 [***** ] > Processing Locus CUFF.861_From_mt_0_4528444_ð6 [***** ] > Processing Locus CUFF.879_From_rsch_4_405516ð6 [***** ] > Processing Locus CUFF.881_From_wil_2_2925323ð6 [***** ] > Processing Locus CUFF.907_From_ws_0_3182508_ð6 [***** ] > Processing Locus CUFF.913_From_wil_2_2834553ð6 [***** ] > Processing Locus CUFF.919_From_ws_0_3347582_ð6 [***** ] > Processing Locus CUFF.919_From_ws_0_3347582_ð6 [***** ] > Processing Locus CUFF.919_From_ws_0_3347582_ð6 [***** ] > Processing Locus CUFF.941_From_wu_0_2824308_ð6 [****** ] > Processing Locus CUFF.941_From_wu_0_2824308_ð6 [****** ] > Processing Locus CUFF.945_From_wu_0_2678387_ð6 [****** ] > Processing Locus CUFF.947_From_wu_0_2654219_ð6 [****** ] > Processing Locus CUFF.949_From_wu_0_2687576_ð6 [****** ] > Processing Locus CUFF.955_From_ws_0_3340488_ð6 [****** ] > Processing Locus CUFF.965_From_zu_0_3238769_ð6 [****** ] > Processing Locus CUFF.965_From_zu_0_3238769_ð6 [****** ] > Processing Locus CUFF.971_From_zu_0_3255169_ð6 [****** ] > Processing Locus CUFF.973_From_zu_0_3242889_ð6 [****** ] > Processing Locus CUFF.977_From_zu_0_3255503_ð6 [****** ] > Processing Locus CUFF.981_From_zu_0_3289907_ð6 [****** ] > Processing Locus CUFF.989_From_zu_0_3289907_ð6 [******* ] > Processing Locus CUFF.991_From_zu_0_3277661_ð6 [******* ] > Processed 77 loci. [*************************] 100% > Map Properties: > Total Map Mass: 4902.82 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:25:11] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.547_From_bur_0_2032354 [ ] 1% > Processing Locus CUFF.555_From_can_0_3217045 [ ] 2% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 6% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 7% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 9% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 10% > Processing Locus CUFF.585_From_ct_1_3247037_ [** ] 11% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 12% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 14% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 15% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 16% > Processing Locus CUFF.613_From_hi_0_2773206_ [**** ] 18% > Processing Locus CUFF.615_From_edi_0_2932438 [**** ] 19% > Processing Locus CUFF.617_From_edi_0_2918156 [***** ] 20% > Processing Locus CUFF.619_From_edi_0_2871668 [***** ] 22% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 23% > Processing Locus CUFF.627_From_edi_0_2889434 [****** ] 24% > Processing Locus CUFF.635_From_ct_1_3241157_ [****** ] 25% > Processing Locus CUFF.661_From_kn_0_3819922_ [****** ] 27% > Processing Locus CUFF.663_From_kn_0_3613403_ [******* ] 28% > Processing Locus CUFF.665_From_hi_0_2939638_ [******* ] 29% > Processing Locus CUFF.671_From_edi_0_2859720 [******* ] 31% > Processing Locus CUFF.677_From_ct_1_3133995_ [******** ] 32% > Processing Locus CUFF.679_From_ler_0_3998410 [******** ] 33% > Processing Locus CUFF.685_From_mt_0_4231054_ [******** ] 35% > Processing Locus CUFF.689_From_ler_0_4018856 [********* ] 36% > Processing Locus CUFF.695_From_mt_0_4217716_ [********* ] 37% > Processing Locus CUFF.697_From_mt_0_4229662_ [********* ] 38% > Processing Locus CUFF.699_From_no_0_2905273_ [********** ] 40% > Processing Locus CUFF.703_From_no_0_2885444_ [********** ] 41% > Processing Locus CUFF.715_From_oy_0_3098144_ [********** ] 42% > Processing Locus CUFF.717_From_oy_0_2966542_ [*********** ] 44% > Processing Locus CUFF.719_From_oy_0_2936927_ [*********** ] 45% > Processing Locus CUFF.729_From_oy_0_3001818_ [*********** ] 46% > Processing Locus CUFF.733_From_no_0_2956652_ [************ ] 48% > Processing Locus CUFF.735_From_po_0_3293868_ [************ ] 49% > Processing Locus CUFF.737_From_ct_1_3132277_ [************ ] 50% > Processing Locus CUFF.749_From_oy_0_3162092_ [************ ] 51% > Processing Locus CUFF.749_From_oy_0_3162092_ [************* ] 53% > Processing Locus CUFF.763_From_rsch_4_403203 [************* ] 54% > Processing Locus CUFF.771_From_po_0_3332479_ [************* ] 55% > Processing Locus CUFF.779_From_rsch_4_421454 [************** ] 57% > Processing Locus CUFF.783_From_oy_0_2965192_ [************** ] 58% > Processing Locus CUFF.791_From_rsch_4_425553 [************** ] 59% > Processing Locus CUFF.805_From_sf_2_2486157_ [*************** ] 61% > Processing Locus CUFF.809_From_sf_2_2682779_ [*************** ] 62% > Processing Locus CUFF.811_From_sf_2_2459023_ [*************** ] 63% > Processing Locus CUFF.817_From_sf_2_2524453_ [**************** ] 64% > Processing Locus CUFF.835_From_tsu_0_3211741 [**************** ] 66% > Processing Locus CUFF.839_From_sf_2_2680171_ [**************** ] 67% > Processing Locus CUFF.839_From_sf_2_2680171_ [***************** ] 68% > Processing Locus CUFF.843_From_rsch_4_429219 [***************** ] 70% > Processing Locus CUFF.861_From_mt_0_4528444_ [***************** ] 71% > Processing Locus CUFF.879_From_rsch_4_405516 [****************** ] 72% > Processing Locus CUFF.881_From_wil_2_2925323 [****************** ] 74% > Processing Locus CUFF.907_From_ws_0_3182508_ [****************** ] 75% > Processing Locus CUFF.913_From_wil_2_2834553 [******************* ] 76% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 77% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 79% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 80% > Processing Locus CUFF.941_From_wu_0_2824308_ [******************** ] 81% > Processing Locus CUFF.941_From_wu_0_2824308_ [******************** ] 83% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************* ] 84% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************* ] 85% > Processing Locus CUFF.949_From_wu_0_2687576_ [********************* ] 87% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************** ] 88% > Processing Locus CUFF.965_From_zu_0_3238769_ [********************** ] 89% > Processing Locus CUFF.965_From_zu_0_3238769_ [********************** ] 90% > Processing Locus CUFF.971_From_zu_0_3255169_ [*********************** ] 92% > Processing Locus CUFF.973_From_zu_0_3242889_ [*********************** ] 93% > Processing Locus CUFF.977_From_zu_0_3255503_ [*********************** ] 94% > Processing Locus CUFF.981_From_zu_0_3289907_ [************************ ] 96% > Processing Locus CUFF.989_From_zu_0_3289907_ [************************ ] 97% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 98% > Processed 77 loci. [*************************] 100% [16:25:11] Loading reference annotation and sequence [16:25:11] Learning bias parameters. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.547_From_bur_0_2032354 [ ] 1% > Processing Locus CUFF.555_From_can_0_3217045 [ ] 2% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 6% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 7% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 9% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 10% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 11% > Processing Locus CUFF.615_From_edi_0_2932438 [*** ] 12% > Processing Locus CUFF.617_From_edi_0_2918156 [*** ] 14% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 15% > Processing Locus CUFF.623_From_hi_0_2778596_ [**** ] 16% > Processing Locus CUFF.627_From_edi_0_2889434 [**** ] 18% > Processing Locus CUFF.635_From_ct_1_3241157_ [**** ] 19% > Processing Locus CUFF.661_From_kn_0_3819922_ [***** ] 20% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 22% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 23% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 24% > Processing Locus CUFF.677_From_ct_1_3133995_ [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 27% > Processing Locus CUFF.685_From_mt_0_4231054_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 31% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 32% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 33% > Processing Locus CUFF.715_From_oy_0_3098144_ [******** ] 35% > Processing Locus CUFF.717_From_oy_0_2966542_ [********* ] 36% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 37% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 38% > Processing Locus CUFF.735_From_po_0_3293868_ [********** ] 40% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 41% > Processing Locus CUFF.749_From_oy_0_3162092_ [********** ] 42% > Processing Locus CUFF.749_From_oy_0_3162092_ [*********** ] 44% > Processing Locus CUFF.763_From_rsch_4_403203 [*********** ] 45% > Processing Locus CUFF.771_From_po_0_3332479_ [*********** ] 46% > Processing Locus CUFF.779_From_rsch_4_421454 [************ ] 48% > Processing Locus CUFF.783_From_oy_0_2965192_ [************ ] 49% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 50% > Processing Locus CUFF.805_From_sf_2_2486157_ [************ ] 51% > Processing Locus CUFF.809_From_sf_2_2682779_ [************* ] 53% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 54% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 55% > Processing Locus CUFF.835_From_tsu_0_3211741 [************** ] 57% > Processing Locus CUFF.839_From_sf_2_2680171_ [************** ] 58% > Processing Locus CUFF.839_From_sf_2_2680171_ [************** ] 59% > Processing Locus CUFF.843_From_rsch_4_429219 [*************** ] 61% > Processing Locus CUFF.861_From_mt_0_4528444_ [*************** ] 62% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 63% > Processing Locus CUFF.881_From_wil_2_2925323 [**************** ] 64% > Processing Locus CUFF.919_From_ws_0_3347582_ [**************** ] 66% > Processing Locus CUFF.941_From_wu_0_2824308_ [**************** ] 67% > Processing Locus CUFF.945_From_wu_0_2678387_ [***************** ] 68% > Processing Locus CUFF.947_From_wu_0_2654219_ [***************** ] 70% > Processing Locus CUFF.949_From_wu_0_2687576_ [***************** ] 71% > Processing Locus CUFF.955_From_ws_0_3340488_ [****************** ] 72% > Processing Locus CUFF.971_From_zu_0_3255169_ [****************** ] 74% > Processing Locus CUFF.973_From_zu_0_3242889_ [****************** ] 75% > Processing Locus CUFF.977_From_zu_0_3255503_ [******************* ] 76% > Processing Locus CUFF.981_From_zu_0_3289907_ [******************* ] 77% > Processing Locus CUFF.989_From_zu_0_3289907_ [******************* ] 79% > Processing Locus CUFF.991_From_zu_0_3277661_ [******************** ] 80% > Processed 63 loci. [*************************] 100% [16:25:11] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.547_From_bur_0_2032354 [ ] 1% > Processing Locus CUFF.555_From_can_0_3217045 [ ] 2% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 3% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 6% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 7% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 9% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 10% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 11% > Processing Locus CUFF.615_From_edi_0_2932438 [*** ] 12% > Processing Locus CUFF.617_From_edi_0_2918156 [*** ] 14% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 15% > Processing Locus CUFF.623_From_hi_0_2778596_ [**** ] 16% > Processing Locus CUFF.627_From_edi_0_2889434 [**** ] 18% > Processing Locus CUFF.635_From_ct_1_3241157_ [**** ] 19% > Processing Locus CUFF.661_From_kn_0_3819922_ [***** ] 20% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 22% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 23% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 24% > Processing Locus CUFF.677_From_ct_1_3133995_ [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 27% > Processing Locus CUFF.685_From_mt_0_4231054_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 31% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 32% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 33% > Processing Locus CUFF.715_From_oy_0_3098144_ [******** ] 35% > Processing Locus CUFF.717_From_oy_0_2966542_ [********* ] 36% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 37% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 38% > Processing Locus CUFF.735_From_po_0_3293868_ [********** ] 40% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 41% > Processing Locus CUFF.749_From_oy_0_3162092_ [********** ] 42% > Processing Locus CUFF.749_From_oy_0_3162092_ [*********** ] 44% > Processing Locus CUFF.763_From_rsch_4_403203 [*********** ] 45% > Processing Locus CUFF.771_From_po_0_3332479_ [*********** ] 46% > Processing Locus CUFF.779_From_rsch_4_421454 [************ ] 48% > Processing Locus CUFF.783_From_oy_0_2965192_ [************ ] 49% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 50% > Processing Locus CUFF.805_From_sf_2_2486157_ [************ ] 51% > Processing Locus CUFF.809_From_sf_2_2682779_ [************* ] 53% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 54% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 55% > Processing Locus CUFF.835_From_tsu_0_3211741 [************** ] 57% > Processing Locus CUFF.839_From_sf_2_2680171_ [************** ] 58% > Processing Locus CUFF.839_From_sf_2_2680171_ [************** ] 59% > Processing Locus CUFF.843_From_rsch_4_429219 [*************** ] 61% > Processing Locus CUFF.861_From_mt_0_4528444_ [*************** ] 62% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 63% > Processing Locus CUFF.881_From_wil_2_2925323 [**************** ] 64% > Processing Locus CUFF.919_From_ws_0_3347582_ [**************** ] 66% > Processing Locus CUFF.941_From_wu_0_2824308_ [**************** ] 67% > Processing Locus CUFF.945_From_wu_0_2678387_ [***************** ] 68% > Processing Locus CUFF.947_From_wu_0_2654219_ [***************** ] 70% > Processing Locus CUFF.949_From_wu_0_2687576_ [***************** ] 71% > Processing Locus CUFF.955_From_ws_0_3340488_ [****************** ] 72% > Processing Locus CUFF.971_From_zu_0_3255169_ [****************** ] 74% > Processing Locus CUFF.973_From_zu_0_3242889_ [****************** ] 75% > Processing Locus CUFF.977_From_zu_0_3255503_ [******************* ] 76% > Processing Locus CUFF.981_From_zu_0_3289907_ [******************* ] 77% > Processing Locus CUFF.989_From_zu_0_3289907_ [******************* ] 79% > Processing Locus CUFF.991_From_zu_0_3277661_ [******************** ] 80% > Processed 63 loci. [*************************] 100% [Mon Apr 4 16:25:13 2011] Joining segment hits [Mon Apr 4 16:25:15 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:50 elapsed] [Mon Apr 4 16:25:18 2011] Retrieving sequences for splices [Mon Apr 4 16:25:18 2011] Indexing splices [Mon Apr 4 16:25:18 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:25:20 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:25:22 2011] Mapping reads against segment_juncs with Bowtie cufflinks -p 4 -o ./Mt_0 -r ngene.fa ./Mt_0/accepted_hits.bam [Mon Apr 4 16:25:24 2011] Joining segment hits [16:25:24] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399Õ [ ] > Processing Locus CUFF.525_From_bur_0_1863298Õ [ ] > Processing Locus CUFF.533_From_bur_0_2020452Õ [ ] > Processing Locus CUFF.563_From_bur_0_2020452Õ [ ] > Processing Locus CUFF.567_From_can_0_3258779Õ [ ] > Processing Locus CUFF.571_From_can_0_3076940Õ [ ] > Processing Locus CUFF.573_From_can_0_3233581Õ [ ] > Processing Locus CUFF.575_From_ct_1_3082021_Õ [ ] > Processing Locus CUFF.579_From_ct_1_3133451_Õ [ ] > Processing Locus CUFF.583_From_ct_1_3302721_Õ [ ] > Processing Locus CUFF.585_From_ct_1_3247037_Õ [* ] > Processing Locus CUFF.585_From_ct_1_3247037_Õ [* ] > Processing Locus CUFF.593_From_can_0_3270131Õ [* ] > Processing Locus CUFF.593_From_can_0_3270131Õ [* ] > Processing Locus CUFF.595_From_ct_1_3302721_Õ [* ] > Processing Locus CUFF.597_From_edi_0_2759827Õ [* ] > Processing Locus CUFF.615_From_edi_0_2932438Õ [* ] > Processing Locus CUFF.621_From_edi_0_2934714Õ [* ] > Processing Locus CUFF.621_From_edi_0_2934714Õ [* ] > Processing Locus CUFF.621_From_edi_0_2934714Õ [* ] > Processing Locus CUFF.621_From_edi_0_2934714Õ [* ] > Processing Locus CUFF.623_From_hi_0_2778596_Õ [* ] > Processing Locus CUFF.627_From_edi_0_2889434Õ [* ] > Processing Locus CUFF.629_From_kn_0_3594465_Õ [* ] > Processing Locus CUFF.641_From_kn_0_3605300_Õ [** ] > Processing Locus CUFF.655_From_hi_0_2795398_Õ [** ] > Processing Locus CUFF.661_From_kn_0_3819922_Õ [** ] > Processing Locus CUFF.661_From_kn_0_3819922_Õ [** ] > Processing Locus CUFF.661_From_kn_0_3819922_Õ [** ] > Processing Locus CUFF.663_From_kn_0_3613403_Õ [** ] > Processing Locus CUFF.665_From_hi_0_2939638_Õ [** ] > Processing Locus CUFF.671_From_edi_0_2859720Õ [** ] > Processing Locus CUFF.675_From_mt_0_4213448_Õ [** ] > Processing Locus CUFF.677_From_ct_1_3133995_Õ [** ] > Processing Locus CUFF.679_From_ler_0_3998410Õ [** ] > Processing Locus CUFF.681_From_mt_0_4399784_Õ [** ] > Processing Locus CUFF.685_From_mt_0_4231054_Õ [*** ] > Processing Locus CUFF.687_From_mt_0_4230874_Õ [*** ] > Processing Locus CUFF.689_From_ler_0_4018856Õ [*** ] > Processing Locus CUFF.693_From_no_0_2934639_Õ [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_Õ [*** ] > Processing Locus CUFF.697_From_mt_0_4229662_Õ [*** ] > Processing Locus CUFF.699_From_no_0_2905273_Õ [*** ] > Processing Locus CUFF.703_From_no_0_2885444_Õ [*** ] > Processing Locus CUFF.709_From_no_0_3101262_Õ [*** ] > Processing Locus CUFF.711_From_no_0_3088052_Õ [**** ] > Processing Locus CUFF.725_From_no_0_3116640_Õ [**** ] > Processing Locus CUFF.729_From_oy_0_3001818_Õ [**** ] > Processing Locus CUFF.733_From_no_0_2956652_Õ [**** ] > Processing Locus CUFF.739_From_po_0_3340213_Õ [**** ] > Processing Locus CUFF.747_From_po_0_3299272_Õ [**** ] > Processing Locus CUFF.755_From_mt_0_4193196_Õ [**** ] > Processing Locus CUFF.761_From_po_0_3606391_Õ [**** ] > Processing Locus CUFF.763_From_rsch_4_403203Õ [**** ] > Processing Locus CUFF.771_From_po_0_3332479_Õ [**** ] > Processing Locus CUFF.773_From_po_0_3606391_Õ [***** ] > Processing Locus CUFF.779_From_rsch_4_421454Õ [***** ] > Processing Locus CUFF.783_From_oy_0_2965192_Õ [***** ] > Processing Locus CUFF.785_From_no_0_3128142_Õ [***** ] > Processing Locus CUFF.785_From_no_0_3128142_Õ [***** ] > Processing Locus CUFF.789_From_rsch_4_427544Õ [***** ] > Processing Locus CUFF.791_From_rsch_4_425553Õ [***** ] > Processing Locus CUFF.805_From_sf_2_2486157_Õ [***** ] > Processing Locus CUFF.807_From_sf_2_2488391_Õ [***** ] > Processing Locus CUFF.817_From_sf_2_2524453_Õ [***** ] > Processing Locus CUFF.819_From_tsu_0_3036945Õ [****** ] > Processing Locus CUFF.839_From_sf_2_2680171_Õ [****** ] > Processing Locus CUFF.843_From_rsch_4_429219Õ [****** ] > Processing Locus CUFF.855_From_wil_2_2915899Õ [****** ] > Processing Locus CUFF.861_From_mt_0_4528444_Õ [****** ] > Processing Locus CUFF.879_From_rsch_4_405516Õ [****** ] > Processing Locus CUFF.895_From_tsu_0_3215821Õ [****** ] > Processing Locus CUFF.901_From_wil_2_3088151Õ [****** ] > Processing Locus CUFF.907_From_ws_0_3182508_Õ [****** ] > Processing Locus CUFF.913_From_wil_2_2834553Õ [****** ] > Processing Locus CUFF.915_From_ws_0_3349444_Õ [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_Õ [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_Õ [******* ] > Processing Locus CUFF.925_From_ws_0_3371988_Õ [******* ] > Processing Locus CUFF.925_From_ws_0_3371988_Õ [******* ] > Processing Locus CUFF.935_From_ws_0_3380934_Õ [******* ] > Processing Locus CUFF.941_From_wu_0_2824308_Õ [******* ] > Processing Locus CUFF.945_From_wu_0_2678387_Õ [******* ] > Processing Locus CUFF.947_From_wu_0_2654219_Õ [******* ] > Processing Locus CUFF.955_From_ws_0_3340488_Õ [******* ] > Processing Locus CUFF.957_From_ws_0_3381390_Õ [******* ] > Processing Locus CUFF.963_From_zu_0_3092045_Õ [******** ] > Processing Locus CUFF.965_From_zu_0_3238769_Õ [******** ] > Processing Locus CUFF.973_From_zu_0_3242889_Õ [******** ] > Processing Locus CUFF.977_From_zu_0_3255503_Õ [******** ] > Processing Locus CUFF.985_From_zu_0_3280213_Õ [******** ] > Processing Locus CUFF.985_From_zu_0_3280213_Õ [******** ] > Processing Locus CUFF.985_From_zu_0_3280213_Õ [******** ] > Processing Locus CUFF.991_From_zu_0_3277661_Õ [******** ] > Processed 94 loci. [*************************] 100% > Map Properties: > Total Map Mass: 6328.59 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:25:24] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 1% > Processing Locus CUFF.533_From_bur_0_2020452 [ ] 2% > Processing Locus CUFF.563_From_bur_0_2020452 [ ] 3% > Processing Locus CUFF.567_From_can_0_3258779 [* ] 4% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.573_From_can_0_3233581 [* ] 6% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 7% > Processing Locus CUFF.579_From_ct_1_3133451_ [** ] 8% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.585_From_ct_1_3247037_ [** ] 10% > Processing Locus CUFF.585_From_ct_1_3247037_ [** ] 11% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 12% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 13% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 14% > Processing Locus CUFF.597_From_edi_0_2759827 [*** ] 15% > Processing Locus CUFF.615_From_edi_0_2932438 [**** ] 17% > Processing Locus CUFF.621_From_edi_0_2934714 [**** ] 18% > Processing Locus CUFF.621_From_edi_0_2934714 [**** ] 19% > Processing Locus CUFF.621_From_edi_0_2934714 [***** ] 20% > Processing Locus CUFF.621_From_edi_0_2934714 [***** ] 21% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 22% > Processing Locus CUFF.627_From_edi_0_2889434 [***** ] 23% > Processing Locus CUFF.629_From_kn_0_3594465_ [****** ] 24% > Processing Locus CUFF.641_From_kn_0_3605300_ [****** ] 25% > Processing Locus CUFF.655_From_hi_0_2795398_ [****** ] 26% > Processing Locus CUFF.661_From_kn_0_3819922_ [****** ] 27% > Processing Locus CUFF.661_From_kn_0_3819922_ [******* ] 28% > Processing Locus CUFF.661_From_kn_0_3819922_ [******* ] 29% > Processing Locus CUFF.663_From_kn_0_3613403_ [******* ] 30% > Processing Locus CUFF.665_From_hi_0_2939638_ [******* ] 31% > Processing Locus CUFF.671_From_edi_0_2859720 [******** ] 32% > Processing Locus CUFF.675_From_mt_0_4213448_ [******** ] 34% > Processing Locus CUFF.677_From_ct_1_3133995_ [******** ] 35% > Processing Locus CUFF.679_From_ler_0_3998410 [********* ] 36% > Processing Locus CUFF.681_From_mt_0_4399784_ [********* ] 37% > Processing Locus CUFF.685_From_mt_0_4231054_ [********* ] 38% > Processing Locus CUFF.687_From_mt_0_4230874_ [********* ] 39% > Processing Locus CUFF.689_From_ler_0_4018856 [********** ] 40% > Processing Locus CUFF.693_From_no_0_2934639_ [********** ] 41% > Processing Locus CUFF.695_From_mt_0_4217716_ [********** ] 42% > Processing Locus CUFF.697_From_mt_0_4229662_ [********** ] 43% > Processing Locus CUFF.699_From_no_0_2905273_ [*********** ] 44% > Processing Locus CUFF.703_From_no_0_2885444_ [*********** ] 45% > Processing Locus CUFF.709_From_no_0_3101262_ [*********** ] 46% > Processing Locus CUFF.711_From_no_0_3088052_ [*********** ] 47% > Processing Locus CUFF.725_From_no_0_3116640_ [************ ] 48% > Processing Locus CUFF.729_From_oy_0_3001818_ [************ ] 50% > Processing Locus CUFF.733_From_no_0_2956652_ [************ ] 51% > Processing Locus CUFF.739_From_po_0_3340213_ [************* ] 52% > Processing Locus CUFF.747_From_po_0_3299272_ [************* ] 53% > Processing Locus CUFF.755_From_mt_0_4193196_ [************* ] 54% > Processing Locus CUFF.761_From_po_0_3606391_ [************* ] 55% > Processing Locus CUFF.763_From_rsch_4_403203 [************** ] 56% > Processing Locus CUFF.771_From_po_0_3332479_ [************** ] 57% > Processing Locus CUFF.773_From_po_0_3606391_ [************** ] 58% > Processing Locus CUFF.779_From_rsch_4_421454 [************** ] 59% > Processing Locus CUFF.783_From_oy_0_2965192_ [*************** ] 60% > Processing Locus CUFF.785_From_no_0_3128142_ [*************** ] 61% > Processing Locus CUFF.785_From_no_0_3128142_ [*************** ] 62% > Processing Locus CUFF.789_From_rsch_4_427544 [*************** ] 63% > Processing Locus CUFF.791_From_rsch_4_425553 [**************** ] 64% > Processing Locus CUFF.805_From_sf_2_2486157_ [**************** ] 65% > Processing Locus CUFF.807_From_sf_2_2488391_ [**************** ] 67% > Processing Locus CUFF.817_From_sf_2_2524453_ [***************** ] 68% > Processing Locus CUFF.819_From_tsu_0_3036945 [***************** ] 69% > Processing Locus CUFF.839_From_sf_2_2680171_ [***************** ] 70% > Processing Locus CUFF.843_From_rsch_4_429219 [***************** ] 71% > Processing Locus CUFF.855_From_wil_2_2915899 [****************** ] 72% > Processing Locus CUFF.861_From_mt_0_4528444_ [****************** ] 73% > Processing Locus CUFF.879_From_rsch_4_405516 [****************** ] 74% > Processing Locus CUFF.895_From_tsu_0_3215821 [****************** ] 75% > Processing Locus CUFF.901_From_wil_2_3088151 [******************* ] 76% > Processing Locus CUFF.907_From_ws_0_3182508_ [******************* ] 77% > Processing Locus CUFF.913_From_wil_2_2834553 [******************* ] 78% > Processing Locus CUFF.915_From_ws_0_3349444_ [******************* ] 79% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 80% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 81% > Processing Locus CUFF.925_From_ws_0_3371988_ [******************** ] 82% > Processing Locus CUFF.925_From_ws_0_3371988_ [********************* ] 84% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************* ] 85% > Processing Locus CUFF.941_From_wu_0_2824308_ [********************* ] 86% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************* ] 87% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************** ] 88% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************** ] 89% > Processing Locus CUFF.957_From_ws_0_3381390_ [********************** ] 90% > Processing Locus CUFF.963_From_zu_0_3092045_ [********************** ] 91% > Processing Locus CUFF.965_From_zu_0_3238769_ [*********************** ] 92% > Processing Locus CUFF.973_From_zu_0_3242889_ [*********************** ] 93% > Processing Locus CUFF.977_From_zu_0_3255503_ [*********************** ] 94% > Processing Locus CUFF.985_From_zu_0_3280213_ [*********************** ] 95% > Processing Locus CUFF.985_From_zu_0_3280213_ [************************ ] 96% > Processing Locus CUFF.985_From_zu_0_3280213_ [************************ ] 97% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 98% > Processed 94 loci. [*************************] 100% [16:25:24] Loading reference annotation and sequence [16:25:24] Learning bias parameters. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.563_From_bur_0_2020452 [ ] 1% > Processing Locus CUFF.567_From_can_0_3258779 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.573_From_can_0_3233581 [* ] 4% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 5% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 7% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 8% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.597_From_edi_0_2759827 [** ] 10% > Processing Locus CUFF.615_From_edi_0_2932438 [** ] 11% > Processing Locus CUFF.623_From_hi_0_2778596_ [*** ] 12% > Processing Locus CUFF.627_From_edi_0_2889434 [*** ] 13% > Processing Locus CUFF.641_From_kn_0_3605300_ [*** ] 14% > Processing Locus CUFF.655_From_hi_0_2795398_ [*** ] 15% > Processing Locus CUFF.661_From_kn_0_3819922_ [**** ] 17% > Processing Locus CUFF.661_From_kn_0_3819922_ [**** ] 18% > Processing Locus CUFF.663_From_kn_0_3613403_ [**** ] 19% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 20% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 21% > Processing Locus CUFF.675_From_mt_0_4213448_ [***** ] 22% > Processing Locus CUFF.677_From_ct_1_3133995_ [***** ] 23% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 24% > Processing Locus CUFF.681_From_mt_0_4399784_ [****** ] 25% > Processing Locus CUFF.687_From_mt_0_4230874_ [****** ] 26% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 27% > Processing Locus CUFF.693_From_no_0_2934639_ [******* ] 28% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 29% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 30% > Processing Locus CUFF.699_From_no_0_2905273_ [******* ] 31% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 32% > Processing Locus CUFF.709_From_no_0_3101262_ [******** ] 34% > Processing Locus CUFF.725_From_no_0_3116640_ [******** ] 35% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 36% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 37% > Processing Locus CUFF.747_From_po_0_3299272_ [********* ] 38% > Processing Locus CUFF.755_From_mt_0_4193196_ [********* ] 39% > Processing Locus CUFF.761_From_po_0_3606391_ [********** ] 40% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 41% > Processing Locus CUFF.771_From_po_0_3332479_ [********** ] 42% > Processing Locus CUFF.773_From_po_0_3606391_ [********** ] 43% > Processing Locus CUFF.779_From_rsch_4_421454 [*********** ] 44% > Processing Locus CUFF.783_From_oy_0_2965192_ [*********** ] 45% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 46% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 47% > Processing Locus CUFF.789_From_rsch_4_427544 [************ ] 48% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 50% > Processing Locus CUFF.805_From_sf_2_2486157_ [************ ] 51% > Processing Locus CUFF.807_From_sf_2_2488391_ [************* ] 52% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 53% > Processing Locus CUFF.843_From_rsch_4_429219 [************* ] 54% > Processing Locus CUFF.861_From_mt_0_4528444_ [************* ] 55% > Processing Locus CUFF.879_From_rsch_4_405516 [************** ] 56% > Processing Locus CUFF.901_From_wil_2_3088151 [************** ] 57% > Processing Locus CUFF.907_From_ws_0_3182508_ [************** ] 58% > Processing Locus CUFF.915_From_ws_0_3349444_ [************** ] 59% > Processing Locus CUFF.919_From_ws_0_3347582_ [*************** ] 60% > Processing Locus CUFF.941_From_wu_0_2824308_ [*************** ] 61% > Processing Locus CUFF.945_From_wu_0_2678387_ [*************** ] 62% > Processing Locus CUFF.947_From_wu_0_2654219_ [*************** ] 63% > Processing Locus CUFF.955_From_ws_0_3340488_ [**************** ] 64% > Processing Locus CUFF.957_From_ws_0_3381390_ [**************** ] 65% > Processing Locus CUFF.963_From_zu_0_3092045_ [**************** ] 67% > Processing Locus CUFF.973_From_zu_0_3242889_ [***************** ] 68% > Processing Locus CUFF.977_From_zu_0_3255503_ [***************** ] 69% > Processing Locus CUFF.991_From_zu_0_3277661_ [***************** ] 70% > Processed 67 loci. [*************************] 100% [16:25:24] Assembling transcripts and estimating abundances. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.563_From_bur_0_2020452 [ ] 1% > Processing Locus CUFF.567_From_can_0_3258779 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.573_From_can_0_3233581 [* ] 4% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 5% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 7% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 8% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.597_From_edi_0_2759827 [** ] 10% > Processing Locus CUFF.615_From_edi_0_2932438 [** ] 11% > Processing Locus CUFF.623_From_hi_0_2778596_ [*** ] 12% > Processing Locus CUFF.627_From_edi_0_2889434 [*** ] 13% > Processing Locus CUFF.641_From_kn_0_3605300_ [*** ] 14% > Processing Locus CUFF.655_From_hi_0_2795398_ [*** ] 15% > Processing Locus CUFF.661_From_kn_0_3819922_ [**** ] 17% > Processing Locus CUFF.661_From_kn_0_3819922_ [**** ] 18% > Processing Locus CUFF.663_From_kn_0_3613403_ [**** ] 19% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 20% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 21% > Processing Locus CUFF.675_From_mt_0_4213448_ [***** ] 22% > Processing Locus CUFF.677_From_ct_1_3133995_ [***** ] 23% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 24% > Processing Locus CUFF.681_From_mt_0_4399784_ [****** ] 25% > Processing Locus CUFF.687_From_mt_0_4230874_ [****** ] 26% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 27% > Processing Locus CUFF.693_From_no_0_2934639_ [******* ] 28% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 29% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 30% > Processing Locus CUFF.699_From_no_0_2905273_ [******* ] 31% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 32% > Processing Locus CUFF.709_From_no_0_3101262_ [******** ] 34% > Processing Locus CUFF.725_From_no_0_3116640_ [******** ] 35% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 36% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 37% > Processing Locus CUFF.747_From_po_0_3299272_ [********* ] 38% > Processing Locus CUFF.755_From_mt_0_4193196_ [********* ] 39% > Processing Locus CUFF.761_From_po_0_3606391_ [********** ] 40% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 41% > Processing Locus CUFF.771_From_po_0_3332479_ [********** ] 42% > Processing Locus CUFF.773_From_po_0_3606391_ [********** ] 43% > Processing Locus CUFF.779_From_rsch_4_421454 [*********** ] 44% > Processing Locus CUFF.783_From_oy_0_2965192_ [*********** ] 45% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 46% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 47% > Processing Locus CUFF.789_From_rsch_4_427544 [************ ] 48% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 50% > Processing Locus CUFF.805_From_sf_2_2486157_ [************ ] 51% > Processing Locus CUFF.807_From_sf_2_2488391_ [************* ] 52% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 53% > Processing Locus CUFF.843_From_rsch_4_429219 [************* ] 54% > Processing Locus CUFF.861_From_mt_0_4528444_ [************* ] 55% > Processing Locus CUFF.879_From_rsch_4_405516 [************** ] 56% > Processing Locus CUFF.901_From_wil_2_3088151 [************** ] 57% > Processing Locus CUFF.907_From_ws_0_3182508_ [************** ] 58% > Processing Locus CUFF.915_From_ws_0_3349444_ [************** ] 59% > Processing Locus CUFF.919_From_ws_0_3347582_ [*************** ] 60% > Processing Locus CUFF.941_From_wu_0_2824308_ [*************** ] 61% > Processing Locus CUFF.945_From_wu_0_2678387_ [*************** ] 62% > Processing Locus CUFF.947_From_wu_0_2654219_ [*************** ] 63% > Processing Locus CUFF.955_From_ws_0_3340488_ [**************** ] 64% > Processing Locus CUFF.957_From_ws_0_3381390_ [**************** ] 65% > Processing Locus CUFF.963_From_zu_0_3092045_ [**************** ] 67% > Processing Locus CUFF.973_From_zu_0_3242889_ [***************** ] 68% > Processing Locus CUFF.977_From_zu_0_3255503_ [***************** ] 69% > Processing Locus CUFF.991_From_zu_0_3277661_ [***************** ] 70% > Processed 67 loci. [*************************] 100% [Mon Apr 4 16:25:25 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:31 elapsed] file: /data/arabidopsis/xiang/magic_founder/Sf_2_R1/R38_L7_Sf_2_sdlg_R1_nss_barcode_CAT.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Sf_2_R2/R38_L8_Sf_2_sdlg_R2_nss_barcode_CAT.unmap_1.fq file: /data/arabidopsis/xiang/magic_founder/Tsu_0_R1/R38_L7_Tsu_0_sdlg_R1_nss_barcode_GTA.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Tsu_0_R2/R38_L8_Tsu_0_sdlg_R2_nss_barcode_GTA.unmap_1.fq cufflinks -p 4 -o ./Rsch_4 -r ngene.fa ./Rsch_4/accepted_hits.bam [16:25:32] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.525_From_bur_0_1863298 ¾ [ ] > Processing Locus CUFF.529_From_bur_0_1873494 ¾ [ ] > Processing Locus CUFF.551_From_can_0_3122480 ¾ [ ] > Processing Locus CUFF.573_From_can_0_3233581 ¾ [ ] > Processing Locus CUFF.575_From_ct_1_3082021_ ¾ [ ] > Processing Locus CUFF.583_From_ct_1_3302721_ ¾ [ ] > Processing Locus CUFF.593_From_can_0_3270131 ¾ [ ] > Processing Locus CUFF.593_From_can_0_3270131 ¾ [ ] > Processing Locus CUFF.593_From_can_0_3270131 ¾ [ ] > Processing Locus CUFF.595_From_ct_1_3302721_ ¾ [ ] > Processing Locus CUFF.601_From_edi_0_2934714 ¾ [ ] > Processing Locus CUFF.603_From_bur_0_2025286 ¾ [ ] > Processing Locus CUFF.603_From_bur_0_2025286 ¾ [ ] > Processing Locus CUFF.603_From_bur_0_2025286 ¾ [ ] > Processing Locus CUFF.604_From_edi_0_2934714 ¾ [* ] > Processing Locus CUFF.615_From_edi_0_2932438 ¾ [* ] > Processing Locus CUFF.617_From_edi_0_2918156 ¾ [* ] > Processing Locus CUFF.619_From_edi_0_2871668 ¾ [* ] > Processing Locus CUFF.621_From_edi_0_2934714 ¾ [* ] > Processing Locus CUFF.621_From_edi_0_2934714 ¾ [* ] > Processing Locus CUFF.623_From_hi_0_2778596_ ¾ [* ] > Processing Locus CUFF.629_From_kn_0_3594465_ ¾ [* ] > Processing Locus CUFF.635_From_ct_1_3241157_ ¾ [* ] > Processing Locus CUFF.637_From_kn_0_3626969_ ¾ [* ] > Processing Locus CUFF.641_From_kn_0_3605300_ ¾ [** ] > Processing Locus CUFF.645_From_edi_0_2888586 ¾ [** ] > Processing Locus CUFF.649_From_kn_0_3617271_ ¾ [** ] > Processing Locus CUFF.655_From_hi_0_2795398_ ¾ [** ] > Processing Locus CUFF.661_From_kn_0_3819922_ ¾ [** ] > Processing Locus CUFF.661_From_kn_0_3819922_ ¾ [** ] > Processing Locus CUFF.663_From_kn_0_3613403_ ¾ [** ] > Processing Locus CUFF.665_From_hi_0_2939638_ ¾ [** ] > Processing Locus CUFF.671_From_edi_0_2859720 ¾ [** ] > Processing Locus CUFF.679_From_ler_0_3998410 ¾ [** ] > Processing Locus CUFF.687_From_mt_0_4230874_ ¾ [** ] > Processing Locus CUFF.689_From_ler_0_4018856 ¾ [*** ] > Processing Locus CUFF.693_From_no_0_2934639_ ¾ [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_ ¾ [*** ] > Processing Locus CUFF.697_From_mt_0_4229662_ ¾ [*** ] > Processing Locus CUFF.699_From_no_0_2905273_ ¾ [*** ] > Processing Locus CUFF.701_From_no_0_2951521_ ¾ [*** ] > Processing Locus CUFF.703_From_no_0_2885444_ ¾ [*** ] > Processing Locus CUFF.707_From_no_0_2959683_ ¾ [*** ] > Processing Locus CUFF.725_From_no_0_3116640_ ¾ [*** ] > Processing Locus CUFF.733_From_no_0_2956652_ ¾ [**** ] > Processing Locus CUFF.737_From_ct_1_3132277_ ¾ [**** ] > Processing Locus CUFF.741_From_po_0_3382155_ ¾ [**** ] > Processing Locus CUFF.747_From_po_0_3299272_ ¾ [**** ] > Processing Locus CUFF.749_From_oy_0_3162092_ ¾ [**** ] > Processing Locus CUFF.751_From_rsch_4_403485 ¾ [**** ] > Processing Locus CUFF.755_From_mt_0_4193196_ ¾ [**** ] > Processing Locus CUFF.757_From_po_0_3372769_ ¾ [**** ] > Processing Locus CUFF.759_From_no_0_2936769_ ¾ [**** ] > Processing Locus CUFF.763_From_rsch_4_403203 ¾ [**** ] > Processing Locus CUFF.765_From_rsch_4_411079 ¾ [***** ] > Processing Locus CUFF.767_From_rsch_4_411814 ¾ [***** ] > Processing Locus CUFF.769_From_rsch_4_410762 ¾ [***** ] > Processing Locus CUFF.771_From_po_0_3332479_ ¾ [***** ] > Processing Locus CUFF.775_From_rsch_4_409124 ¾ [***** ] > Processing Locus CUFF.777_From_rsch_4_408506 ¾ [***** ] > Processing Locus CUFF.779_From_rsch_4_421454 ¾ [***** ] > Processing Locus CUFF.785_From_no_0_3128142_ ¾ [***** ] > Processing Locus CUFF.785_From_no_0_3128142_ ¾ [***** ] > Processing Locus CUFF.789_From_rsch_4_427544 ¾ [***** ] > Processing Locus CUFF.789_From_rsch_4_427544 ¾ [***** ] > Processing Locus CUFF.791_From_rsch_4_425553 ¾ [****** ] > Processing Locus CUFF.795_From_rsch_4_429714 ¾ [****** ] > Processing Locus CUFF.807_From_sf_2_2488391_ ¾ [****** ] > Processing Locus CUFF.811_From_sf_2_2459023_ ¾ [****** ] > Processing Locus CUFF.817_From_sf_2_2524453_ ¾ [****** ] > Processing Locus CUFF.827_From_rsch_4_427728 ¾ [****** ] > Processing Locus CUFF.831_From_sf_2_2687774_ ¾ [****** ] > Processing Locus CUFF.839_From_sf_2_2680171_ ¾ [****** ] > Processing Locus CUFF.839_From_sf_2_2680171_ ¾ [****** ] > Processing Locus CUFF.843_From_rsch_4_429219 ¾ [****** ] > Processing Locus CUFF.861_From_mt_0_4528444_ ¾ [****** ] > Processing Locus CUFF.871_From_rsch_4_426655 ¾ [******* ] > Processing Locus CUFF.873_From_wil_2_3050523 ¾ [******* ] > Processing Locus CUFF.879_From_rsch_4_405516 ¾ [******* ] > Processing Locus CUFF.885_From_wil_2_3063473 ¾ [******* ] > Processing Locus CUFF.887_From_wil_2_3054893 ¾ [******* ] > Processing Locus CUFF.893_From_ws_0_3190679_ ¾ [******* ] > Processing Locus CUFF.913_From_wil_2_2834553 ¾ [******* ] > Processing Locus CUFF.917_From_ws_0_3371988_ ¾ [******* ] > Processing Locus CUFF.925_From_ws_0_3371988_ ¾ [******* ] > Processing Locus CUFF.931_From_wu_0_2679395_ ¾ [******** ] > Processing Locus CUFF.935_From_ws_0_3380934_ ¾ [******** ] > Processing Locus CUFF.945_From_wu_0_2678387_ ¾ [******** ] > Processing Locus CUFF.947_From_wu_0_2654219_ ¾ [******** ] > Processing Locus CUFF.949_From_wu_0_2687576_ ¾ [******** ] > Processing Locus CUFF.951_From_wil_2_3087183 ¾ [******** ] > Processing Locus CUFF.955_From_ws_0_3340488_ ¾ [******** ] > Processing Locus CUFF.957_From_ws_0_3381390_ ¾ [******** ] > Processing Locus CUFF.965_From_zu_0_3238769_ ¾ [******** ] > Processing Locus CUFF.967_From_zu_0_3022629_ ¾ [********* ] > Processing Locus CUFF.973_From_zu_0_3242889_ ¾ [********* ] > Processing Locus CUFF.977_From_zu_0_3255503_ ¾ [********* ] > Processing Locus CUFF.987_From_zu_0_3118546_ ¾ [********* ] > Processing Locus CUFF.991_From_zu_0_3277661_ ¾ [********* ] > Processing Locus CUFF.993_From_zu_0_3082201_ ¾ [********* ] > Processed 100 loci. [*************************] 100% > Map Properties: > Total Map Mass: 4628.89 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:25:32] Assembling transcripts and estimating abundances. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 2% > Processing Locus CUFF.573_From_can_0_3233581 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.583_From_ct_1_3302721_ [* ] 5% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 7% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 8% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.601_From_edi_0_2934714 [** ] 10% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 11% > Processing Locus CUFF.603_From_bur_0_2025286 [*** ] 12% > Processing Locus CUFF.603_From_bur_0_2025286 [*** ] 13% > Processing Locus CUFF.604_From_edi_0_2934714 [*** ] 14% > Processing Locus CUFF.615_From_edi_0_2932438 [*** ] 15% > Processing Locus CUFF.617_From_edi_0_2918156 [**** ] 16% > Processing Locus CUFF.619_From_edi_0_2871668 [**** ] 17% > Processing Locus CUFF.621_From_edi_0_2934714 [**** ] 18% > Processing Locus CUFF.621_From_edi_0_2934714 [**** ] 19% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 20% > Processing Locus CUFF.629_From_kn_0_3594465_ [***** ] 21% > Processing Locus CUFF.635_From_ct_1_3241157_ [***** ] 22% > Processing Locus CUFF.637_From_kn_0_3626969_ [***** ] 23% > Processing Locus CUFF.641_From_kn_0_3605300_ [****** ] 24% > Processing Locus CUFF.645_From_edi_0_2888586 [****** ] 25% > Processing Locus CUFF.649_From_kn_0_3617271_ [****** ] 26% > Processing Locus CUFF.655_From_hi_0_2795398_ [****** ] 27% > Processing Locus CUFF.661_From_kn_0_3819922_ [******* ] 28% > Processing Locus CUFF.661_From_kn_0_3819922_ [******* ] 29% > Processing Locus CUFF.663_From_kn_0_3613403_ [******* ] 30% > Processing Locus CUFF.665_From_hi_0_2939638_ [******* ] 31% > Processing Locus CUFF.671_From_edi_0_2859720 [******** ] 32% > Processing Locus CUFF.679_From_ler_0_3998410 [******** ] 33% > Processing Locus CUFF.687_From_mt_0_4230874_ [******** ] 34% > Processing Locus CUFF.689_From_ler_0_4018856 [******** ] 35% > Processing Locus CUFF.693_From_no_0_2934639_ [********* ] 36% > Processing Locus CUFF.695_From_mt_0_4217716_ [********* ] 37% > Processing Locus CUFF.697_From_mt_0_4229662_ [********* ] 38% > Processing Locus CUFF.699_From_no_0_2905273_ [********* ] 39% > Processing Locus CUFF.701_From_no_0_2951521_ [********** ] 40% > Processing Locus CUFF.703_From_no_0_2885444_ [********** ] 41% > Processing Locus CUFF.707_From_no_0_2959683_ [********** ] 42% > Processing Locus CUFF.725_From_no_0_3116640_ [********** ] 43% > Processing Locus CUFF.733_From_no_0_2956652_ [*********** ] 44% > Processing Locus CUFF.737_From_ct_1_3132277_ [*********** ] 45% > Processing Locus CUFF.741_From_po_0_3382155_ [*********** ] 46% > Processing Locus CUFF.747_From_po_0_3299272_ [*********** ] 47% > Processing Locus CUFF.749_From_oy_0_3162092_ [************ ] 48% > Processing Locus CUFF.751_From_rsch_4_403485 [************ ] 49% > Processing Locus CUFF.755_From_mt_0_4193196_ [************ ] 50% > Processing Locus CUFF.757_From_po_0_3372769_ [************ ] 51% > Processing Locus CUFF.759_From_no_0_2936769_ [************* ] 52% > Processing Locus CUFF.763_From_rsch_4_403203 [************* ] 53% > Processing Locus CUFF.765_From_rsch_4_411079 [************* ] 54% > Processing Locus CUFF.767_From_rsch_4_411814 [************* ] 55% > Processing Locus CUFF.769_From_rsch_4_410762 [************** ] 56% > Processing Locus CUFF.771_From_po_0_3332479_ [************** ] 57% > Processing Locus CUFF.775_From_rsch_4_409124 [************** ] 58% > Processing Locus CUFF.777_From_rsch_4_408506 [************** ] 59% > Processing Locus CUFF.779_From_rsch_4_421454 [*************** ] 60% > Processing Locus CUFF.785_From_no_0_3128142_ [*************** ] 61% > Processing Locus CUFF.785_From_no_0_3128142_ [*************** ] 62% > Processing Locus CUFF.789_From_rsch_4_427544 [*************** ] 63% > Processing Locus CUFF.789_From_rsch_4_427544 [**************** ] 64% > Processing Locus CUFF.791_From_rsch_4_425553 [**************** ] 65% > Processing Locus CUFF.795_From_rsch_4_429714 [**************** ] 66% > Processing Locus CUFF.807_From_sf_2_2488391_ [**************** ] 67% > Processing Locus CUFF.811_From_sf_2_2459023_ [***************** ] 68% > Processing Locus CUFF.817_From_sf_2_2524453_ [***************** ] 69% > Processing Locus CUFF.827_From_rsch_4_427728 [***************** ] 70% > Processing Locus CUFF.831_From_sf_2_2687774_ [***************** ] 71% > Processing Locus CUFF.839_From_sf_2_2680171_ [****************** ] 72% > Processing Locus CUFF.839_From_sf_2_2680171_ [****************** ] 73% > Processing Locus CUFF.843_From_rsch_4_429219 [****************** ] 74% > Processing Locus CUFF.861_From_mt_0_4528444_ [****************** ] 75% > Processing Locus CUFF.871_From_rsch_4_426655 [******************* ] 76% > Processing Locus CUFF.873_From_wil_2_3050523 [******************* ] 77% > Processing Locus CUFF.879_From_rsch_4_405516 [******************* ] 78% > Processing Locus CUFF.885_From_wil_2_3063473 [******************* ] 79% > Processing Locus CUFF.887_From_wil_2_3054893 [******************** ] 80% > Processing Locus CUFF.893_From_ws_0_3190679_ [******************** ] 81% > Processing Locus CUFF.913_From_wil_2_2834553 [******************** ] 82% > Processing Locus CUFF.917_From_ws_0_3371988_ [******************** ] 83% > Processing Locus CUFF.925_From_ws_0_3371988_ [********************* ] 84% > Processing Locus CUFF.931_From_wu_0_2679395_ [********************* ] 85% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************* ] 86% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************* ] 87% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************** ] 88% > Processing Locus CUFF.949_From_wu_0_2687576_ [********************** ] 89% > Processing Locus CUFF.951_From_wil_2_3087183 [********************** ] 90% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************** ] 91% > Processing Locus CUFF.957_From_ws_0_3381390_ [*********************** ] 92% > Processing Locus CUFF.965_From_zu_0_3238769_ [*********************** ] 93% > Processing Locus CUFF.967_From_zu_0_3022629_ [*********************** ] 94% > Processing Locus CUFF.973_From_zu_0_3242889_ [*********************** ] 95% > Processing Locus CUFF.977_From_zu_0_3255503_ [************************ ] 96% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 97% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 98% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 99%file: /data/arabidopsis/xiang/magic_founder/Wil_2_R1/R38_L7_Wil_2_sdlg_R1_nss_barcode_TGC.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Wil_2_R2/R38_L8_Wil_2_sdlg_R2_nss_barcode_TGC.unmap_1.fq > Processed 100 loci. [*************************] 100% [16:25:32] Loading reference annotation and sequence [16:25:32] Learning bias parameters. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 2% > Processing Locus CUFF.573_From_can_0_3233581 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 5% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 6% > Processing Locus CUFF.601_From_edi_0_2934714 [* ] 7% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 8% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 9% > Processing Locus CUFF.604_From_edi_0_2934714 [** ] 10% > Processing Locus CUFF.615_From_edi_0_2932438 [** ] 11% > Processing Locus CUFF.617_From_edi_0_2918156 [*** ] 12% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 13% > Processing Locus CUFF.621_From_edi_0_2934714 [*** ] 14% > Processing Locus CUFF.635_From_ct_1_3241157_ [*** ] 15% > Processing Locus CUFF.645_From_edi_0_2888586 [**** ] 16% > Processing Locus CUFF.649_From_kn_0_3617271_ [**** ] 17% > Processing Locus CUFF.655_From_hi_0_2795398_ [**** ] 18% > Processing Locus CUFF.661_From_kn_0_3819922_ [**** ] 19% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 20% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 21% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 22% > Processing Locus CUFF.679_From_ler_0_3998410 [***** ] 23% > Processing Locus CUFF.687_From_mt_0_4230874_ [****** ] 24% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 25% > Processing Locus CUFF.693_From_no_0_2934639_ [****** ] 26% > Processing Locus CUFF.695_From_mt_0_4217716_ [****** ] 27% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 28% > Processing Locus CUFF.699_From_no_0_2905273_ [******* ] 29% > Processing Locus CUFF.703_From_no_0_2885444_ [******* ] 30% > Processing Locus CUFF.707_From_no_0_2959683_ [******* ] 31% > Processing Locus CUFF.725_From_no_0_3116640_ [******** ] 32% > Processing Locus CUFF.733_From_no_0_2956652_ [******** ] 33% > Processing Locus CUFF.737_From_ct_1_3132277_ [******** ] 34% > Processing Locus CUFF.747_From_po_0_3299272_ [******** ] 35% > Processing Locus CUFF.749_From_oy_0_3162092_ [********* ] 36% > Processing Locus CUFF.751_From_rsch_4_403485 [********* ] 37% > Processing Locus CUFF.755_From_mt_0_4193196_ [********* ] 38% > Processing Locus CUFF.757_From_po_0_3372769_ [********* ] 39% > Processing Locus CUFF.759_From_no_0_2936769_ [********** ] 40% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 41% > Processing Locus CUFF.765_From_rsch_4_411079 [********** ] 42% > Processing Locus CUFF.769_From_rsch_4_410762 [********** ] 43% > Processing Locus CUFF.771_From_po_0_3332479_ [*********** ] 44% > Processing Locus CUFF.777_From_rsch_4_408506 [*********** ] 45% > Processing Locus CUFF.779_From_rsch_4_421454 [*********** ] 46% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 47% > Processing Locus CUFF.785_From_no_0_3128142_ [************ ] 48% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 49% > Processing Locus CUFF.795_From_rsch_4_429714 [************ ] 50% > Processing Locus CUFF.807_From_sf_2_2488391_ [************ ] 51% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 52% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 53% > Processing Locus CUFF.827_From_rsch_4_427728 [************* ] 54% > Processing Locus CUFF.839_From_sf_2_2680171_ [************* ] 55% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 56% > Processing Locus CUFF.861_From_mt_0_4528444_ [************** ] 57% > Processing Locus CUFF.871_From_rsch_4_426655 [************** ] 58% > Processing Locus CUFF.879_From_rsch_4_405516 [************** ] 59% > Processing Locus CUFF.887_From_wil_2_3054893 [*************** ] 60% > Processing Locus CUFF.931_From_wu_0_2679395_ [*************** ] 61% > Processing Locus CUFF.935_From_ws_0_3380934_ [*************** ] 62% > Processing Locus CUFF.947_From_wu_0_2654219_ [*************** ] 63% > Processing Locus CUFF.949_From_wu_0_2687576_ [**************** ] 64% > Processing Locus CUFF.955_From_ws_0_3340488_ [**************** ] 65% > Processing Locus CUFF.957_From_ws_0_3381390_ [**************** ] 66% > Processing Locus CUFF.973_From_zu_0_3242889_ [**************** ] 67% > Processing Locus CUFF.977_From_zu_0_3255503_ [***************** ] 68% > Processing Locus CUFF.987_From_zu_0_3118546_ [***************** ] 69% > Processing Locus CUFF.991_From_zu_0_3277661_ [***************** ] 70% > Processing Locus CUFF.993_From_zu_0_3082201_ [***************** ] 71% > Processed 72 loci. [*************************] 100% [16:25:32] Assembling transcripts and estimating abundances. > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 2% > Processing Locus CUFF.573_From_can_0_3233581 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 5% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 6% > Processing Locus CUFF.601_From_edi_0_2934714 [* ] 7% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 8% > Processing Locus CUFF.603_From_bur_0_2025286 [** ] 9% > Processing Locus CUFF.604_From_edi_0_2934714 [** ] 10% > Processing Locus CUFF.615_From_edi_0_2932438 [** ] 11% > Processing Locus CUFF.617_From_edi_0_2918156 [*** ] 12% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 13% > Processing Locus CUFF.621_From_edi_0_2934714 [*** ] 14% > Processing Locus CUFF.635_From_ct_1_3241157_ [*** ] 15% > Processing Locus CUFF.645_From_edi_0_2888586 [**** ] 16% > Processing Locus CUFF.649_From_kn_0_3617271_ [**** ] 17% > Processing Locus CUFF.655_From_hi_0_2795398_ [**** ] 18% > Processing Locus CUFF.661_From_kn_0_3819922_ [**** ] 19% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 20% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 21% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 22% > Processing Locus CUFF.679_From_ler_0_3998410 [***** ] 23% > Processing Locus CUFF.687_From_mt_0_4230874_ [****** ] 24% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 25% > Processing Locus CUFF.693_From_no_0_2934639_ [****** ] 26% > Processing Locus CUFF.695_From_mt_0_4217716_ [****** ] 27% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 28% > Processing Locus CUFF.699_From_no_0_2905273_ [******* ] 29% > Processing Locus CUFF.703_From_no_0_2885444_ [******* ] 30% > Processing Locus CUFF.707_From_no_0_2959683_ [******* ] 31% > Processing Locus CUFF.725_From_no_0_3116640_ [******** ] 32% > Processing Locus CUFF.733_From_no_0_2956652_ [******** ] 33% > Processing Locus CUFF.737_From_ct_1_3132277_ [******** ] 34% > Processing Locus CUFF.747_From_po_0_3299272_ [******** ] 35% > Processing Locus CUFF.749_From_oy_0_3162092_ [********* ] 36% > Processing Locus CUFF.751_From_rsch_4_403485 [********* ] 37% > Processing Locus CUFF.755_From_mt_0_4193196_ [********* ] 38% > Processing Locus CUFF.757_From_po_0_3372769_ [********* ] 39% > Processing Locus CUFF.759_From_no_0_2936769_ [********** ] 40% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 41% > Processing Locus CUFF.765_From_rsch_4_411079 [********** ] 42% > Processing Locus CUFF.769_From_rsch_4_410762 [********** ] 43% > Processing Locus CUFF.771_From_po_0_3332479_ [*********** ] 44% > Processing Locus CUFF.777_From_rsch_4_408506 [*********** ] 45% > Processing Locus CUFF.779_From_rsch_4_421454 [*********** ] 46% > Processing Locus CUFF.785_From_no_0_3128142_ [*********** ] 47% > Processing Locus CUFF.785_From_no_0_3128142_ [************ ] 48% > Processing Locus CUFF.791_From_rsch_4_425553 [************ ] 49% > Processing Locus CUFF.795_From_rsch_4_429714 [************ ] 50% > Processing Locus CUFF.807_From_sf_2_2488391_ [************ ] 51% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 52% > Processing Locus CUFF.817_From_sf_2_2524453_ [************* ] 53% > Processing Locus CUFF.827_From_rsch_4_427728 [************* ] 54% > Processing Locus CUFF.839_From_sf_2_2680171_ [************* ] 55% > Processing Locus CUFF.843_From_rsch_4_429219 [************** ] 56% > Processing Locus CUFF.861_From_mt_0_4528444_ [************** ] 57% > Processing Locus CUFF.871_From_rsch_4_426655 [************** ] 58% > Processing Locus CUFF.879_From_rsch_4_405516 [************** ] 59% > Processing Locus CUFF.887_From_wil_2_3054893 [*************** ] 60% > Processing Locus CUFF.931_From_wu_0_2679395_ [*************** ] 61% > Processing Locus CUFF.935_From_ws_0_3380934_ [*************** ] 62% > Processing Locus CUFF.947_From_wu_0_2654219_ [*************** ] 63% > Processing Locus CUFF.949_From_wu_0_2687576_ [**************** ] 64% > Processing Locus CUFF.955_From_ws_0_3340488_ [**************** ] 65% > Processing Locus CUFF.957_From_ws_0_3381390_ [**************** ] 66% > Processing Locus CUFF.973_From_zu_0_3242889_ [**************** ] 67% > Processing Locus CUFF.977_From_zu_0_3255503_ [***************** ] 68% > Processing Locus CUFF.987_From_zu_0_3118546_ [***************** ] 69% > Processing Locus CUFF.991_From_zu_0_3277661_ [***************** ] 70% > Processing Locus CUFF.993_From_zu_0_3082201_ [***************** ] 71% > Processed 72 loci. [*************************] 100% file: /data/arabidopsis/xiang/magic_founder/Ws_0_R1/R39_L5_Ws_0_sdlg_R1_nss_barcode_ACG.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Ws_0_R2/R39_L6_Ws_0_sdlg_R2_nss_barcode_ACG.unmap_1.fq $RNAGI/rnagi.sh -o ./Sf_2 -n ngene.fa Sf_2.Tongene.merge.fq reference: ngene.fa $RNAGI/rnagi.sh -o ./Tsu_0 -n ngene.fa Tsu_0.Tongene.merge.fq reference: ngene.fa $RNAGI/rnagi.sh -o ./Ws_0 -n ngene.fa Ws_0.Tongene.merge.fq reference: ngene.fa $RNAGI/rnagi.sh -o ./Wil_2 -n ngene.fa Wil_2.Tongene.merge.fq reference: ngene.fa tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Ws_0 ngene.fa ./Ws_0/Ws_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:25:44 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:25:44 2011] Preparing output location ./Ws_0// [Mon Apr 4 16:25:44 2011] Checking for Bowtie index files [Mon Apr 4 16:25:44 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:25:44 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:25:44 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:25:44 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:25:44 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Wil_2 ngene.fa ./Wil_2/Wil_2.Tongene.merge.flt_1.fq [Mon Apr 4 16:25:48 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:25:48 2011] Preparing output location ./Wil_2// [Mon Apr 4 16:25:48 2011] Checking for Bowtie index files [Mon Apr 4 16:25:48 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:25:48 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:25:48 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:25:48 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:25:49 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Tsu_0 ngene.fa ./Tsu_0/Tsu_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:25:55 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:25:55 2011] Preparing output location ./Tsu_0// [Mon Apr 4 16:25:55 2011] Checking for Bowtie index files [Mon Apr 4 16:25:55 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:25:55 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:25:55 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:25:55 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:25:55 2011] Checking reads min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Sf_2 ngene.fa ./Sf_2/Sf_2.Tongene.merge.flt_1.fq [Mon Apr 4 16:25:57 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:25:57 2011] Preparing output location ./Sf_2// [Mon Apr 4 16:25:57 2011] Checking for Bowtie index files [Mon Apr 4 16:25:57 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:25:57 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:25:57 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:25:57 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:25:58 2011] Checking reads [Mon Apr 4 16:25:58 2011] Mapping reads against ngene.fa with Bowtie file: /data/arabidopsis/xiang/magic_founder/Wu_0_R1/R39_L5_Wu_0_sdlg_R1_nss_barcode_CAT.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Wu_0_R2/R39_L6_Wu_0_sdlg_R2_nss_barcode_CAT.unmap_1.fq $RNAGI/rnagi.sh -o ./Wu_0 -n ngene.fa Wu_0.Tongene.merge.fq reference: ngene.fa [Mon Apr 4 16:26:04 2011] Joining segment hits min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:26:12 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:26:13 2011] Mapping reads against ngene.fa with Bowtie(1/3) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:26:16 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:26:17 2011] Joining segment hits [Mon Apr 4 16:26:17 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:26:17 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:26:20 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:26:24 2011] Joining segment hits [Mon Apr 4 16:26:25 2011] Joining segment hits [Mon Apr 4 16:26:25 2011] Searching for junctions via segment mapping tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Wu_0 ngene.fa ./Wu_0/Wu_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:26:27 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:26:27 2011] Preparing output location ./Wu_0// [Mon Apr 4 16:26:27 2011] Checking for Bowtie index files [Mon Apr 4 16:26:27 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:26:27 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:26:27 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:26:27 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:26:27 2011] Checking reads [Mon Apr 4 16:26:40 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:26:41 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:26:41 2011] Retrieving sequences for splices [Mon Apr 4 16:26:41 2011] Indexing splices [Mon Apr 4 16:26:41 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:26:42 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:26:43 2011] Mapping reads against segment_juncs with Bowtie min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:26:46 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:26:46 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:26:46 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:26:47 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:26:48 2011] Joining segment hits [Mon Apr 4 16:26:49 2011] Reporting output tracks [Mon Apr 4 16:26:50 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:26:51 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:26:51 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:26:52 2011] Mapping reads against ngene.fa with Bowtie(3/3) ----------------------------------------------- Run complete [00:01:08 elapsed] [Mon Apr 4 16:26:57 2011] Searching for junctions via segment mapping [Mon Apr 4 16:26:58 2011] Searching for junctions via segment mapping [Mon Apr 4 16:26:58 2011] Searching for junctions via segment mapping [Mon Apr 4 16:26:58 2011] Joining segment hits cufflinks -p 4 -o ./Ws_0 -r ngene.fa ./Ws_0/accepted_hits.bam [16:27:00] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399Å{ [ ] > Processing Locus CUFF.525_From_bur_0_1863298Å{ [ ] > Processing Locus CUFF.529_From_bur_0_1873494Å{ [ ] > Processing Locus CUFF.545_From_bur_0_1856286Å{ [ ] > Processing Locus CUFF.551_From_can_0_3122480Å{ [ ] > Processing Locus CUFF.561_From_can_0_3189753Å{ [ ] > Processing Locus CUFF.571_From_can_0_3076940Å{ [ ] > Processing Locus CUFF.575_From_ct_1_3082021_Å{ [ ] > Processing Locus CUFF.577_From_ct_1_3125173_Å{ [ ] > Processing Locus CUFF.579_From_ct_1_3133451_Å{ [ ] > Processing Locus CUFF.583_From_ct_1_3302721_Å{ [* ] > Processing Locus CUFF.585_From_ct_1_3247037_Å{ [* ] > Processing Locus CUFF.589_From_edi_0_2723255Å{ [* ] > Processing Locus CUFF.593_From_can_0_3270131Å{ [* ] > Processing Locus CUFF.593_From_can_0_3270131Å{ [* ] > Processing Locus CUFF.593_From_can_0_3270131Å{ [* ] > Processing Locus CUFF.595_From_ct_1_3302721_Å{ [* ] > Processing Locus CUFF.609_From_hi_0_2755116_Å{ [* ] > Processing Locus CUFF.619_From_edi_0_2871668Å{ [* ] > Processing Locus CUFF.619_From_edi_0_2871668Å{ [* ] > Processing Locus CUFF.623_From_hi_0_2778596_Å{ [* ] > Processing Locus CUFF.625_From_hi_0_2964064_Å{ [* ] > Processing Locus CUFF.625_From_hi_0_2964064_Å{ [* ] > Processing Locus CUFF.629_From_kn_0_3594465_Å{ [** ] > Processing Locus CUFF.649_From_kn_0_3617271_Å{ [** ] > Processing Locus CUFF.651_From_ler_0_3967940Å{ [** ] > Processing Locus CUFF.657_From_ler_0_3998132Å{ [** ] > Processing Locus CUFF.663_From_kn_0_3613403_Å{ [** ] > Processing Locus CUFF.665_From_hi_0_2939638_Å{ [** ] > Processing Locus CUFF.673_From_ler_0_4224097Å{ [** ] > Processing Locus CUFF.679_From_ler_0_3998410Å{ [** ] > Processing Locus CUFF.683_From_ler_0_4165287Å{ [** ] > Processing Locus CUFF.685_From_mt_0_4231054_Å{ [** ] > Processing Locus CUFF.687_From_mt_0_4230874_Å{ [*** ] > Processing Locus CUFF.689_From_ler_0_4018856Å{ [*** ] > Processing Locus CUFF.691_From_hi_0_2961678_Å{ [*** ] > Processing Locus CUFF.695_From_mt_0_4217716_Å{ [*** ] > Processing Locus CUFF.697_From_mt_0_4229662_Å{ [*** ] > Processing Locus CUFF.699_From_no_0_2905273_Å{ [*** ] > Processing Locus CUFF.703_From_no_0_2885444_Å{ [*** ] > Processing Locus CUFF.705_From_no_0_3113578_Å{ [*** ] > Processing Locus CUFF.725_From_no_0_3116640_Å{ [*** ] > Processing Locus CUFF.729_From_oy_0_3001818_Å{ [**** ] > Processing Locus CUFF.731_From_po_0_3324652_Å{ [**** ] > Processing Locus CUFF.733_From_no_0_2956652_Å{ [**** ] > Processing Locus CUFF.737_From_ct_1_3132277_Å{ [**** ] > Processing Locus CUFF.741_From_po_0_3382155_Å{ [**** ] > Processing Locus CUFF.751_From_rsch_4_403485Å{ [**** ] > Processing Locus CUFF.755_From_mt_0_4193196_Å{ [**** ] > Processing Locus CUFF.763_From_rsch_4_403203Å{ [**** ] > Processing Locus CUFF.785_From_no_0_3128142_Å{ [**** ] > Processing Locus CUFF.785_From_no_0_3128142_Å{ [**** ] > Processing Locus CUFF.785_From_no_0_3128142_Å{ [**** ] > Processing Locus CUFF.789_From_rsch_4_427544Å{ [**** ] > Processing Locus CUFF.811_From_sf_2_2459023_Å{ [***** ] > Processing Locus CUFF.817_From_sf_2_2524453_Å{ [***** ] > Processing Locus CUFF.829_From_tsu_0_3135135Å{ [***** ] > Processing Locus CUFF.861_From_mt_0_4528444_Å{ [***** ] > Processing Locus CUFF.861_From_mt_0_4528444_Å{ [***** ] > Processing Locus CUFF.867_From_wil_2_2945095Å{ [***** ] > Processing Locus CUFF.879_From_rsch_4_405516Å{ [***** ] > Processing Locus CUFF.881_From_wil_2_2925323Å{ [***** ] > Processing Locus CUFF.887_From_wil_2_3054893Å{ [***** ] > Processing Locus CUFF.889_From_ws_0_3181530_Å{ [***** ] > Processing Locus CUFF.891_From_wil_2_3079625Å{ [****** ] > Processing Locus CUFF.901_From_wil_2_3088151Å{ [****** ] > Processing Locus CUFF.901_From_wil_2_3088151Å{ [****** ] > Processing Locus CUFF.905_From_ws_0_3339092_Å{ [****** ] > Processing Locus CUFF.907_From_ws_0_3182508_Å{ [****** ] > Processing Locus CUFF.913_From_wil_2_2834553Å{ [****** ] > Processing Locus CUFF.915_From_ws_0_3349444_Å{ [****** ] > Processing Locus CUFF.917_From_ws_0_3371988_Å{ [****** ] > Processing Locus CUFF.917_From_ws_0_3371988_Å{ [****** ] > Processing Locus CUFF.919_From_ws_0_3347582_Å{ [****** ] > Processing Locus CUFF.919_From_ws_0_3347582_Å{ [****** ] > Processing Locus CUFF.919_From_ws_0_3347582_Å{ [****** ] > Processing Locus CUFF.919_From_ws_0_3347582_Å{ [****** ] > Processing Locus CUFF.921_From_wil_2_3077447Å{ [****** ] > Processing Locus CUFF.923_From_ws_0_3382728_Å{ [****** ] > Processing Locus CUFF.925_From_ws_0_3371988_Å{ [******* ] > Processing Locus CUFF.929_From_ws_0_3382728_Å{ [******* ] > Processing Locus CUFF.931_From_wu_0_2679395_Å{ [******* ] > Processing Locus CUFF.935_From_ws_0_3380934_Å{ [******* ] > Processing Locus CUFF.937_From_ws_0_3373604_Å{ [******* ] > Processing Locus CUFF.945_From_wu_0_2678387_Å{ [******* ] > Processing Locus CUFF.947_From_wu_0_2654219_Å{ [******* ] > Processing Locus CUFF.949_From_wu_0_2687576_Å{ [******* ] > Processing Locus CUFF.953_From_ws_0_3382500_Å{ [******* ] > Processing Locus CUFF.955_From_ws_0_3340488_Å{ [******** ] > Processing Locus CUFF.957_From_ws_0_3381390_Å{ [******** ] > Processing Locus CUFF.959_From_ws_0_3344070_Å{ [******** ] > Processing Locus CUFF.983_From_zu_0_3243571_Å{ [******** ] > Processing Locus CUFF.987_From_zu_0_3118546_Å{ [******** ] > Processing Locus CUFF.993_From_zu_0_3082201_Å{ [******** ] > Processed 94 loci. [*************************] 100% > Map Properties: > Total Map Mass: 3892.00 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:27:00] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.525_From_bur_0_1863298 [ ] 1% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 2% > Processing Locus CUFF.545_From_bur_0_1856286 [ ] 3% > Processing Locus CUFF.551_From_can_0_3122480 [* ] 4% > Processing Locus CUFF.561_From_can_0_3189753 [* ] 5% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 6% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 7% > Processing Locus CUFF.577_From_ct_1_3125173_ [** ] 8% > Processing Locus CUFF.579_From_ct_1_3133451_ [** ] 9% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 10% > Processing Locus CUFF.585_From_ct_1_3247037_ [** ] 11% > Processing Locus CUFF.589_From_edi_0_2723255 [*** ] 12% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 13% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 14% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 15% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 17% > Processing Locus CUFF.609_From_hi_0_2755116_ [**** ] 18% > Processing Locus CUFF.619_From_edi_0_2871668 [**** ] 19% > Processing Locus CUFF.619_From_edi_0_2871668 [***** ] 20% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 21% > Processing Locus CUFF.625_From_hi_0_2964064_ [***** ] 22% > Processing Locus CUFF.625_From_hi_0_2964064_ [***** ] 23% > Processing Locus CUFF.629_From_kn_0_3594465_ [****** ] 24% > Processing Locus CUFF.649_From_kn_0_3617271_ [****** ] 25% > Processing Locus CUFF.651_From_ler_0_3967940 [****** ] 26% > Processing Locus CUFF.657_From_ler_0_3998132 [****** ] 27% > Processing Locus CUFF.663_From_kn_0_3613403_ [******* ] 28% > Processing Locus CUFF.665_From_hi_0_2939638_ [******* ] 29% > Processing Locus CUFF.673_From_ler_0_4224097 [******* ] 30% > Processing Locus CUFF.679_From_ler_0_3998410 [******* ] 31% > Processing Locus CUFF.683_From_ler_0_4165287 [******** ] 32% > Processing Locus CUFF.685_From_mt_0_4231054_ [******** ] 34% > Processing Locus CUFF.687_From_mt_0_4230874_ [******** ] 35% > Processing Locus CUFF.689_From_ler_0_4018856 [********* ] 36% > Processing Locus CUFF.691_From_hi_0_2961678_ [********* ] 37% > Processing Locus CUFF.695_From_mt_0_4217716_ [********* ] 38% > Processing Locus CUFF.697_From_mt_0_4229662_ [********* ] 39% > Processing Locus CUFF.699_From_no_0_2905273_ [********** ] 40% > Processing Locus CUFF.703_From_no_0_2885444_ [********** ] 41% > Processing Locus CUFF.705_From_no_0_3113578_ [********** ] 42% > Processing Locus CUFF.725_From_no_0_3116640_ [********** ] 43% > Processing Locus CUFF.729_From_oy_0_3001818_ [*********** ] 44% > Processing Locus CUFF.731_From_po_0_3324652_ [*********** ] 45% > Processing Locus CUFF.733_From_no_0_2956652_ [*********** ] 46% > Processing Locus CUFF.737_From_ct_1_3132277_ [*********** ] 47% > Processing Locus CUFF.741_From_po_0_3382155_ [************ ] 48% > Processing Locus CUFF.751_From_rsch_4_403485 [************ ] 50% > Processing Locus CUFF.755_From_mt_0_4193196_ [************ ] 51% > Processing Locus CUFF.763_From_rsch_4_403203 [************* ] 52% > Processing Locus CUFF.785_From_no_0_3128142_ [************* ] 53% > Processing Locus CUFF.785_From_no_0_3128142_ [************* ] 54% > Processing Locus CUFF.785_From_no_0_3128142_ [************* ] 55% > Processing Locus CUFF.789_From_rsch_4_427544 [************** ] 56% > Processing Locus CUFF.811_From_sf_2_2459023_ [************** ] 57% > Processing Locus CUFF.817_From_sf_2_2524453_ [************** ] 58% > Processing Locus CUFF.829_From_tsu_0_3135135 [************** ] 59% > Processing Locus CUFF.861_From_mt_0_4528444_ [*************** ] 60% > Processing Locus CUFF.861_From_mt_0_4528444_ [*************** ] 61% > Processing Locus CUFF.867_From_wil_2_2945095 [*************** ] 62% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 63% > Processing Locus CUFF.881_From_wil_2_2925323 [**************** ] 64% > Processing Locus CUFF.887_From_wil_2_3054893 [**************** ] 65% > Processing Locus CUFF.889_From_ws_0_3181530_ [**************** ] 67% > Processing Locus CUFF.891_From_wil_2_3079625 [***************** ] 68% > Processing Locus CUFF.901_From_wil_2_3088151 [***************** ] 69% > Processing Locus CUFF.901_From_wil_2_3088151 [***************** ] 70% > Processing Locus CUFF.905_From_ws_0_3339092_ [***************** ] 71% > Processing Locus CUFF.907_From_ws_0_3182508_ [****************** ] 72% > Processing Locus CUFF.913_From_wil_2_2834553 [****************** ] 73% > Processing Locus CUFF.915_From_ws_0_3349444_ [****************** ] 74% > Processing Locus CUFF.917_From_ws_0_3371988_ [****************** ] 75% > Processing Locus CUFF.917_From_ws_0_3371988_ [******************* ] 76% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 77% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 78% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 79% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 80% > Processing Locus CUFF.921_From_wil_2_3077447 [******************** ] 81% > Processing Locus CUFF.923_From_ws_0_3382728_ [******************** ] 82% > Processing Locus CUFF.925_From_ws_0_3371988_ [********************* ] 84% > Processing Locus CUFF.929_From_ws_0_3382728_ [********************* ] 85% > Processing Locus CUFF.931_From_wu_0_2679395_ [********************* ] 86% > Processing Locus CUFF.935_From_ws_0_3380934_ [********************* ] 87% > Processing Locus CUFF.937_From_ws_0_3373604_ [********************** ] 88% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************** ] 89% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************** ] 90% > Processing Locus CUFF.949_From_wu_0_2687576_ [********************** ] 91% > Processing Locus CUFF.953_From_ws_0_3382500_ [*********************** ] 92% > Processing Locus CUFF.955_From_ws_0_3340488_ [*********************** ] 93% > Processing Locus CUFF.957_From_ws_0_3381390_ [*********************** ] 94% > Processing Locus CUFF.959_From_ws_0_3344070_ [*********************** ] 95% > Processing Locus CUFF.983_From_zu_0_3243571_ [************************ ] 96% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 97% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 98% > Processed 94 loci. [*************************] 100% [16:27:00] Loading reference annotation and sequence [16:27:00] Learning bias parameters. > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 0% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 5% > Processing Locus CUFF.589_From_edi_0_2723255 [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 7% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 8% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 10% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 11% > Processing Locus CUFF.651_From_ler_0_3967940 [*** ] 12% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 13% > Processing Locus CUFF.665_From_hi_0_2939638_ [*** ] 14% > Processing Locus CUFF.673_From_ler_0_4224097 [*** ] 15% > Processing Locus CUFF.679_From_ler_0_3998410 [**** ] 17% > Processing Locus CUFF.683_From_ler_0_4165287 [**** ] 18% > Processing Locus CUFF.687_From_mt_0_4230874_ [**** ] 19% > Processing Locus CUFF.689_From_ler_0_4018856 [***** ] 20% > Processing Locus CUFF.691_From_hi_0_2961678_ [***** ] 21% > Processing Locus CUFF.695_From_mt_0_4217716_ [***** ] 22% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 23% > Processing Locus CUFF.699_From_no_0_2905273_ [****** ] 24% > Processing Locus CUFF.705_From_no_0_3113578_ [****** ] 25% > Processing Locus CUFF.725_From_no_0_3116640_ [****** ] 26% > Processing Locus CUFF.729_From_oy_0_3001818_ [****** ] 27% > Processing Locus CUFF.731_From_po_0_3324652_ [******* ] 28% > Processing Locus CUFF.733_From_no_0_2956652_ [******* ] 29% > Processing Locus CUFF.737_From_ct_1_3132277_ [******* ] 30% > Processing Locus CUFF.741_From_po_0_3382155_ [******* ] 31% > Processing Locus CUFF.755_From_mt_0_4193196_ [******** ] 32% > Processing Locus CUFF.763_From_rsch_4_403203 [******** ] 34% > Processing Locus CUFF.785_From_no_0_3128142_ [******** ] 35% > Processing Locus CUFF.785_From_no_0_3128142_ [********* ] 36% > Processing Locus CUFF.789_From_rsch_4_427544 [********* ] 37% > Processing Locus CUFF.811_From_sf_2_2459023_ [********* ] 38% > Processing Locus CUFF.817_From_sf_2_2524453_ [********* ] 39% > Processing Locus CUFF.879_From_rsch_4_405516 [********** ] 40% > Processing Locus CUFF.881_From_wil_2_2925323 [********** ] 41% > Processing Locus CUFF.887_From_wil_2_3054893 [********** ] 42% > Processing Locus CUFF.889_From_ws_0_3181530_ [********** ] 43% > Processing Locus CUFF.891_From_wil_2_3079625 [*********** ] 44% > Processing Locus CUFF.901_From_wil_2_3088151 [*********** ] 45% > Processing Locus CUFF.901_From_wil_2_3088151 [*********** ] 46% > Processing Locus CUFF.905_From_ws_0_3339092_ [*********** ] 47% > Processing Locus CUFF.915_From_ws_0_3349444_ [************ ] 48% > Processing Locus CUFF.923_From_ws_0_3382728_ [************ ] 50% > Processing Locus CUFF.925_From_ws_0_3371988_ [************ ] 51% > Processing Locus CUFF.929_From_ws_0_3382728_ [************* ] 52% > Processing Locus CUFF.935_From_ws_0_3380934_ [************* ] 53% > Processing Locus CUFF.937_From_ws_0_3373604_ [************* ] 54% > Processing Locus CUFF.953_From_ws_0_3382500_ [************* ] 55% > Processing Locus CUFF.957_From_ws_0_3381390_ [************** ] 56% > Processing Locus CUFF.959_From_ws_0_3344070_ [************** ] 57% > Processing Locus CUFF.987_From_zu_0_3118546_ [************** ] 58% > Processed 56 loci. [*************************] 100% [16:27:00] Assembling transcripts and estimating abundances. > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 0% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.579_From_ct_1_3133451_ [* ] 5% > Processing Locus CUFF.589_From_edi_0_2723255 [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 7% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 8% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 10% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 11% > Processing Locus CUFF.651_From_ler_0_3967940 [*** ] 12% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 13% > Processing Locus CUFF.665_From_hi_0_2939638_ [*** ] 14% > Processing Locus CUFF.673_From_ler_0_4224097 [*** ] 15% > Processing Locus CUFF.679_From_ler_0_3998410 [**** ] 17% > Processing Locus CUFF.683_From_ler_0_4165287 [**** ] 18% > Processing Locus CUFF.687_From_mt_0_4230874_ [**** ] 19% > Processing Locus CUFF.689_From_ler_0_4018856 [***** ] 20% > Processing Locus CUFF.691_From_hi_0_2961678_ [***** ] 21% > Processing Locus CUFF.695_From_mt_0_4217716_ [***** ] 22% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 23% > Processing Locus CUFF.699_From_no_0_2905273_ [****** ] 24% > Processing Locus CUFF.705_From_no_0_3113578_ [****** ] 25% > Processing Locus CUFF.725_From_no_0_3116640_ [****** ] 26% > Processing Locus CUFF.729_From_oy_0_3001818_ [****** ] 27% > Processing Locus CUFF.731_From_po_0_3324652_ [******* ] 28% > Processing Locus CUFF.733_From_no_0_2956652_ [******* ] 29% > Processing Locus CUFF.737_From_ct_1_3132277_ [******* ] 30% > Processing Locus CUFF.741_From_po_0_3382155_ [******* ] 31% > Processing Locus CUFF.755_From_mt_0_4193196_ [******** ] 32% > Processing Locus CUFF.763_From_rsch_4_403203 [******** ] 34% > Processing Locus CUFF.785_From_no_0_3128142_ [******** ] 35% > Processing Locus CUFF.785_From_no_0_3128142_ [********* ] 36% > Processing Locus CUFF.789_From_rsch_4_427544 [********* ] 37% > Processing Locus CUFF.811_From_sf_2_2459023_ [********* ] 38% > Processing Locus CUFF.817_From_sf_2_2524453_ [********* ] 39% > Processing Locus CUFF.879_From_rsch_4_405516 [********** ] 40% > Processing Locus CUFF.881_From_wil_2_2925323 [********** ] 41% > Processing Locus CUFF.887_From_wil_2_3054893 [********** ] 42% > Processing Locus CUFF.889_From_ws_0_3181530_ [********** ] 43% > Processing Locus CUFF.891_From_wil_2_3079625 [*********** ] 44% > Processing Locus CUFF.901_From_wil_2_3088151 [*********** ] 45% > Processing Locus CUFF.901_From_wil_2_3088151 [*********** ] 46% > Processing Locus CUFF.905_From_ws_0_3339092_ [*********** ] 47% > Processing Locus CUFF.915_From_ws_0_3349444_ [************ ] 48% > Processing Locus CUFF.923_From_ws_0_3382728_ [************ ] 50% > Processing Locus CUFF.925_From_ws_0_3371988_ [************ ] 51% > Processing Locus CUFF.929_From_ws_0_3382728_ [************* ] 52% > Processing Locus CUFF.935_From_ws_0_3380934_ [************* ] 53% > Processing Locus CUFF.937_From_ws_0_3373604_ [************* ] 54% > Processing Locus CUFF.953_From_ws_0_3382500_ [************* ] 55% > Processing Locus CUFF.957_From_ws_0_3381390_ [************** ] 56% > Processing Locus CUFF.959_From_ws_0_3344070_ [************** ] 57% > Processing Locus CUFF.987_From_zu_0_3118546_ [************** ] 58% > Processed 56 loci. [*************************] 100% [Mon Apr 4 16:27:15 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:27:18 2011] Retrieving sequences for splices [Mon Apr 4 16:27:18 2011] Indexing splices [Mon Apr 4 16:27:18 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:18 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:27:19 2011] Retrieving sequences for splices [Mon Apr 4 16:27:19 2011] Indexing splices [Mon Apr 4 16:27:19 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:20 2011] Retrieving sequences for splices [Mon Apr 4 16:27:20 2011] Indexing splices [Mon Apr 4 16:27:20 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:21 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:22 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:22 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:23 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:23 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:27:25 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:25 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:25 2011] Joining segment hits [Mon Apr 4 16:27:27 2011] Joining segment hits [Mon Apr 4 16:27:27 2011] Reporting output tracks [Mon Apr 4 16:27:27 2011] Joining segment hits [Mon Apr 4 16:27:27 2011] Searching for junctions via segment mapping [Mon Apr 4 16:27:28 2011] Reporting output tracks [Mon Apr 4 16:27:28 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:33 elapsed] ----------------------------------------------- Run complete [00:01:32 elapsed] ----------------------------------------------- Run complete [00:01:41 elapsed] cufflinks -p 4 -o ./Tsu_0 -r ngene.fa ./Tsu_0/accepted_hits.bam [16:27:33] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_1804399âÝ [ ] > Processing Locus CUFF.529_From_bur_0_1873494âÝ [ ] > Processing Locus CUFF.533_From_bur_0_2020452âÝ [ ] > Processing Locus CUFF.533_From_bur_0_2020452âÝ [ ] > Processing Locus CUFF.545_From_bur_0_1856286âÝ [ ] > Processing Locus CUFF.563_From_bur_0_2020452âÝ [ ] > Processing Locus CUFF.563_From_bur_0_2020452âÝ [ ] > Processing Locus CUFF.571_From_can_0_3076940âÝ [ ] > Processing Locus CUFF.575_From_ct_1_3082021_âÝ [ ] > Processing Locus CUFF.583_From_ct_1_3302721_âÝ [ ] > Processing Locus CUFF.585_From_ct_1_3247037_âÝ [ ] > Processing Locus CUFF.593_From_can_0_3270131âÝ [ ] > Processing Locus CUFF.593_From_can_0_3270131âÝ [ ] > Processing Locus CUFF.593_From_can_0_3270131âÝ [ ] > Processing Locus CUFF.595_From_ct_1_3302721_âÝ [* ] > Processing Locus CUFF.607_From_edi_0_2891226âÝ [* ] > Processing Locus CUFF.615_From_edi_0_2932438âÝ [* ] > Processing Locus CUFF.617_From_edi_0_2918156âÝ [* ] > Processing Locus CUFF.619_From_edi_0_2871668âÝ [* ] > Processing Locus CUFF.623_From_hi_0_2778596_âÝ [* ] > Processing Locus CUFF.635_From_ct_1_3241157_âÝ [* ] > Processing Locus CUFF.655_From_hi_0_2795398_âÝ [* ] > Processing Locus CUFF.663_From_kn_0_3613403_âÝ [* ] > Processing Locus CUFF.671_From_edi_0_2859720âÝ [** ] > Processing Locus CUFF.673_From_ler_0_4224097âÝ [** ] > Processing Locus CUFF.675_From_mt_0_4213448_âÝ [** ] > Processing Locus CUFF.679_From_ler_0_3998410âÝ [** ] > Processing Locus CUFF.685_From_mt_0_4231054_âÝ [** ] > Processing Locus CUFF.687_From_mt_0_4230874_âÝ [** ] > Processing Locus CUFF.689_From_ler_0_4018856âÝ [** ] > Processing Locus CUFF.695_From_mt_0_4217716_âÝ [** ] > Processing Locus CUFF.697_From_mt_0_4229662_âÝ [** ] > Processing Locus CUFF.699_From_no_0_2905273_âÝ [** ] > Processing Locus CUFF.703_From_no_0_2885444_âÝ [*** ] > Processing Locus CUFF.709_From_no_0_3101262_âÝ [*** ] > Processing Locus CUFF.729_From_oy_0_3001818_âÝ [*** ] > Processing Locus CUFF.733_From_no_0_2956652_âÝ [*** ] > Processing Locus CUFF.745_From_po_0_3507160_âÝ [*** ] > Processing Locus CUFF.747_From_po_0_3299272_âÝ [*** ] > Processing Locus CUFF.749_From_oy_0_3162092_âÝ [*** ] > Processing Locus CUFF.751_From_rsch_4_403485âÝ [*** ] > Processing Locus CUFF.753_From_oy_0_3121110_âÝ [*** ] > Processing Locus CUFF.757_From_po_0_3372769_âÝ [**** ] > Processing Locus CUFF.761_From_po_0_3606391_âÝ [**** ] > Processing Locus CUFF.761_From_po_0_3606391_âÝ [**** ] > Processing Locus CUFF.763_From_rsch_4_403203âÝ [**** ] > Processing Locus CUFF.773_From_po_0_3606391_âÝ [**** ] > Processing Locus CUFF.773_From_po_0_3606391_âÝ [**** ] > Processing Locus CUFF.773_From_po_0_3606391_âÝ [**** ] > Processing Locus CUFF.779_From_rsch_4_421454âÝ [**** ] > Processing Locus CUFF.781_From_rsch_4_427756âÝ [**** ] > Processing Locus CUFF.783_From_oy_0_2965192_âÝ [**** ] > Processing Locus CUFF.787_From_rsch_4_427756âÝ [**** ] > Processing Locus CUFF.789_From_rsch_4_427544âÝ [**** ] > Processing Locus CUFF.791_From_rsch_4_425553âÝ [**** ] > Processing Locus CUFF.795_From_rsch_4_429714âÝ [***** ] > Processing Locus CUFF.805_From_sf_2_2486157_âÝ [***** ] > Processing Locus CUFF.811_From_sf_2_2459023_âÝ [***** ] > Processing Locus CUFF.813_From_tsu_0_2970253âÝ [***** ] > Processing Locus CUFF.817_From_sf_2_2524453_âÝ [***** ] > Processing Locus CUFF.819_From_tsu_0_3036945âÝ [***** ] > Processing Locus CUFF.821_From_tsu_0_3175121âÝ [***** ] > Processing Locus CUFF.823_From_tsu_0_3175121âÝ [***** ] > Processing Locus CUFF.827_From_rsch_4_427728âÝ [***** ] > Processing Locus CUFF.829_From_tsu_0_3135135âÝ [****** ] > Processing Locus CUFF.833_From_tsu_0_3208747âÝ [****** ] > Processing Locus CUFF.835_From_tsu_0_3211741âÝ [****** ] > Processing Locus CUFF.837_From_tsu_0_3215671âÝ [****** ] > Processing Locus CUFF.837_From_tsu_0_3215671âÝ [****** ] > Processing Locus CUFF.843_From_rsch_4_429219âÝ [****** ] > Processing Locus CUFF.847_From_tsu_0_3242833âÝ [****** ] > Processing Locus CUFF.855_From_wil_2_2915899âÝ [****** ] > Processing Locus CUFF.859_From_tsu_0_3215737âÝ [****** ] > Processing Locus CUFF.869_From_sf_2_2701328_âÝ [****** ] > Processing Locus CUFF.873_From_wil_2_3050523âÝ [****** ] > Processing Locus CUFF.877_From_sf_2_2687786_âÝ [******* ] > Processing Locus CUFF.879_From_rsch_4_405516âÝ [******* ] > Processing Locus CUFF.887_From_wil_2_3054893âÝ [******* ] > Processing Locus CUFF.895_From_tsu_0_3215821âÝ [******* ] > Processing Locus CUFF.901_From_wil_2_3088151âÝ [******* ] > Processing Locus CUFF.901_From_wil_2_3088151âÝ [******* ] > Processing Locus CUFF.907_From_ws_0_3182508_âÝ [******* ] > Processing Locus CUFF.913_From_wil_2_2834553âÝ [******* ] > Processing Locus CUFF.933_From_tsu_0_3212935âÝ [******* ] > Processing Locus CUFF.937_From_ws_0_3373604_âÝ [******* ] > Processing Locus CUFF.943_From_zu_0_3075813_âÝ [******** ] > Processing Locus CUFF.945_From_wu_0_2678387_âÝ [******** ] > Processing Locus CUFF.947_From_wu_0_2654219_âÝ [******** ] > Processing Locus CUFF.949_From_wu_0_2687576_âÝ [******** ] > Processing Locus CUFF.957_From_ws_0_3381390_âÝ [******** ] > Processing Locus CUFF.963_From_zu_0_3092045_âÝ [******** ] > Processing Locus CUFF.969_From_zu_0_3190435_âÝ [******** ] > Processing Locus CUFF.973_From_zu_0_3242889_âÝ [******** ] > Processing Locus CUFF.977_From_zu_0_3255503_âÝ [******** ] > Processing Locus CUFF.985_From_zu_0_3280213_âÝ [********* ] > Processing Locus CUFF.991_From_zu_0_3277661_âÝ [********* ] > Processing Locus CUFF.993_From_zu_0_3082201_âÝ [********* ] > Processed 97 loci. [*************************] 100% > Map Properties: > Total Map Mass: 6284.84 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:27:33] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.533_From_bur_0_2020452 [ ] 2% > Processing Locus CUFF.533_From_bur_0_2020452 [ ] 3% > Processing Locus CUFF.545_From_bur_0_1856286 [* ] 4% > Processing Locus CUFF.563_From_bur_0_2020452 [* ] 5% > Processing Locus CUFF.563_From_bur_0_2020452 [* ] 6% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 7% > Processing Locus CUFF.575_From_ct_1_3082021_ [** ] 8% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 9% > Processing Locus CUFF.585_From_ct_1_3247037_ [** ] 10% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 11% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 12% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 13% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 14% > Processing Locus CUFF.607_From_edi_0_2891226 [*** ] 15% > Processing Locus CUFF.615_From_edi_0_2932438 [**** ] 16% > Processing Locus CUFF.617_From_edi_0_2918156 [**** ] 17% > Processing Locus CUFF.619_From_edi_0_2871668 [**** ] 18% > Processing Locus CUFF.623_From_hi_0_2778596_ [**** ] 19% > Processing Locus CUFF.635_From_ct_1_3241157_ [***** ] 20% > Processing Locus CUFF.655_From_hi_0_2795398_ [***** ] 21% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 22% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 23% > Processing Locus CUFF.673_From_ler_0_4224097 [****** ] 24% > Processing Locus CUFF.675_From_mt_0_4213448_ [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 26% > Processing Locus CUFF.685_From_mt_0_4231054_ [****** ] 27% > Processing Locus CUFF.687_From_mt_0_4230874_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 30% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 31% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 32% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 34% > Processing Locus CUFF.709_From_no_0_3101262_ [******** ] 35% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 36% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 37% > Processing Locus CUFF.745_From_po_0_3507160_ [********* ] 38% > Processing Locus CUFF.747_From_po_0_3299272_ [********* ] 39% > Processing Locus CUFF.749_From_oy_0_3162092_ [********** ] 40% > Processing Locus CUFF.751_From_rsch_4_403485 [********** ] 41% > Processing Locus CUFF.753_From_oy_0_3121110_ [********** ] 42% > Processing Locus CUFF.757_From_po_0_3372769_ [********** ] 43% > Processing Locus CUFF.761_From_po_0_3606391_ [*********** ] 44% > Processing Locus CUFF.761_From_po_0_3606391_ [*********** ] 45% > Processing Locus CUFF.763_From_rsch_4_403203 [*********** ] 46% > Processing Locus CUFF.773_From_po_0_3606391_ [*********** ] 47% > Processing Locus CUFF.773_From_po_0_3606391_ [************ ] 48% > Processing Locus CUFF.773_From_po_0_3606391_ [************ ] 49% > Processing Locus CUFF.779_From_rsch_4_421454 [************ ] 50% > Processing Locus CUFF.781_From_rsch_4_427756 [************ ] 51% > Processing Locus CUFF.783_From_oy_0_2965192_ [************* ] 52% > Processing Locus CUFF.787_From_rsch_4_427756 [************* ] 53% > Processing Locus CUFF.789_From_rsch_4_427544 [************* ] 54% > Processing Locus CUFF.791_From_rsch_4_425553 [************* ] 55% > Processing Locus CUFF.795_From_rsch_4_429714 [************** ] 56% > Processing Locus CUFF.805_From_sf_2_2486157_ [************** ] 57% > Processing Locus CUFF.811_From_sf_2_2459023_ [************** ] 58% > Processing Locus CUFF.813_From_tsu_0_2970253 [************** ] 59% > Processing Locus CUFF.817_From_sf_2_2524453_ [*************** ] 60% > Processing Locus CUFF.819_From_tsu_0_3036945 [*************** ] 61% > Processing Locus CUFF.821_From_tsu_0_3175121 [*************** ] 62% > Processing Locus CUFF.823_From_tsu_0_3175121 [*************** ] 63% > Processing Locus CUFF.827_From_rsch_4_427728 [**************** ] 64% > Processing Locus CUFF.829_From_tsu_0_3135135 [**************** ] 65% > Processing Locus CUFF.833_From_tsu_0_3208747 [**************** ] 67% > Processing Locus CUFF.835_From_tsu_0_3211741 [***************** ] 68% > Processing Locus CUFF.837_From_tsu_0_3215671 [***************** ] 69% > Processing Locus CUFF.837_From_tsu_0_3215671 [***************** ] 70% > Processing Locus CUFF.843_From_rsch_4_429219 [***************** ] 71% > Processing Locus CUFF.847_From_tsu_0_3242833 [****************** ] 72% > Processing Locus CUFF.855_From_wil_2_2915899 [****************** ] 73% > Processing Locus CUFF.859_From_tsu_0_3215737 [****************** ] 74% > Processing Locus CUFF.869_From_sf_2_2701328_ [****************** ] 75% > Processing Locus CUFF.873_From_wil_2_3050523 [******************* ] 76% > Processing Locus CUFF.877_From_sf_2_2687786_ [******************* ] 77% > Processing Locus CUFF.879_From_rsch_4_405516 [******************* ] 78% > Processing Locus CUFF.887_From_wil_2_3054893 [******************* ] 79% > Processing Locus CUFF.895_From_tsu_0_3215821 [******************** ] 80% > Processing Locus CUFF.901_From_wil_2_3088151 [******************** ] 81% > Processing Locus CUFF.901_From_wil_2_3088151 [******************** ] 82% > Processing Locus CUFF.907_From_ws_0_3182508_ [******************** ] 83% > Processing Locus CUFF.913_From_wil_2_2834553 [********************* ] 84% > Processing Locus CUFF.933_From_tsu_0_3212935 [********************* ] 85% > Processing Locus CUFF.937_From_ws_0_3373604_ [********************* ] 86% > Processing Locus CUFF.943_From_zu_0_3075813_ [********************* ] 87% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************** ] 88% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************** ] 89% > Processing Locus CUFF.949_From_wu_0_2687576_ [********************** ] 90% > Processing Locus CUFF.957_From_ws_0_3381390_ [********************** ] 91% > Processing Locus CUFF.963_From_zu_0_3092045_ [*********************** ] 92% > Processing Locus CUFF.969_From_zu_0_3190435_ [*********************** ] 93% > Processing Locus CUFF.973_From_zu_0_3242889_ [*********************** ] 94% > Processing Locus CUFF.977_From_zu_0_3255503_ [*********************** ] 95% > Processing Locus CUFF.985_From_zu_0_3280213_ [************************ ] 96% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 97% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 98% > Processed 97 loci. [*************************] 100% [16:27:33] Loading reference annotation and sequence [16:27:33] Learning bias parameters. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.563_From_bur_0_2020452 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 5% > Processing Locus CUFF.615_From_edi_0_2932438 [* ] 6% > Processing Locus CUFF.617_From_edi_0_2918156 [* ] 7% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 8% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 9% > Processing Locus CUFF.635_From_ct_1_3241157_ [** ] 10% > Processing Locus CUFF.655_From_hi_0_2795398_ [** ] 11% > Processing Locus CUFF.671_From_edi_0_2859720 [*** ] 12% > Processing Locus CUFF.675_From_mt_0_4213448_ [*** ] 13% > Processing Locus CUFF.685_From_mt_0_4231054_ [*** ] 14% > Processing Locus CUFF.687_From_mt_0_4230874_ [*** ] 15% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 16% > Processing Locus CUFF.695_From_mt_0_4217716_ [**** ] 17% > Processing Locus CUFF.697_From_mt_0_4229662_ [**** ] 18% > Processing Locus CUFF.709_From_no_0_3101262_ [**** ] 19% > Processing Locus CUFF.729_From_oy_0_3001818_ [***** ] 20% > Processing Locus CUFF.745_From_po_0_3507160_ [***** ] 21% > Processing Locus CUFF.747_From_po_0_3299272_ [***** ] 22% > Processing Locus CUFF.751_From_rsch_4_403485 [***** ] 23% > Processing Locus CUFF.757_From_po_0_3372769_ [****** ] 24% > Processing Locus CUFF.779_From_rsch_4_421454 [****** ] 25% > Processing Locus CUFF.781_From_rsch_4_427756 [****** ] 26% > Processing Locus CUFF.783_From_oy_0_2965192_ [****** ] 27% > Processing Locus CUFF.787_From_rsch_4_427756 [******* ] 28% > Processing Locus CUFF.789_From_rsch_4_427544 [******* ] 29% > Processing Locus CUFF.791_From_rsch_4_425553 [******* ] 30% > Processing Locus CUFF.795_From_rsch_4_429714 [******* ] 31% > Processing Locus CUFF.805_From_sf_2_2486157_ [******** ] 32% > Processing Locus CUFF.811_From_sf_2_2459023_ [******** ] 34% > Processing Locus CUFF.813_From_tsu_0_2970253 [******** ] 35% > Processing Locus CUFF.817_From_sf_2_2524453_ [********* ] 36% > Processing Locus CUFF.821_From_tsu_0_3175121 [********* ] 37% > Processing Locus CUFF.827_From_rsch_4_427728 [********* ] 38% > Processing Locus CUFF.833_From_tsu_0_3208747 [********* ] 39% > Processing Locus CUFF.835_From_tsu_0_3211741 [********** ] 40% > Processing Locus CUFF.837_From_tsu_0_3215671 [********** ] 41% > Processing Locus CUFF.837_From_tsu_0_3215671 [********** ] 42% > Processing Locus CUFF.843_From_rsch_4_429219 [********** ] 43% > Processing Locus CUFF.847_From_tsu_0_3242833 [*********** ] 44% > Processing Locus CUFF.859_From_tsu_0_3215737 [*********** ] 45% > Processing Locus CUFF.873_From_wil_2_3050523 [*********** ] 46% > Processing Locus CUFF.877_From_sf_2_2687786_ [*********** ] 47% > Processing Locus CUFF.879_From_rsch_4_405516 [************ ] 48% > Processing Locus CUFF.895_From_tsu_0_3215821 [************ ] 49% > Processing Locus CUFF.901_From_wil_2_3088151 [************ ] 50% > Processing Locus CUFF.933_From_tsu_0_3212935 [************ ] 51% > Processing Locus CUFF.937_From_ws_0_3373604_ [************* ] 52% > Processing Locus CUFF.947_From_wu_0_2654219_ [************* ] 53% > Processing Locus CUFF.949_From_wu_0_2687576_ [************* ] 54% > Processing Locus CUFF.957_From_ws_0_3381390_ [************* ] 55% > Processing Locus CUFF.973_From_zu_0_3242889_ [************** ] 56% > Processing Locus CUFF.977_From_zu_0_3255503_ [************** ] 57% > Processing Locus CUFF.985_From_zu_0_3280213_ [************** ] 58% > Processing Locus CUFF.991_From_zu_0_3277661_ [************** ] 59% > Processing Locus CUFF.993_From_zu_0_3082201_ [*************** ] 60% > Processed 60 loci. [*************************] 100% [16:27:33] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.563_From_bur_0_2020452 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 5% > Processing Locus CUFF.615_From_edi_0_2932438 [* ] 6% > Processing Locus CUFF.617_From_edi_0_2918156 [* ] 7% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 8% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 9% > Processing Locus CUFF.635_From_ct_1_3241157_ [** ] 10% > Processing Locus CUFF.655_From_hi_0_2795398_ [** ] 11% > Processing Locus CUFF.671_From_edi_0_2859720 [*** ] 12% > Processing Locus CUFF.675_From_mt_0_4213448_ [*** ] 13% > Processing Locus CUFF.685_From_mt_0_4231054_ [*** ] 14% > Processing Locus CUFF.687_From_mt_0_4230874_ [*** ] 15% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 16% > Processing Locus CUFF.695_From_mt_0_4217716_ [**** ] 17% > Processing Locus CUFF.697_From_mt_0_4229662_ [**** ] 18% > Processing Locus CUFF.709_From_no_0_3101262_ [**** ] 19% > Processing Locus CUFF.729_From_oy_0_3001818_ [***** ] 20% > Processing Locus CUFF.745_From_po_0_3507160_ [***** ] 21% > Processing Locus CUFF.747_From_po_0_3299272_ [***** ] 22% > Processing Locus CUFF.751_From_rsch_4_403485 [***** ] 23% > Processing Locus CUFF.757_From_po_0_3372769_ [****** ] 24% > Processing Locus CUFF.779_From_rsch_4_421454 [****** ] 25% > Processing Locus CUFF.781_From_rsch_4_427756 [****** ] 26% > Processing Locus CUFF.783_From_oy_0_2965192_ [****** ] 27% > Processing Locus CUFF.787_From_rsch_4_427756 [******* ] 28% > Processing Locus CUFF.789_From_rsch_4_427544 [******* ] 29% > Processing Locus CUFF.791_From_rsch_4_425553 [******* ] 30% > Processing Locus CUFF.795_From_rsch_4_429714 [******* ] 31% > Processing Locus CUFF.805_From_sf_2_2486157_ [******** ] 32% > Processing Locus CUFF.811_From_sf_2_2459023_ [******** ] 34% > Processing Locus CUFF.813_From_tsu_0_2970253 [******** ] 35% > Processing Locus CUFF.817_From_sf_2_2524453_ [********* ] 36% > Processing Locus CUFF.821_From_tsu_0_3175121 [********* ] 37% > Processing Locus CUFF.827_From_rsch_4_427728 [********* ] 38% > Processing Locus CUFF.833_From_tsu_0_3208747 [********* ] 39% > Processing Locus CUFF.835_From_tsu_0_3211741 [********** ] 40% > Processing Locus CUFF.837_From_tsu_0_3215671 [********** ] 41% > Processing Locus CUFF.837_From_tsu_0_3215671 [********** ] 42% > Processing Locus CUFF.843_From_rsch_4_429219 [********** ] 43% > Processing Locus CUFF.847_From_tsu_0_3242833 [*********** ] 44% > Processing Locus CUFF.859_From_tsu_0_3215737 [*********** ] 45% > Processing Locus CUFF.873_From_wil_2_3050523 [*********** ] 46% > Processing Locus CUFF.877_From_sf_2_2687786_ [*********** ] 47% > Processing Locus CUFF.879_From_rsch_4_405516 [************ ] 48% > Processing Locus CUFF.895_From_tsu_0_3215821 [************ ] 49% > Processing Locus CUFF.901_From_wil_2_3088151 [************ ] 50% > Processing Locus CUFF.933_From_tsu_0_3212935 [************ ] 51% > Processing Locus CUFF.937_From_ws_0_3373604_ [************* ] 52% > Processing Locus CUFF.947_From_wu_0_2654219_ [************* ] 53% > Processing Locus CUFF.949_From_wu_0_2687576_ [************* ] 54% > Processing Locus CUFF.957_From_ws_0_3381390_ [************* ] 55% > Processing Locus CUFF.973_From_zu_0_3242889_ [************** ] 56% > Processing Locus CUFF.977_From_zu_0_3255503_ [************** ] 57% > Processing Locus CUFF.985_From_zu_0_3280213_ [************** ] 58% > Processing Locus CUFF.991_From_zu_0_3277661_ [************** ] 59% > Processing Locus CUFF.993_From_zu_0_3082201_ [*************** ] 60% > Processed 60 loci. [*************************] 100% cufflinks -p 4 -o ./Sf_2 -r ngene.fa ./Sf_2/accepted_hits.bam [16:27:34] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.529_From_bur_0_18734941¼ [ ] > Processing Locus CUFF.551_From_can_0_31224801¼ [ ] > Processing Locus CUFF.561_From_can_0_31897531¼ [ ] > Processing Locus CUFF.567_From_can_0_32587791¼ [ ] > Processing Locus CUFF.567_From_can_0_32587791¼ [ ] > Processing Locus CUFF.567_From_can_0_32587791¼ [ ] > Processing Locus CUFF.571_From_can_0_30769401¼ [ ] > Processing Locus CUFF.575_From_ct_1_3082021_1¼ [ ] > Processing Locus CUFF.577_From_ct_1_3125173_1¼ [ ] > Processing Locus CUFF.579_From_ct_1_3133451_1¼ [ ] > Processing Locus CUFF.581_From_can_0_32184591¼ [ ] > Processing Locus CUFF.583_From_ct_1_3302721_1¼ [ ] > Processing Locus CUFF.585_From_ct_1_3247037_1¼ [* ] > Processing Locus CUFF.593_From_can_0_32701311¼ [* ] > Processing Locus CUFF.593_From_can_0_32701311¼ [* ] > Processing Locus CUFF.595_From_ct_1_3302721_1¼ [* ] > Processing Locus CUFF.599_From_edi_0_27447021¼ [* ] > Processing Locus CUFF.607_From_edi_0_28912261¼ [* ] > Processing Locus CUFF.619_From_edi_0_28716681¼ [* ] > Processing Locus CUFF.621_From_edi_0_29347141¼ [* ] > Processing Locus CUFF.623_From_hi_0_2778596_1¼ [* ] > Processing Locus CUFF.641_From_kn_0_3605300_1¼ [* ] > Processing Locus CUFF.661_From_kn_0_3819922_1¼ [** ] > Processing Locus CUFF.663_From_kn_0_3613403_1¼ [** ] > Processing Locus CUFF.665_From_hi_0_2939638_1¼ [** ] > Processing Locus CUFF.677_From_ct_1_3133995_1¼ [** ] > Processing Locus CUFF.679_From_ler_0_39984101¼ [** ] > Processing Locus CUFF.685_From_mt_0_4231054_1¼ [** ] > Processing Locus CUFF.689_From_ler_0_40188561¼ [** ] > Processing Locus CUFF.695_From_mt_0_4217716_1¼ [** ] > Processing Locus CUFF.697_From_mt_0_4229662_1¼ [** ] > Processing Locus CUFF.699_From_no_0_2905273_1¼ [** ] > Processing Locus CUFF.703_From_no_0_2885444_1¼ [*** ] > Processing Locus CUFF.711_From_no_0_3088052_1¼ [*** ] > Processing Locus CUFF.715_From_oy_0_3098144_1¼ [*** ] > Processing Locus CUFF.723_From_po_0_3306688_1¼ [*** ] > Processing Locus CUFF.733_From_no_0_2956652_1¼ [*** ] > Processing Locus CUFF.741_From_po_0_3382155_1¼ [*** ] > Processing Locus CUFF.743_From_po_0_3330421_1¼ [*** ] > Processing Locus CUFF.759_From_no_0_2936769_1¼ [*** ] > Processing Locus CUFF.763_From_rsch_4_4032031¼ [*** ] > Processing Locus CUFF.771_From_po_0_3332479_1¼ [**** ] > Processing Locus CUFF.779_From_rsch_4_4214541¼ [**** ] > Processing Locus CUFF.781_From_rsch_4_4277561¼ [**** ] > Processing Locus CUFF.787_From_rsch_4_4277561¼ [**** ] > Processing Locus CUFF.789_From_rsch_4_4275441¼ [**** ] > Processing Locus CUFF.793_From_sf_2_2504999_1¼ [**** ] > Processing Locus CUFF.797_From_sf_2_2676583_1¼ [**** ] > Processing Locus CUFF.801_From_sf_2_2532172_1¼ [**** ] > Processing Locus CUFF.805_From_sf_2_2486157_1¼ [**** ] > Processing Locus CUFF.807_From_sf_2_2488391_1¼ [**** ] > Processing Locus CUFF.809_From_sf_2_2682779_1¼ [***** ] > Processing Locus CUFF.811_From_sf_2_2459023_1¼ [***** ] > Processing Locus CUFF.815_From_sf_2_2671632_1¼ [***** ] > Processing Locus CUFF.817_From_sf_2_2524453_1¼ [***** ] > Processing Locus CUFF.821_From_tsu_0_31751211¼ [***** ] > Processing Locus CUFF.823_From_tsu_0_31751211¼ [***** ] > Processing Locus CUFF.831_From_sf_2_2687774_1¼ [***** ] > Processing Locus CUFF.837_From_tsu_0_32156711¼ [***** ] > Processing Locus CUFF.837_From_tsu_0_32156711¼ [***** ] > Processing Locus CUFF.839_From_sf_2_2680171_1¼ [***** ] > Processing Locus CUFF.841_From_tsu_0_32432731¼ [****** ] > Processing Locus CUFF.845_From_tsu_0_32432731¼ [****** ] > Processing Locus CUFF.857_From_sf_2_2653966_1¼ [****** ] > Processing Locus CUFF.861_From_mt_0_4528444_1¼ [****** ] > Processing Locus CUFF.869_From_sf_2_2701328_1¼ [****** ] > Processing Locus CUFF.873_From_wil_2_30505231¼ [****** ] > Processing Locus CUFF.877_From_sf_2_2687786_1¼ [****** ] > Processing Locus CUFF.879_From_rsch_4_4055161¼ [****** ] > Processing Locus CUFF.887_From_wil_2_30548931¼ [****** ] > Processing Locus CUFF.895_From_tsu_0_32158211¼ [****** ] > Processing Locus CUFF.899_From_ws_0_3190963_1¼ [******* ] > Processing Locus CUFF.901_From_wil_2_30881511¼ [******* ] > Processing Locus CUFF.901_From_wil_2_30881511¼ [******* ] > Processing Locus CUFF.901_From_wil_2_30881511¼ [******* ] > Processing Locus CUFF.907_From_ws_0_3182508_1¼ [******* ] > Processing Locus CUFF.909_From_wil_2_30522731¼ [******* ] > Processing Locus CUFF.913_From_wil_2_28345531¼ [******* ] > Processing Locus CUFF.937_From_ws_0_3373604_1¼ [******* ] > Processing Locus CUFF.945_From_wu_0_2678387_1¼ [******* ] > Processing Locus CUFF.947_From_wu_0_2654219_1¼ [******* ] > Processing Locus CUFF.949_From_wu_0_2687576_1¼ [******* ] > Processing Locus CUFF.951_From_wil_2_30871831¼ [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_1¼ [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_1¼ [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_1¼ [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_1¼ [******** ] > Processing Locus CUFF.953_From_ws_0_3382500_1¼ [******** ] > Processing Locus CUFF.955_From_ws_0_3340488_1¼ [******** ] > Processing Locus CUFF.967_From_zu_0_3022629_1¼ [******** ] > Processing Locus CUFF.971_From_zu_0_3255169_1¼ [******** ] > Processing Locus CUFF.987_From_zu_0_3118546_1¼ [******** ] > Processing Locus CUFF.993_From_zu_0_3082201_1¼ [******** ] > Processed 93 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5360.89 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:27:34] Assembling transcripts and estimating abundances. > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 0% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.567_From_can_0_3258779 [ ] 3% > Processing Locus CUFF.567_From_can_0_3258779 [* ] 4% > Processing Locus CUFF.567_From_can_0_3258779 [* ] 5% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 6% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 7% > Processing Locus CUFF.577_From_ct_1_3125173_ [** ] 8% > Processing Locus CUFF.579_From_ct_1_3133451_ [** ] 9% > Processing Locus CUFF.581_From_can_0_3218459 [** ] 10% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 11% > Processing Locus CUFF.585_From_ct_1_3247037_ [*** ] 12% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 13% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 15% > Processing Locus CUFF.595_From_ct_1_3302721_ [**** ] 16% > Processing Locus CUFF.599_From_edi_0_2744702 [**** ] 17% > Processing Locus CUFF.607_From_edi_0_2891226 [**** ] 18% > Processing Locus CUFF.619_From_edi_0_2871668 [**** ] 19% > Processing Locus CUFF.621_From_edi_0_2934714 [***** ] 20% > Processing Locus CUFF.623_From_hi_0_2778596_ [***** ] 21% > Processing Locus CUFF.641_From_kn_0_3605300_ [***** ] 22% > Processing Locus CUFF.661_From_kn_0_3819922_ [***** ] 23% > Processing Locus CUFF.663_From_kn_0_3613403_ [****** ] 24% > Processing Locus CUFF.665_From_hi_0_2939638_ [****** ] 25% > Processing Locus CUFF.677_From_ct_1_3133995_ [****** ] 26% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 27% > Processing Locus CUFF.685_From_mt_0_4231054_ [******* ] 29% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 30% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 31% > Processing Locus CUFF.697_From_mt_0_4229662_ [******** ] 32% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 33% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 34% > Processing Locus CUFF.711_From_no_0_3088052_ [******** ] 35% > Processing Locus CUFF.715_From_oy_0_3098144_ [********* ] 36% > Processing Locus CUFF.723_From_po_0_3306688_ [********* ] 37% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 38% > Processing Locus CUFF.741_From_po_0_3382155_ [********* ] 39% > Processing Locus CUFF.743_From_po_0_3330421_ [********** ] 40% > Processing Locus CUFF.759_From_no_0_2936769_ [********** ] 41% > Processing Locus CUFF.763_From_rsch_4_403203 [********** ] 43% > Processing Locus CUFF.771_From_po_0_3332479_ [*********** ] 44% > Processing Locus CUFF.779_From_rsch_4_421454 [*********** ] 45% > Processing Locus CUFF.781_From_rsch_4_427756 [*********** ] 46% > Processing Locus CUFF.787_From_rsch_4_427756 [*********** ] 47% > Processing Locus CUFF.789_From_rsch_4_427544 [************ ] 48% > Processing Locus CUFF.793_From_sf_2_2504999_ [************ ] 49% > Processing Locus CUFF.797_From_sf_2_2676583_ [************ ] 50% > Processing Locus CUFF.801_From_sf_2_2532172_ [************ ] 51% > Processing Locus CUFF.805_From_sf_2_2486157_ [************* ] 52% > Processing Locus CUFF.807_From_sf_2_2488391_ [************* ] 53% > Processing Locus CUFF.809_From_sf_2_2682779_ [************* ] 54% > Processing Locus CUFF.811_From_sf_2_2459023_ [************* ] 55% > Processing Locus CUFF.815_From_sf_2_2671632_ [************** ] 56% > Processing Locus CUFF.817_From_sf_2_2524453_ [************** ] 58% > Processing Locus CUFF.821_From_tsu_0_3175121 [************** ] 59% > Processing Locus CUFF.823_From_tsu_0_3175121 [*************** ] 60% > Processing Locus CUFF.831_From_sf_2_2687774_ [*************** ] 61% > Processing Locus CUFF.837_From_tsu_0_3215671 [*************** ] 62% > Processing Locus CUFF.837_From_tsu_0_3215671 [*************** ] 63% > Processing Locus CUFF.839_From_sf_2_2680171_ [**************** ] 64% > Processing Locus CUFF.841_From_tsu_0_3243273 [**************** ] 65% > Processing Locus CUFF.845_From_tsu_0_3243273 [**************** ] 66% > Processing Locus CUFF.857_From_sf_2_2653966_ [**************** ] 67% > Processing Locus CUFF.861_From_mt_0_4528444_ [***************** ] 68% > Processing Locus CUFF.869_From_sf_2_2701328_ [***************** ] 69% > Processing Locus CUFF.873_From_wil_2_3050523 [***************** ] 70% > Processing Locus CUFF.877_From_sf_2_2687786_ [****************** ] 72% > Processing Locus CUFF.879_From_rsch_4_405516 [****************** ] 73% > Processing Locus CUFF.887_From_wil_2_3054893 [****************** ] 74% > Processing Locus CUFF.895_From_tsu_0_3215821 [****************** ] 75% > Processing Locus CUFF.899_From_ws_0_3190963_ [******************* ] 76% > Processing Locus CUFF.901_From_wil_2_3088151 [******************* ] 77% > Processing Locus CUFF.901_From_wil_2_3088151 [******************* ] 78% > Processing Locus CUFF.901_From_wil_2_3088151 [******************* ] 79% > Processing Locus CUFF.907_From_ws_0_3182508_ [******************** ] 80% > Processing Locus CUFF.909_From_wil_2_3052273 [******************** ] 81% > Processing Locus CUFF.913_From_wil_2_2834553 [******************** ] 82% > Processing Locus CUFF.937_From_ws_0_3373604_ [******************** ] 83% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************* ] 84% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************* ] 86% > Processing Locus CUFF.949_From_wu_0_2687576_ [********************* ] 87% > Processing Locus CUFF.951_From_wil_2_3087183 [********************** ] 88% > Processing Locus CUFF.953_From_ws_0_3382500_ [********************** ] 89% > Processing Locus CUFF.953_From_ws_0_3382500_ [********************** ] 90% > Processing Locus CUFF.953_From_ws_0_3382500_ [********************** ] 91% > Processing Locus CUFF.953_From_ws_0_3382500_ [*********************** ] 92% > Processing Locus CUFF.953_From_ws_0_3382500_ [*********************** ] 93% > Processing Locus CUFF.955_From_ws_0_3340488_ [*********************** ] 94% > Processing Locus CUFF.967_From_zu_0_3022629_ [*********************** ] 95% > Processing Locus CUFF.971_From_zu_0_3255169_ [************************ ] 96% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 97% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 98% > Processed 93 loci. [*************************] 100% [16:27:34] Loading reference annotation and sequence [16:27:34] Learning bias parameters. > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 0% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.577_From_ct_1_3125173_ [* ] 4% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 5% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 7% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 8% > Processing Locus CUFF.599_From_edi_0_2744702 [** ] 9% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 10% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 11% > Processing Locus CUFF.641_From_kn_0_3605300_ [*** ] 12% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 13% > Processing Locus CUFF.665_From_hi_0_2939638_ [*** ] 15% > Processing Locus CUFF.677_From_ct_1_3133995_ [**** ] 16% > Processing Locus CUFF.685_From_mt_0_4231054_ [**** ] 17% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 18% > Processing Locus CUFF.695_From_mt_0_4217716_ [**** ] 19% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 20% > Processing Locus CUFF.711_From_no_0_3088052_ [***** ] 21% > Processing Locus CUFF.715_From_oy_0_3098144_ [***** ] 22% > Processing Locus CUFF.723_From_po_0_3306688_ [***** ] 23% > Processing Locus CUFF.733_From_no_0_2956652_ [****** ] 24% > Processing Locus CUFF.743_From_po_0_3330421_ [****** ] 25% > Processing Locus CUFF.763_From_rsch_4_403203 [****** ] 26% > Processing Locus CUFF.771_From_po_0_3332479_ [****** ] 27% > Processing Locus CUFF.781_From_rsch_4_427756 [******* ] 29% > Processing Locus CUFF.787_From_rsch_4_427756 [******* ] 30% > Processing Locus CUFF.789_From_rsch_4_427544 [******* ] 31% > Processing Locus CUFF.793_From_sf_2_2504999_ [******** ] 32% > Processing Locus CUFF.797_From_sf_2_2676583_ [******** ] 33% > Processing Locus CUFF.801_From_sf_2_2532172_ [******** ] 34% > Processing Locus CUFF.805_From_sf_2_2486157_ [******** ] 35% > Processing Locus CUFF.807_From_sf_2_2488391_ [********* ] 36% > Processing Locus CUFF.809_From_sf_2_2682779_ [********* ] 37% > Processing Locus CUFF.811_From_sf_2_2459023_ [********* ] 38% > Processing Locus CUFF.815_From_sf_2_2671632_ [********* ] 39% > Processing Locus CUFF.817_From_sf_2_2524453_ [********** ] 40% > Processing Locus CUFF.821_From_tsu_0_3175121 [********** ] 41% > Processing Locus CUFF.831_From_sf_2_2687774_ [********** ] 43% > Processing Locus CUFF.839_From_sf_2_2680171_ [*********** ] 44% > Processing Locus CUFF.841_From_tsu_0_3243273 [*********** ] 45% > Processing Locus CUFF.845_From_tsu_0_3243273 [*********** ] 46% > Processing Locus CUFF.857_From_sf_2_2653966_ [*********** ] 47% > Processing Locus CUFF.861_From_mt_0_4528444_ [************ ] 48% > Processing Locus CUFF.869_From_sf_2_2701328_ [************ ] 49% > Processing Locus CUFF.873_From_wil_2_3050523 [************ ] 50% > Processing Locus CUFF.877_From_sf_2_2687786_ [************ ] 51% > Processing Locus CUFF.879_From_rsch_4_405516 [************* ] 52% > Processing Locus CUFF.887_From_wil_2_3054893 [************* ] 53% > Processing Locus CUFF.895_From_tsu_0_3215821 [************* ] 54% > Processing Locus CUFF.899_From_ws_0_3190963_ [************* ] 55% > Processing Locus CUFF.901_From_wil_2_3088151 [************** ] 56% > Processing Locus CUFF.907_From_ws_0_3182508_ [************** ] 58% > Processing Locus CUFF.909_From_wil_2_3052273 [************** ] 59% > Processing Locus CUFF.913_From_wil_2_2834553 [*************** ] 60% > Processing Locus CUFF.937_From_ws_0_3373604_ [*************** ] 61% > Processing Locus CUFF.949_From_wu_0_2687576_ [*************** ] 62% > Processing Locus CUFF.953_From_ws_0_3382500_ [*************** ] 63% > Processing Locus CUFF.953_From_ws_0_3382500_ [**************** ] 64% > Processing Locus CUFF.955_From_ws_0_3340488_ [**************** ] 65% > Processing Locus CUFF.967_From_zu_0_3022629_ [**************** ] 66% > Processing Locus CUFF.971_From_zu_0_3255169_ [**************** ] 67% > Processing Locus CUFF.987_From_zu_0_3118546_ [***************** ] 68% > Processing Locus CUFF.993_From_zu_0_3082201_ [***************** ] 69% > Processed 66 loci. [*************************] 100% [16:27:34] Assembling transcripts and estimating abundances. > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 0% > Processing Locus CUFF.551_From_can_0_3122480 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.577_From_ct_1_3125173_ [* ] 4% > Processing Locus CUFF.581_From_can_0_3218459 [* ] 5% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 7% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 8% > Processing Locus CUFF.599_From_edi_0_2744702 [** ] 9% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 10% > Processing Locus CUFF.623_From_hi_0_2778596_ [** ] 11% > Processing Locus CUFF.641_From_kn_0_3605300_ [*** ] 12% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 13% > Processing Locus CUFF.665_From_hi_0_2939638_ [*** ] 15% > Processing Locus CUFF.677_From_ct_1_3133995_ [**** ] 16% > Processing Locus CUFF.685_From_mt_0_4231054_ [**** ] 17% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 18% > Processing Locus CUFF.695_From_mt_0_4217716_ [**** ] 19% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 20% > Processing Locus CUFF.711_From_no_0_3088052_ [***** ] 21% > Processing Locus CUFF.715_From_oy_0_3098144_ [***** ] 22% > Processing Locus CUFF.723_From_po_0_3306688_ [***** ] 23% > Processing Locus CUFF.733_From_no_0_2956652_ [****** ] 24% > Processing Locus CUFF.743_From_po_0_3330421_ [****** ] 25% > Processing Locus CUFF.763_From_rsch_4_403203 [****** ] 26% > Processing Locus CUFF.771_From_po_0_3332479_ [****** ] 27% > Processing Locus CUFF.781_From_rsch_4_427756 [******* ] 29% > Processing Locus CUFF.787_From_rsch_4_427756 [******* ] 30% > Processing Locus CUFF.789_From_rsch_4_427544 [******* ] 31% > Processing Locus CUFF.793_From_sf_2_2504999_ [******** ] 32% > Processing Locus CUFF.797_From_sf_2_2676583_ [******** ] 33% > Processing Locus CUFF.801_From_sf_2_2532172_ [******** ] 34% > Processing Locus CUFF.805_From_sf_2_2486157_ [******** ] 35% > Processing Locus CUFF.807_From_sf_2_2488391_ [********* ] 36% > Processing Locus CUFF.809_From_sf_2_2682779_ [********* ] 37% > Processing Locus CUFF.811_From_sf_2_2459023_ [********* ] 38% > Processing Locus CUFF.815_From_sf_2_2671632_ [********* ] 39% > Processing Locus CUFF.817_From_sf_2_2524453_ [********** ] 40% > Processing Locus CUFF.821_From_tsu_0_3175121 [********** ] 41% > Processing Locus CUFF.831_From_sf_2_2687774_ [********** ] 43% > Processing Locus CUFF.839_From_sf_2_2680171_ [*********** ] 44% > Processing Locus CUFF.841_From_tsu_0_3243273 [*********** ] 45% > Processing Locus CUFF.845_From_tsu_0_3243273 [*********** ] 46% > Processing Locus CUFF.857_From_sf_2_2653966_ [*********** ] 47% > Processing Locus CUFF.861_From_mt_0_4528444_ [************ ] 48% > Processing Locus CUFF.869_From_sf_2_2701328_ [************ ] 49% > Processing Locus CUFF.873_From_wil_2_3050523 [************ ] 50% > Processing Locus CUFF.877_From_sf_2_2687786_ [************ ] 51% > Processing Locus CUFF.879_From_rsch_4_405516 [************* ] 52% > Processing Locus CUFF.887_From_wil_2_3054893 [************* ] 53% > Processing Locus CUFF.895_From_tsu_0_3215821 [************* ] 54% > Processing Locus CUFF.899_From_ws_0_3190963_ [************* ] 55% > Processing Locus CUFF.901_From_wil_2_3088151 [************** ] 56% > Processing Locus CUFF.907_From_ws_0_3182508_ [************** ] 58% > Processing Locus CUFF.909_From_wil_2_3052273 [************** ] 59% > Processing Locus CUFF.913_From_wil_2_2834553 [*************** ] 60% > Processing Locus CUFF.937_From_ws_0_3373604_ [*************** ] 61% > Processing Locus CUFF.949_From_wu_0_2687576_ [*************** ] 62% > Processing Locus CUFF.953_From_ws_0_3382500_ [*************** ] 63% > Processing Locus CUFF.953_From_ws_0_3382500_ [**************** ] 64% > Processing Locus CUFF.955_From_ws_0_3340488_ [**************** ] 65% > Processing Locus CUFF.967_From_zu_0_3022629_ [**************** ] 66% > Processing Locus CUFF.971_From_zu_0_3255169_ [**************** ] 67% > Processing Locus CUFF.987_From_zu_0_3118546_ [***************** ] 68% > Processing Locus CUFF.993_From_zu_0_3082201_ [***************** ] 69% > Processed 66 loci. [*************************] 100% cufflinks -p 4 -o ./Wil_2 -r ngene.fa ./Wil_2/accepted_hits.bam [16:27:34] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.523_From_bur_0_18043994W [ ] > Processing Locus CUFF.529_From_bur_0_18734944W [ ] > Processing Locus CUFF.553_From_can_0_32236554W [ ] > Processing Locus CUFF.559_From_can_0_32312054W [ ] > Processing Locus CUFF.561_From_can_0_31897534W [ ] > Processing Locus CUFF.571_From_can_0_30769404W [ ] > Processing Locus CUFF.575_From_ct_1_3082021_4W [ ] > Processing Locus CUFF.583_From_ct_1_3302721_4W [ ] > Processing Locus CUFF.589_From_edi_0_27232554W [ ] > Processing Locus CUFF.593_From_can_0_32701314W [ ] > Processing Locus CUFF.593_From_can_0_32701314W [ ] > Processing Locus CUFF.593_From_can_0_32701314W [ ] > Processing Locus CUFF.595_From_ct_1_3302721_4W [* ] > Processing Locus CUFF.609_From_hi_0_2755116_4W [* ] > Processing Locus CUFF.613_From_hi_0_2773206_4W [* ] > Processing Locus CUFF.619_From_edi_0_28716684W [* ] > Processing Locus CUFF.623_From_hi_0_2778596_4W [* ] > Processing Locus CUFF.641_From_kn_0_3605300_4W [* ] > Processing Locus CUFF.655_From_hi_0_2795398_4W [* ] > Processing Locus CUFF.663_From_kn_0_3613403_4W [* ] > Processing Locus CUFF.671_From_edi_0_28597204W [* ] > Processing Locus CUFF.673_From_ler_0_42240974W [** ] > Processing Locus CUFF.679_From_ler_0_39984104W [** ] > Processing Locus CUFF.685_From_mt_0_4231054_4W [** ] > Processing Locus CUFF.687_From_mt_0_4230874_4W [** ] > Processing Locus CUFF.689_From_ler_0_40188564W [** ] > Processing Locus CUFF.691_From_hi_0_2961678_4W [** ] > Processing Locus CUFF.695_From_mt_0_4217716_4W [** ] > Processing Locus CUFF.697_From_mt_0_4229662_4W [** ] > Processing Locus CUFF.699_From_no_0_2905273_4W [** ] > Processing Locus CUFF.703_From_no_0_2885444_4W [** ] > Processing Locus CUFF.729_From_oy_0_3001818_4W [*** ] > Processing Locus CUFF.733_From_no_0_2956652_4W [*** ] > Processing Locus CUFF.737_From_ct_1_3132277_4W [*** ] > Processing Locus CUFF.749_From_oy_0_3162092_4W [*** ] > Processing Locus CUFF.749_From_oy_0_3162092_4W [*** ] > Processing Locus CUFF.755_From_mt_0_4193196_4W [*** ] > Processing Locus CUFF.763_From_rsch_4_4032034W [*** ] > Processing Locus CUFF.779_From_rsch_4_4214544W [*** ] > Processing Locus CUFF.791_From_rsch_4_4255534W [*** ] > Processing Locus CUFF.795_From_rsch_4_4297144W [*** ] > Processing Locus CUFF.801_From_sf_2_2532172_4W [**** ] > Processing Locus CUFF.805_From_sf_2_2486157_4W [**** ] > Processing Locus CUFF.817_From_sf_2_2524453_4W [**** ] > Processing Locus CUFF.819_From_tsu_0_30369454W [**** ] > Processing Locus CUFF.829_From_tsu_0_31351354W [**** ] > Processing Locus CUFF.831_From_sf_2_2687774_4W [**** ] > Processing Locus CUFF.837_From_tsu_0_32156714W [**** ] > Processing Locus CUFF.837_From_tsu_0_32156714W [**** ] > Processing Locus CUFF.843_From_rsch_4_4292194W [**** ] > Processing Locus CUFF.851_From_wil_2_29061374W [**** ] > Processing Locus CUFF.853_From_wil_2_29205294W [**** ] > Processing Locus CUFF.855_From_wil_2_29158994W [***** ] > Processing Locus CUFF.861_From_mt_0_4528444_4W [***** ] > Processing Locus CUFF.863_From_wil_2_30084614W [***** ] > Processing Locus CUFF.865_From_wil_2_28924854W [***** ] > Processing Locus CUFF.867_From_wil_2_29450954W [***** ] > Processing Locus CUFF.869_From_sf_2_2701328_4W [***** ] > Processing Locus CUFF.871_From_rsch_4_4266554W [***** ] > Processing Locus CUFF.873_From_wil_2_30505234W [***** ] > Processing Locus CUFF.875_From_wil_2_30529514W [***** ] > Processing Locus CUFF.879_From_rsch_4_4055164W [****** ] > Processing Locus CUFF.881_From_wil_2_29253234W [****** ] > Processing Locus CUFF.883_From_wil_2_30662294W [****** ] > Processing Locus CUFF.885_From_wil_2_30634734W [****** ] > Processing Locus CUFF.887_From_wil_2_30548934W [****** ] > Processing Locus CUFF.893_From_ws_0_3190679_4W [****** ] > Processing Locus CUFF.897_From_ws_0_3298283_4W [****** ] > Processing Locus CUFF.901_From_wil_2_30881514W [****** ] > Processing Locus CUFF.903_From_wil_2_30895414W [****** ] > Processing Locus CUFF.907_From_ws_0_3182508_4W [****** ] > Processing Locus CUFF.909_From_wil_2_30522734W [******* ] > Processing Locus CUFF.911_From_wil_2_30687374W [******* ] > Processing Locus CUFF.913_From_wil_2_28345534W [******* ] > Processing Locus CUFF.917_From_ws_0_3371988_4W [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_4W [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_4W [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_4W [******* ] > Processing Locus CUFF.921_From_wil_2_30774474W [******* ] > Processing Locus CUFF.925_From_ws_0_3371988_4W [******* ] > Processing Locus CUFF.935_From_ws_0_3380934_4W [******* ] > Processing Locus CUFF.941_From_wu_0_2824308_4W [******* ] > Processing Locus CUFF.943_From_zu_0_3075813_4W [******** ] > Processing Locus CUFF.945_From_wu_0_2678387_4W [******** ] > Processing Locus CUFF.947_From_wu_0_2654219_4W [******** ] > Processing Locus CUFF.949_From_wu_0_2687576_4W [******** ] > Processing Locus CUFF.951_From_wil_2_30871834W [******** ] > Processing Locus CUFF.955_From_ws_0_3340488_4W [******** ] > Processing Locus CUFF.957_From_ws_0_3381390_4W [******** ] > Processing Locus CUFF.963_From_zu_0_3092045_4W [******** ] > Processing Locus CUFF.965_From_zu_0_3238769_4W [******** ] > Processing Locus CUFF.969_From_zu_0_3190435_4W [********* ] > Processing Locus CUFF.973_From_zu_0_3242889_4W [********* ] > Processing Locus CUFF.977_From_zu_0_3255503_4W [********* ] > Processing Locus CUFF.983_From_zu_0_3243571_4W [********* ] > Processing Locus CUFF.987_From_zu_0_3118546_4W [********* ] > Processing Locus CUFF.991_From_zu_0_3277661_4W [********* ] > Processing Locus CUFF.993_From_zu_0_3082201_4W [********* ] > Processed 98 loci. [*************************] 100% > Map Properties: > Total Map Mass: 9653.69 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:27:34] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.553_From_can_0_3223655 [ ] 2% > Processing Locus CUFF.559_From_can_0_3231205 [ ] 3% > Processing Locus CUFF.561_From_can_0_3189753 [* ] 4% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 6% > Processing Locus CUFF.583_From_ct_1_3302721_ [* ] 7% > Processing Locus CUFF.589_From_edi_0_2723255 [** ] 8% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 9% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 10% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 11% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 12% > Processing Locus CUFF.609_From_hi_0_2755116_ [*** ] 13% > Processing Locus CUFF.613_From_hi_0_2773206_ [*** ] 14% > Processing Locus CUFF.619_From_edi_0_2871668 [*** ] 15% > Processing Locus CUFF.623_From_hi_0_2778596_ [**** ] 16% > Processing Locus CUFF.641_From_kn_0_3605300_ [**** ] 17% > Processing Locus CUFF.655_From_hi_0_2795398_ [**** ] 18% > Processing Locus CUFF.663_From_kn_0_3613403_ [**** ] 19% > Processing Locus CUFF.671_From_edi_0_2859720 [***** ] 20% > Processing Locus CUFF.673_From_ler_0_4224097 [***** ] 21% > Processing Locus CUFF.679_From_ler_0_3998410 [***** ] 22% > Processing Locus CUFF.685_From_mt_0_4231054_ [***** ] 23% > Processing Locus CUFF.687_From_mt_0_4230874_ [****** ] 24% > Processing Locus CUFF.689_From_ler_0_4018856 [****** ] 25% > Processing Locus CUFF.691_From_hi_0_2961678_ [****** ] 26% > Processing Locus CUFF.695_From_mt_0_4217716_ [****** ] 27% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 28% > Processing Locus CUFF.699_From_no_0_2905273_ [******* ] 29% > Processing Locus CUFF.703_From_no_0_2885444_ [******* ] 30% > Processing Locus CUFF.729_From_oy_0_3001818_ [******* ] 31% > Processing Locus CUFF.733_From_no_0_2956652_ [******** ] 32% > Processing Locus CUFF.737_From_ct_1_3132277_ [******** ] 33% > Processing Locus CUFF.749_From_oy_0_3162092_ [******** ] 34% > Processing Locus CUFF.749_From_oy_0_3162092_ [******** ] 35% > Processing Locus CUFF.755_From_mt_0_4193196_ [********* ] 36% > Processing Locus CUFF.763_From_rsch_4_403203 [********* ] 37% > Processing Locus CUFF.779_From_rsch_4_421454 [********* ] 38% > Processing Locus CUFF.791_From_rsch_4_425553 [********* ] 39% > Processing Locus CUFF.795_From_rsch_4_429714 [********** ] 40% > Processing Locus CUFF.801_From_sf_2_2532172_ [********** ] 41% > Processing Locus CUFF.805_From_sf_2_2486157_ [********** ] 42% > Processing Locus CUFF.817_From_sf_2_2524453_ [********** ] 43% > Processing Locus CUFF.819_From_tsu_0_3036945 [*********** ] 44% > Processing Locus CUFF.829_From_tsu_0_3135135 [*********** ] 45% > Processing Locus CUFF.831_From_sf_2_2687774_ [*********** ] 46% > Processing Locus CUFF.837_From_tsu_0_3215671 [*********** ] 47% > Processing Locus CUFF.837_From_tsu_0_3215671 [************ ] 48% > Processing Locus CUFF.843_From_rsch_4_429219 [************ ] 50% > Processing Locus CUFF.851_From_wil_2_2906137 [************ ] 51% > Processing Locus CUFF.853_From_wil_2_2920529 [************* ] 52% > Processing Locus CUFF.855_From_wil_2_2915899 [************* ] 53% > Processing Locus CUFF.861_From_mt_0_4528444_ [************* ] 54% > Processing Locus CUFF.863_From_wil_2_3008461 [************* ] 55% > Processing Locus CUFF.865_From_wil_2_2892485 [************** ] 56% > Processing Locus CUFF.867_From_wil_2_2945095 [************** ] 57% > Processing Locus CUFF.869_From_sf_2_2701328_ [************** ] 58% > Processing Locus CUFF.871_From_rsch_4_426655 [************** ] 59% > Processing Locus CUFF.873_From_wil_2_3050523 [*************** ] 60% > Processing Locus CUFF.875_From_wil_2_3052951 [*************** ] 61% > Processing Locus CUFF.879_From_rsch_4_405516 [*************** ] 62% > Processing Locus CUFF.881_From_wil_2_2925323 [*************** ] 63% > Processing Locus CUFF.883_From_wil_2_3066229 [**************** ] 64% > Processing Locus CUFF.885_From_wil_2_3063473 [**************** ] 65% > Processing Locus CUFF.887_From_wil_2_3054893 [**************** ] 66% > Processing Locus CUFF.893_From_ws_0_3190679_ [**************** ] 67% > Processing Locus CUFF.897_From_ws_0_3298283_ [***************** ] 68% > Processing Locus CUFF.901_From_wil_2_3088151 [***************** ] 69% > Processing Locus CUFF.903_From_wil_2_3089541 [***************** ] 70% > Processing Locus CUFF.907_From_ws_0_3182508_ [***************** ] 71% > Processing Locus CUFF.909_From_wil_2_3052273 [****************** ] 72% > Processing Locus CUFF.911_From_wil_2_3068737 [****************** ] 73% > Processing Locus CUFF.913_From_wil_2_2834553 [****************** ] 74% > Processing Locus CUFF.917_From_ws_0_3371988_ [****************** ] 75% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 76% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 77% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 78% > Processing Locus CUFF.921_From_wil_2_3077447 [******************* ] 79% > Processing Locus CUFF.925_From_ws_0_3371988_ [******************** ] 80% > Processing Locus CUFF.935_From_ws_0_3380934_ [******************** ] 81% > Processing Locus CUFF.941_From_wu_0_2824308_ [******************** ] 82% > Processing Locus CUFF.943_From_zu_0_3075813_ [******************** ] 83% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************* ] 84% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************* ] 85% > Processing Locus CUFF.949_From_wu_0_2687576_ [********************* ] 86% > Processing Locus CUFF.951_From_wil_2_3087183 [********************* ] 87% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************** ] 88% > Processing Locus CUFF.957_From_ws_0_3381390_ [********************** ] 89% > Processing Locus CUFF.963_From_zu_0_3092045_ [********************** ] 90% > Processing Locus CUFF.965_From_zu_0_3238769_ [********************** ] 91% > Processing Locus CUFF.969_From_zu_0_3190435_ [*********************** ] 92% > Processing Locus CUFF.973_From_zu_0_3242889_ [*********************** ] 93% > Processing Locus CUFF.977_From_zu_0_3255503_ [*********************** ] 94% > Processing Locus CUFF.983_From_zu_0_3243571_ [*********************** ] 95% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 96% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 97% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 98% > Processed 98 loci. [*************************] 100% [16:27:34] Loading reference annotation and sequence [16:27:34] Learning bias parameters. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.553_From_can_0_3223655 [ ] 2% > Processing Locus CUFF.559_From_can_0_3231205 [ ] 3% > Processing Locus CUFF.561_From_can_0_3189753 [* ] 4% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 7% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 8% > Processing Locus CUFF.613_From_hi_0_2773206_ [** ] 9% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 10% > Processing Locus CUFF.641_From_kn_0_3605300_ [** ] 11% > Processing Locus CUFF.655_From_hi_0_2795398_ [*** ] 12% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 13% > Processing Locus CUFF.671_From_edi_0_2859720 [*** ] 14% > Processing Locus CUFF.673_From_ler_0_4224097 [*** ] 15% > Processing Locus CUFF.679_From_ler_0_3998410 [**** ] 16% > Processing Locus CUFF.685_From_mt_0_4231054_ [**** ] 17% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 18% > Processing Locus CUFF.691_From_hi_0_2961678_ [**** ] 19% > Processing Locus CUFF.695_From_mt_0_4217716_ [***** ] 20% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 21% > Processing Locus CUFF.699_From_no_0_2905273_ [***** ] 22% > Processing Locus CUFF.703_From_no_0_2885444_ [***** ] 23% > Processing Locus CUFF.729_From_oy_0_3001818_ [****** ] 24% > Processing Locus CUFF.733_From_no_0_2956652_ [****** ] 25% > Processing Locus CUFF.737_From_ct_1_3132277_ [****** ] 26% > Processing Locus CUFF.755_From_mt_0_4193196_ [****** ] 27% > Processing Locus CUFF.763_From_rsch_4_403203 [******* ] 28% > Processing Locus CUFF.779_From_rsch_4_421454 [******* ] 29% > Processing Locus CUFF.791_From_rsch_4_425553 [******* ] 30% > Processing Locus CUFF.795_From_rsch_4_429714 [******* ] 31% > Processing Locus CUFF.801_From_sf_2_2532172_ [******** ] 32% > Processing Locus CUFF.805_From_sf_2_2486157_ [******** ] 33% > Processing Locus CUFF.817_From_sf_2_2524453_ [******** ] 34% > Processing Locus CUFF.831_From_sf_2_2687774_ [******** ] 35% > Processing Locus CUFF.843_From_rsch_4_429219 [********* ] 36% > Processing Locus CUFF.851_From_wil_2_2906137 [********* ] 37% > Processing Locus CUFF.853_From_wil_2_2920529 [********* ] 38% > Processing Locus CUFF.861_From_mt_0_4528444_ [********* ] 39% > Processing Locus CUFF.863_From_wil_2_3008461 [********** ] 40% > Processing Locus CUFF.867_From_wil_2_2945095 [********** ] 41% > Processing Locus CUFF.869_From_sf_2_2701328_ [********** ] 42% > Processing Locus CUFF.871_From_rsch_4_426655 [********** ] 43% > Processing Locus CUFF.873_From_wil_2_3050523 [*********** ] 44% > Processing Locus CUFF.875_From_wil_2_3052951 [*********** ] 45% > Processing Locus CUFF.879_From_rsch_4_405516 [*********** ] 46% > Processing Locus CUFF.881_From_wil_2_2925323 [*********** ] 47% > Processing Locus CUFF.883_From_wil_2_3066229 [************ ] 48% > Processing Locus CUFF.885_From_wil_2_3063473 [************ ] 50% > Processing Locus CUFF.887_From_wil_2_3054893 [************ ] 51% > Processing Locus CUFF.897_From_ws_0_3298283_ [************* ] 52% > Processing Locus CUFF.901_From_wil_2_3088151 [************* ] 53% > Processing Locus CUFF.903_From_wil_2_3089541 [************* ] 54% > Processing Locus CUFF.907_From_ws_0_3182508_ [************* ] 55% > Processing Locus CUFF.909_From_wil_2_3052273 [************** ] 56% > Processing Locus CUFF.911_From_wil_2_3068737 [************** ] 57% > Processing Locus CUFF.913_From_wil_2_2834553 [************** ] 58% > Processing Locus CUFF.921_From_wil_2_3077447 [************** ] 59% > Processing Locus CUFF.925_From_ws_0_3371988_ [*************** ] 60% > Processing Locus CUFF.935_From_ws_0_3380934_ [*************** ] 61% > Processing Locus CUFF.945_From_wu_0_2678387_ [*************** ] 62% > Processing Locus CUFF.947_From_wu_0_2654219_ [*************** ] 63% > Processing Locus CUFF.949_From_wu_0_2687576_ [**************** ] 64% > Processing Locus CUFF.951_From_wil_2_3087183 [**************** ] 65% > Processing Locus CUFF.955_From_ws_0_3340488_ [**************** ] 66% > Processing Locus CUFF.957_From_ws_0_3381390_ [**************** ] 67% > Processing Locus CUFF.969_From_zu_0_3190435_ [***************** ] 68% > Processing Locus CUFF.973_From_zu_0_3242889_ [***************** ] 69% > Processing Locus CUFF.977_From_zu_0_3255503_ [***************** ] 70% > Processing Locus CUFF.983_From_zu_0_3243571_ [***************** ] 71% > Processing Locus CUFF.987_From_zu_0_3118546_ [****************** ] 72% > Processing Locus CUFF.991_From_zu_0_3277661_ [****************** ] 73% > Processing Locus CUFF.993_From_zu_0_3082201_ [****************** ] 74% > Processed 74 loci. [*************************] 100% [16:27:34] Assembling transcripts and estimating abundances. > Processing Locus CUFF.523_From_bur_0_1804399 [ ] 0% > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 1% > Processing Locus CUFF.553_From_can_0_3223655 [ ] 2% > Processing Locus CUFF.559_From_can_0_3231205 [ ] 3% > Processing Locus CUFF.561_From_can_0_3189753 [* ] 4% > Processing Locus CUFF.571_From_can_0_3076940 [* ] 5% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 6% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 7% > Processing Locus CUFF.595_From_ct_1_3302721_ [** ] 8% > Processing Locus CUFF.613_From_hi_0_2773206_ [** ] 9% > Processing Locus CUFF.619_From_edi_0_2871668 [** ] 10% > Processing Locus CUFF.641_From_kn_0_3605300_ [** ] 11% > Processing Locus CUFF.655_From_hi_0_2795398_ [*** ] 12% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 13% > Processing Locus CUFF.671_From_edi_0_2859720 [*** ] 14% > Processing Locus CUFF.673_From_ler_0_4224097 [*** ] 15% > Processing Locus CUFF.679_From_ler_0_3998410 [**** ] 16% > Processing Locus CUFF.685_From_mt_0_4231054_ [**** ] 17% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 18% > Processing Locus CUFF.691_From_hi_0_2961678_ [**** ] 19% > Processing Locus CUFF.695_From_mt_0_4217716_ [***** ] 20% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 21% > Processing Locus CUFF.699_From_no_0_2905273_ [***** ] 22% > Processing Locus CUFF.703_From_no_0_2885444_ [***** ] 23% > Processing Locus CUFF.729_From_oy_0_3001818_ [****** ] 24% > Processing Locus CUFF.733_From_no_0_2956652_ [****** ] 25% > Processing Locus CUFF.737_From_ct_1_3132277_ [****** ] 26% > Processing Locus CUFF.755_From_mt_0_4193196_ [****** ] 27% > Processing Locus CUFF.763_From_rsch_4_403203 [******* ] 28% > Processing Locus CUFF.779_From_rsch_4_421454 [******* ] 29% > Processing Locus CUFF.791_From_rsch_4_425553 [******* ] 30% > Processing Locus CUFF.795_From_rsch_4_429714 [******* ] 31% > Processing Locus CUFF.801_From_sf_2_2532172_ [******** ] 32% > Processing Locus CUFF.805_From_sf_2_2486157_ [******** ] 33% > Processing Locus CUFF.817_From_sf_2_2524453_ [******** ] 34% > Processing Locus CUFF.831_From_sf_2_2687774_ [******** ] 35% > Processing Locus CUFF.843_From_rsch_4_429219 [********* ] 36% > Processing Locus CUFF.851_From_wil_2_2906137 [********* ] 37% > Processing Locus CUFF.853_From_wil_2_2920529 [********* ] 38% > Processing Locus CUFF.861_From_mt_0_4528444_ [********* ] 39% > Processing Locus CUFF.863_From_wil_2_3008461 [********** ] 40% > Processing Locus CUFF.867_From_wil_2_2945095 [********** ] 41% > Processing Locus CUFF.869_From_sf_2_2701328_ [********** ] 42% > Processing Locus CUFF.871_From_rsch_4_426655 [********** ] 43% > Processing Locus CUFF.873_From_wil_2_3050523 [*********** ] 44% > Processing Locus CUFF.875_From_wil_2_3052951 [*********** ] 45% > Processing Locus CUFF.879_From_rsch_4_405516 [*********** ] 46% > Processing Locus CUFF.881_From_wil_2_2925323 [*********** ] 47% > Processing Locus CUFF.883_From_wil_2_3066229 [************ ] 48% > Processing Locus CUFF.885_From_wil_2_3063473 [************ ] 50% > Processing Locus CUFF.887_From_wil_2_3054893 [************ ] 51% > Processing Locus CUFF.897_From_ws_0_3298283_ [************* ] 52% > Processing Locus CUFF.901_From_wil_2_3088151 [************* ] 53% > Processing Locus CUFF.903_From_wil_2_3089541 [************* ] 54% > Processing Locus CUFF.907_From_ws_0_3182508_ [************* ] 55% > Processing Locus CUFF.909_From_wil_2_3052273 [************** ] 56% > Processing Locus CUFF.911_From_wil_2_3068737 [************** ] 57% > Processing Locus CUFF.913_From_wil_2_2834553 [************** ] 58% > Processing Locus CUFF.921_From_wil_2_3077447 [************** ] 59% > Processing Locus CUFF.925_From_ws_0_3371988_ [*************** ] 60% > Processing Locus CUFF.935_From_ws_0_3380934_ [*************** ] 61% > Processing Locus CUFF.945_From_wu_0_2678387_ [*************** ] 62% > Processing Locus CUFF.947_From_wu_0_2654219_ [*************** ] 63% > Processing Locus CUFF.949_From_wu_0_2687576_ [**************** ] 64% > Processing Locus CUFF.951_From_wil_2_3087183 [**************** ] 65% > Processing Locus CUFF.955_From_ws_0_3340488_ [**************** ] 66% > Processing Locus CUFF.957_From_ws_0_3381390_ [**************** ] 67% > Processing Locus CUFF.969_From_zu_0_3190435_ [***************** ] 68% > Processing Locus CUFF.973_From_zu_0_3242889_ [***************** ] 69% > Processing Locus CUFF.977_From_zu_0_3255503_ [***************** ] 70% > Processing Locus CUFF.983_From_zu_0_3243571_ [***************** ] 71% > Processing Locus CUFF.987_From_zu_0_3118546_ [****************** ] 72% > Processing Locus CUFF.991_From_zu_0_3277661_ [****************** ] 73% > Processing Locus CUFF.993_From_zu_0_3082201_ [****************** ] 74% > Processed 74 loci. [*************************] 100% [Mon Apr 4 16:27:42 2011] Retrieving sequences for splices [Mon Apr 4 16:27:42 2011] Indexing splices [Mon Apr 4 16:27:42 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:45 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:47 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:27:49 2011] Joining segment hits [Mon Apr 4 16:27:52 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:26 elapsed] cufflinks -p 4 -o ./Wu_0 -r ngene.fa ./Wu_0/accepted_hits.bam [16:27:58] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.531_From_bur_0_1868430xa [ ] > Processing Locus CUFF.555_From_can_0_3217045xa [ ] > Processing Locus CUFF.561_From_can_0_3189753xa [ ] > Processing Locus CUFF.571_From_can_0_3076940xa [ ] > Processing Locus CUFF.575_From_ct_1_3082021_xa [ ] > Processing Locus CUFF.583_From_ct_1_3302721_xa [ ] > Processing Locus CUFF.585_From_ct_1_3247037_xa [ ] > Processing Locus CUFF.585_From_ct_1_3247037_xa [ ] > Processing Locus CUFF.593_From_can_0_3270131xa [ ] > Processing Locus CUFF.593_From_can_0_3270131xa [ ] > Processing Locus CUFF.593_From_can_0_3270131xa [ ] > Processing Locus CUFF.595_From_ct_1_3302721_xa [ ] > Processing Locus CUFF.609_From_hi_0_2755116_xa [ ] > Processing Locus CUFF.623_From_hi_0_2778596_xa [* ] > Processing Locus CUFF.627_From_edi_0_2889434xa [* ] > Processing Locus CUFF.629_From_kn_0_3594465_xa [* ] > Processing Locus CUFF.635_From_ct_1_3241157_xa [* ] > Processing Locus CUFF.637_From_kn_0_3626969_xa [* ] > Processing Locus CUFF.639_From_hi_0_2916184_xa [* ] > Processing Locus CUFF.649_From_kn_0_3617271_xa [* ] > Processing Locus CUFF.663_From_kn_0_3613403_xa [* ] > Processing Locus CUFF.669_From_ler_0_4225073xa [* ] > Processing Locus CUFF.671_From_edi_0_2859720xa [** ] > Processing Locus CUFF.679_From_ler_0_3998410xa [** ] > Processing Locus CUFF.683_From_ler_0_4165287xa [** ] > Processing Locus CUFF.685_From_mt_0_4231054_xa [** ] > Processing Locus CUFF.689_From_ler_0_4018856xa [** ] > Processing Locus CUFF.691_From_hi_0_2961678_xa [** ] > Processing Locus CUFF.695_From_mt_0_4217716_xa [** ] > Processing Locus CUFF.697_From_mt_0_4229662_xa [** ] > Processing Locus CUFF.699_From_no_0_2905273_xa [** ] > Processing Locus CUFF.701_From_no_0_2951521_xa [** ] > Processing Locus CUFF.703_From_no_0_2885444_xa [*** ] > Processing Locus CUFF.707_From_no_0_2959683_xa [*** ] > Processing Locus CUFF.715_From_oy_0_3098144_xa [*** ] > Processing Locus CUFF.729_From_oy_0_3001818_xa [*** ] > Processing Locus CUFF.733_From_no_0_2956652_xa [*** ] > Processing Locus CUFF.737_From_ct_1_3132277_xa [*** ] > Processing Locus CUFF.739_From_po_0_3340213_xa [*** ] > Processing Locus CUFF.751_From_rsch_4_403485xa [*** ] > Processing Locus CUFF.755_From_mt_0_4193196_xa [*** ] > Processing Locus CUFF.757_From_po_0_3372769_xa [**** ] > Processing Locus CUFF.763_From_rsch_4_403203xa [**** ] > Processing Locus CUFF.767_From_rsch_4_411814xa [**** ] > Processing Locus CUFF.775_From_rsch_4_409124xa [**** ] > Processing Locus CUFF.783_From_oy_0_2965192_xa [**** ] > Processing Locus CUFF.785_From_no_0_3128142_xa [**** ] > Processing Locus CUFF.785_From_no_0_3128142_xa [**** ] > Processing Locus CUFF.799_From_sf_2_2662232_xa [**** ] > Processing Locus CUFF.801_From_sf_2_2532172_xa [**** ] > Processing Locus CUFF.805_From_sf_2_2486157_xa [**** ] > Processing Locus CUFF.811_From_sf_2_2459023_xa [**** ] > Processing Locus CUFF.817_From_sf_2_2524453_xa [***** ] > Processing Locus CUFF.819_From_tsu_0_3036945xa [***** ] > Processing Locus CUFF.831_From_sf_2_2687774_xa [***** ] > Processing Locus CUFF.839_From_sf_2_2680171_xa [***** ] > Processing Locus CUFF.855_From_wil_2_2915899xa [***** ] > Processing Locus CUFF.861_From_mt_0_4528444_xa [***** ] > Processing Locus CUFF.873_From_wil_2_3050523xa [***** ] > Processing Locus CUFF.877_From_sf_2_2687786_xa [***** ] > Processing Locus CUFF.879_From_rsch_4_405516xa [***** ] > Processing Locus CUFF.881_From_wil_2_2925323xa [****** ] > Processing Locus CUFF.887_From_wil_2_3054893xa [****** ] > Processing Locus CUFF.891_From_wil_2_3079625xa [****** ] > Processing Locus CUFF.907_From_ws_0_3182508_xa [****** ] > Processing Locus CUFF.909_From_wil_2_3052273xa [****** ] > Processing Locus CUFF.913_From_wil_2_2834553xa [****** ] > Processing Locus CUFF.917_From_ws_0_3371988_xa [****** ] > Processing Locus CUFF.919_From_ws_0_3347582_xa [****** ] > Processing Locus CUFF.919_From_ws_0_3347582_xa [****** ] > Processing Locus CUFF.925_From_ws_0_3371988_xa [****** ] > Processing Locus CUFF.927_From_wu_0_2655481_xa [****** ] > Processing Locus CUFF.931_From_wu_0_2679395_xa [******* ] > Processing Locus CUFF.935_From_ws_0_3380934_xa [******* ] > Processing Locus CUFF.941_From_wu_0_2824308_xa [******* ] > Processing Locus CUFF.945_From_wu_0_2678387_xa [******* ] > Processing Locus CUFF.947_From_wu_0_2654219_xa [******* ] > Processing Locus CUFF.949_From_wu_0_2687576_xa [******* ] > Processing Locus CUFF.955_From_ws_0_3340488_xa [******* ] > Processing Locus CUFF.957_From_ws_0_3381390_xa [******* ] > Processing Locus CUFF.963_From_zu_0_3092045_xa [******* ] > Processing Locus CUFF.965_From_zu_0_3238769_xa [******** ] > Processing Locus CUFF.967_From_zu_0_3022629_xa [******** ] > Processing Locus CUFF.969_From_zu_0_3190435_xa [******** ] > Processing Locus CUFF.983_From_zu_0_3243571_xa [******** ] > Processing Locus CUFF.983_From_zu_0_3243571_xa [******** ] > Processing Locus CUFF.987_From_zu_0_3118546_xa [******** ] > Processing Locus CUFF.993_From_zu_0_3082201_xa [******** ] > Processed 88 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5366.90 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:27:58] Assembling transcripts and estimating abundances. > Processing Locus CUFF.531_From_bur_0_1868430 [ ] 0% > Processing Locus CUFF.555_From_can_0_3217045 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.583_From_ct_1_3302721_ [* ] 5% > Processing Locus CUFF.585_From_ct_1_3247037_ [* ] 6% > Processing Locus CUFF.585_From_ct_1_3247037_ [* ] 7% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 9% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 10% > Processing Locus CUFF.593_From_can_0_3270131 [** ] 11% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 12% > Processing Locus CUFF.609_From_hi_0_2755116_ [*** ] 13% > Processing Locus CUFF.623_From_hi_0_2778596_ [*** ] 14% > Processing Locus CUFF.627_From_edi_0_2889434 [*** ] 15% > Processing Locus CUFF.629_From_kn_0_3594465_ [**** ] 17% > Processing Locus CUFF.635_From_ct_1_3241157_ [**** ] 18% > Processing Locus CUFF.637_From_kn_0_3626969_ [**** ] 19% > Processing Locus CUFF.639_From_hi_0_2916184_ [***** ] 20% > Processing Locus CUFF.649_From_kn_0_3617271_ [***** ] 21% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 22% > Processing Locus CUFF.669_From_ler_0_4225073 [***** ] 23% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 26% > Processing Locus CUFF.683_From_ler_0_4165287 [****** ] 27% > Processing Locus CUFF.685_From_mt_0_4231054_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.691_From_hi_0_2961678_ [******* ] 30% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 31% > Processing Locus CUFF.697_From_mt_0_4229662_ [******** ] 32% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 34% > Processing Locus CUFF.701_From_no_0_2951521_ [******** ] 35% > Processing Locus CUFF.703_From_no_0_2885444_ [********* ] 36% > Processing Locus CUFF.707_From_no_0_2959683_ [********* ] 37% > Processing Locus CUFF.715_From_oy_0_3098144_ [********* ] 38% > Processing Locus CUFF.729_From_oy_0_3001818_ [********* ] 39% > Processing Locus CUFF.733_From_no_0_2956652_ [********** ] 40% > Processing Locus CUFF.737_From_ct_1_3132277_ [********** ] 42% > Processing Locus CUFF.739_From_po_0_3340213_ [********** ] 43% > Processing Locus CUFF.751_From_rsch_4_403485 [*********** ] 44% > Processing Locus CUFF.755_From_mt_0_4193196_ [*********** ] 45% > Processing Locus CUFF.757_From_po_0_3372769_ [*********** ] 46% > Processing Locus CUFF.763_From_rsch_4_403203 [*********** ] 47% > Processing Locus CUFF.767_From_rsch_4_411814 [************ ] 48% > Processing Locus CUFF.775_From_rsch_4_409124 [************ ] 50% > Processing Locus CUFF.783_From_oy_0_2965192_ [************ ] 51% > Processing Locus CUFF.785_From_no_0_3128142_ [************* ] 52% > Processing Locus CUFF.785_From_no_0_3128142_ [************* ] 53% > Processing Locus CUFF.799_From_sf_2_2662232_ [************* ] 54% > Processing Locus CUFF.801_From_sf_2_2532172_ [************* ] 55% > Processing Locus CUFF.805_From_sf_2_2486157_ [************** ] 56% > Processing Locus CUFF.811_From_sf_2_2459023_ [************** ] 57% > Processing Locus CUFF.817_From_sf_2_2524453_ [************** ] 59% > Processing Locus CUFF.819_From_tsu_0_3036945 [*************** ] 60% > Processing Locus CUFF.831_From_sf_2_2687774_ [*************** ] 61% > Processing Locus CUFF.839_From_sf_2_2680171_ [*************** ] 62% > Processing Locus CUFF.855_From_wil_2_2915899 [*************** ] 63% > Processing Locus CUFF.861_From_mt_0_4528444_ [**************** ] 64% > Processing Locus CUFF.873_From_wil_2_3050523 [**************** ] 65% > Processing Locus CUFF.877_From_sf_2_2687786_ [**************** ] 67% > Processing Locus CUFF.879_From_rsch_4_405516 [***************** ] 68% > Processing Locus CUFF.881_From_wil_2_2925323 [***************** ] 69% > Processing Locus CUFF.887_From_wil_2_3054893 [***************** ] 70% > Processing Locus CUFF.891_From_wil_2_3079625 [***************** ] 71% > Processing Locus CUFF.907_From_ws_0_3182508_ [****************** ] 72% > Processing Locus CUFF.909_From_wil_2_3052273 [****************** ] 73% > Processing Locus CUFF.913_From_wil_2_2834553 [****************** ] 75% > Processing Locus CUFF.917_From_ws_0_3371988_ [******************* ] 76% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 77% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************* ] 78% > Processing Locus CUFF.925_From_ws_0_3371988_ [******************* ] 79% > Processing Locus CUFF.927_From_wu_0_2655481_ [******************** ] 80% > Processing Locus CUFF.931_From_wu_0_2679395_ [******************** ] 81% > Processing Locus CUFF.935_From_ws_0_3380934_ [******************** ] 82% > Processing Locus CUFF.941_From_wu_0_2824308_ [********************* ] 84% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************* ] 85% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************* ] 86% > Processing Locus CUFF.949_From_wu_0_2687576_ [********************* ] 87% > Processing Locus CUFF.955_From_ws_0_3340488_ [********************** ] 88% > Processing Locus CUFF.957_From_ws_0_3381390_ [********************** ] 89% > Processing Locus CUFF.963_From_zu_0_3092045_ [********************** ] 90% > Processing Locus CUFF.965_From_zu_0_3238769_ [*********************** ] 92% > Processing Locus CUFF.967_From_zu_0_3022629_ [*********************** ] 93% > Processing Locus CUFF.969_From_zu_0_3190435_ [*********************** ] 94% > Processing Locus CUFF.983_From_zu_0_3243571_ [*********************** ] 95% > Processing Locus CUFF.983_From_zu_0_3243571_ [************************ ] 96% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 97% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 98% > Processed 88 loci. [*************************] 100% [16:27:58] Loading reference annotation and sequence [16:27:58] Learning bias parameters. > Processing Locus CUFF.531_From_bur_0_1868430 [ ] 0% > Processing Locus CUFF.555_From_can_0_3217045 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 5% > Processing Locus CUFF.623_From_hi_0_2778596_ [* ] 6% > Processing Locus CUFF.627_From_edi_0_2889434 [* ] 7% > Processing Locus CUFF.629_From_kn_0_3594465_ [** ] 9% > Processing Locus CUFF.635_From_ct_1_3241157_ [** ] 10% > Processing Locus CUFF.637_From_kn_0_3626969_ [** ] 11% > Processing Locus CUFF.639_From_hi_0_2916184_ [*** ] 12% > Processing Locus CUFF.649_From_kn_0_3617271_ [*** ] 13% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 14% > Processing Locus CUFF.669_From_ler_0_4225073 [*** ] 15% > Processing Locus CUFF.671_From_edi_0_2859720 [**** ] 17% > Processing Locus CUFF.679_From_ler_0_3998410 [**** ] 18% > Processing Locus CUFF.685_From_mt_0_4231054_ [**** ] 19% > Processing Locus CUFF.689_From_ler_0_4018856 [***** ] 20% > Processing Locus CUFF.691_From_hi_0_2961678_ [***** ] 21% > Processing Locus CUFF.695_From_mt_0_4217716_ [***** ] 22% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 23% > Processing Locus CUFF.699_From_no_0_2905273_ [****** ] 25% > Processing Locus CUFF.701_From_no_0_2951521_ [****** ] 26% > Processing Locus CUFF.703_From_no_0_2885444_ [****** ] 27% > Processing Locus CUFF.707_From_no_0_2959683_ [******* ] 28% > Processing Locus CUFF.715_From_oy_0_3098144_ [******* ] 29% > Processing Locus CUFF.729_From_oy_0_3001818_ [******* ] 30% > Processing Locus CUFF.733_From_no_0_2956652_ [******* ] 31% > Processing Locus CUFF.737_From_ct_1_3132277_ [******** ] 32% > Processing Locus CUFF.751_From_rsch_4_403485 [******** ] 34% > Processing Locus CUFF.755_From_mt_0_4193196_ [******** ] 35% > Processing Locus CUFF.757_From_po_0_3372769_ [********* ] 36% > Processing Locus CUFF.763_From_rsch_4_403203 [********* ] 37% > Processing Locus CUFF.767_From_rsch_4_411814 [********* ] 38% > Processing Locus CUFF.775_From_rsch_4_409124 [********* ] 39% > Processing Locus CUFF.785_From_no_0_3128142_ [********** ] 40% > Processing Locus CUFF.799_From_sf_2_2662232_ [********** ] 42% > Processing Locus CUFF.801_From_sf_2_2532172_ [********** ] 43% > Processing Locus CUFF.805_From_sf_2_2486157_ [*********** ] 44% > Processing Locus CUFF.811_From_sf_2_2459023_ [*********** ] 45% > Processing Locus CUFF.817_From_sf_2_2524453_ [*********** ] 46% > Processing Locus CUFF.831_From_sf_2_2687774_ [*********** ] 47% > Processing Locus CUFF.839_From_sf_2_2680171_ [************ ] 48% > Processing Locus CUFF.861_From_mt_0_4528444_ [************ ] 50% > Processing Locus CUFF.873_From_wil_2_3050523 [************ ] 51% > Processing Locus CUFF.877_From_sf_2_2687786_ [************* ] 52% > Processing Locus CUFF.879_From_rsch_4_405516 [************* ] 53% > Processing Locus CUFF.881_From_wil_2_2925323 [************* ] 54% > Processing Locus CUFF.887_From_wil_2_3054893 [************* ] 55% > Processing Locus CUFF.907_From_ws_0_3182508_ [************** ] 56% > Processing Locus CUFF.909_From_wil_2_3052273 [************** ] 57% > Processing Locus CUFF.919_From_ws_0_3347582_ [************** ] 59% > Processing Locus CUFF.919_From_ws_0_3347582_ [*************** ] 60% > Processing Locus CUFF.925_From_ws_0_3371988_ [*************** ] 61% > Processing Locus CUFF.927_From_wu_0_2655481_ [*************** ] 62% > Processing Locus CUFF.931_From_wu_0_2679395_ [*************** ] 63% > Processing Locus CUFF.935_From_ws_0_3380934_ [**************** ] 64% > Processing Locus CUFF.941_From_wu_0_2824308_ [**************** ] 65% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 67% > Processing Locus CUFF.947_From_wu_0_2654219_ [***************** ] 68% > Processing Locus CUFF.949_From_wu_0_2687576_ [***************** ] 69% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 70% > Processing Locus CUFF.957_From_ws_0_3381390_ [***************** ] 71% > Processing Locus CUFF.963_From_zu_0_3092045_ [****************** ] 72% > Processing Locus CUFF.967_From_zu_0_3022629_ [****************** ] 73% > Processing Locus CUFF.969_From_zu_0_3190435_ [****************** ] 75% > Processing Locus CUFF.983_From_zu_0_3243571_ [******************* ] 76% > Processing Locus CUFF.987_From_zu_0_3118546_ [******************* ] 77% > Processing Locus CUFF.993_From_zu_0_3082201_ [******************* ] 78% > Processed 70 loci. [*************************] 100% [16:27:58] Assembling transcripts and estimating abundances. > Processing Locus CUFF.531_From_bur_0_1868430 [ ] 0% > Processing Locus CUFF.555_From_can_0_3217045 [ ] 1% > Processing Locus CUFF.561_From_can_0_3189753 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 5% > Processing Locus CUFF.623_From_hi_0_2778596_ [* ] 6% > Processing Locus CUFF.627_From_edi_0_2889434 [* ] 7% > Processing Locus CUFF.629_From_kn_0_3594465_ [** ] 9% > Processing Locus CUFF.635_From_ct_1_3241157_ [** ] 10% > Processing Locus CUFF.637_From_kn_0_3626969_ [** ] 11% > Processing Locus CUFF.639_From_hi_0_2916184_ [*** ] 12% > Processing Locus CUFF.649_From_kn_0_3617271_ [*** ] 13% > Processing Locus CUFF.663_From_kn_0_3613403_ [*** ] 14% > Processing Locus CUFF.669_From_ler_0_4225073 [*** ] 15% > Processing Locus CUFF.671_From_edi_0_2859720 [**** ] 17% > Processing Locus CUFF.679_From_ler_0_3998410 [**** ] 18% > Processing Locus CUFF.685_From_mt_0_4231054_ [**** ] 19% > Processing Locus CUFF.689_From_ler_0_4018856 [***** ] 20% > Processing Locus CUFF.691_From_hi_0_2961678_ [***** ] 21% > Processing Locus CUFF.695_From_mt_0_4217716_ [***** ] 22% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 23% > Processing Locus CUFF.699_From_no_0_2905273_ [****** ] 25% > Processing Locus CUFF.701_From_no_0_2951521_ [****** ] 26% > Processing Locus CUFF.703_From_no_0_2885444_ [****** ] 27% > Processing Locus CUFF.707_From_no_0_2959683_ [******* ] 28% > Processing Locus CUFF.715_From_oy_0_3098144_ [******* ] 29% > Processing Locus CUFF.729_From_oy_0_3001818_ [******* ] 30% > Processing Locus CUFF.733_From_no_0_2956652_ [******* ] 31% > Processing Locus CUFF.737_From_ct_1_3132277_ [******** ] 32% > Processing Locus CUFF.751_From_rsch_4_403485 [******** ] 34% > Processing Locus CUFF.755_From_mt_0_4193196_ [******** ] 35% > Processing Locus CUFF.757_From_po_0_3372769_ [********* ] 36% > Processing Locus CUFF.763_From_rsch_4_403203 [********* ] 37% > Processing Locus CUFF.767_From_rsch_4_411814 [********* ] 38% > Processing Locus CUFF.775_From_rsch_4_409124 [********* ] 39% > Processing Locus CUFF.785_From_no_0_3128142_ [********** ] 40% > Processing Locus CUFF.799_From_sf_2_2662232_ [********** ] 42% > Processing Locus CUFF.801_From_sf_2_2532172_ [********** ] 43% > Processing Locus CUFF.805_From_sf_2_2486157_ [*********** ] 44% > Processing Locus CUFF.811_From_sf_2_2459023_ [*********** ] 45% > Processing Locus CUFF.817_From_sf_2_2524453_ [*********** ] 46% > Processing Locus CUFF.831_From_sf_2_2687774_ [*********** ] 47% > Processing Locus CUFF.839_From_sf_2_2680171_ [************ ] 48% > Processing Locus CUFF.861_From_mt_0_4528444_ [************ ] 50% > Processing Locus CUFF.873_From_wil_2_3050523 [************ ] 51% > Processing Locus CUFF.877_From_sf_2_2687786_ [************* ] 52% > Processing Locus CUFF.879_From_rsch_4_405516 [************* ] 53% > Processing Locus CUFF.881_From_wil_2_2925323 [************* ] 54% > Processing Locus CUFF.887_From_wil_2_3054893 [************* ] 55% > Processing Locus CUFF.907_From_ws_0_3182508_ [************** ] 56% > Processing Locus CUFF.909_From_wil_2_3052273 [************** ] 57% > Processing Locus CUFF.919_From_ws_0_3347582_ [************** ] 59% > Processing Locus CUFF.919_From_ws_0_3347582_ [*************** ] 60% > Processing Locus CUFF.925_From_ws_0_3371988_ [*************** ] 61% > Processing Locus CUFF.927_From_wu_0_2655481_ [*************** ] 62% > Processing Locus CUFF.931_From_wu_0_2679395_ [*************** ] 63% > Processing Locus CUFF.935_From_ws_0_3380934_ [**************** ] 64% > Processing Locus CUFF.941_From_wu_0_2824308_ [**************** ] 65% > Processing Locus CUFF.945_From_wu_0_2678387_ [**************** ] 67% > Processing Locus CUFF.947_From_wu_0_2654219_ [***************** ] 68% > Processing Locus CUFF.949_From_wu_0_2687576_ [***************** ] 69% > Processing Locus CUFF.955_From_ws_0_3340488_ [***************** ] 70% > Processing Locus CUFF.957_From_ws_0_3381390_ [***************** ] 71% > Processing Locus CUFF.963_From_zu_0_3092045_ [****************** ] 72% > Processing Locus CUFF.967_From_zu_0_3022629_ [****************** ] 73% > Processing Locus CUFF.969_From_zu_0_3190435_ [****************** ] 75% > Processing Locus CUFF.983_From_zu_0_3243571_ [******************* ] 76% > Processing Locus CUFF.987_From_zu_0_3118546_ [******************* ] 77% > Processing Locus CUFF.993_From_zu_0_3082201_ [******************* ] 78% > Processed 70 loci. [*************************] 100% file: /data/arabidopsis/xiang/magic_founder/Zu_0_R1/R39_L5_Zu_0_sdlg_R1_nss_barcode_GTA.unmap_1.fq /data/arabidopsis/xiang/magic_founder/Zu_0_R2/R39_L6_Zu_0_sdlg_R2_nss_barcode_GTA.unmap_1.fq $RNAGI/rnagi.sh -o ./Zu_0 -n ngene.fa Zu_0.Tongene.merge.fq reference: ngene.fa tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Zu_0 ngene.fa ./Zu_0/Zu_0.Tongene.merge.flt_1.fq [Mon Apr 4 16:28:20 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 16:28:20 2011] Preparing output location ./Zu_0// [Mon Apr 4 16:28:20 2011] Checking for Bowtie index files [Mon Apr 4 16:28:20 2011] Checking for reference FASTA file Warning: Could not find FASTA file ngene.fa.fa [Mon Apr 4 16:28:20 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 16:28:20 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 16:28:20 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 16:28:20 2011] Checking reads min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 16:28:36 2011] Mapping reads against ngene.fa with Bowtie [Mon Apr 4 16:28:41 2011] Joining segment hits [Mon Apr 4 16:28:53 2011] Mapping reads against ngene.fa with Bowtie(1/3) [Mon Apr 4 16:28:57 2011] Mapping reads against ngene.fa with Bowtie(2/3) [Mon Apr 4 16:29:01 2011] Mapping reads against ngene.fa with Bowtie(3/3) [Mon Apr 4 16:29:05 2011] Searching for junctions via segment mapping [Mon Apr 4 16:29:23 2011] Retrieving sequences for splices [Mon Apr 4 16:29:23 2011] Indexing splices [Mon Apr 4 16:29:24 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:29:26 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:29:28 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 16:29:30 2011] Joining segment hits [Mon Apr 4 16:29:32 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:15 elapsed] cufflinks -p 4 -o ./Zu_0 -r ngene.fa ./Zu_0/accepted_hits.bam [16:29:41] Inspecting reads and determining fragment length distribution. > Processing Locus CUFF.529_From_bur_0_1873494õ [ ] > Processing Locus CUFF.533_From_bur_0_2020452õ [ ] > Processing Locus CUFF.535_From_bur_0_1969548õ [ ] > Processing Locus CUFF.543_From_can_0_3017860õ [ ] > Processing Locus CUFF.553_From_can_0_3223655õ [ ] > Processing Locus CUFF.559_From_can_0_3231205õ [ ] > Processing Locus CUFF.563_From_bur_0_2020452õ [ ] > Processing Locus CUFF.563_From_bur_0_2020452õ [ ] > Processing Locus CUFF.567_From_can_0_3258779õ [ ] > Processing Locus CUFF.567_From_can_0_3258779õ [ ] > Processing Locus CUFF.571_From_can_0_3076940õ [ ] > Processing Locus CUFF.575_From_ct_1_3082021_õ [ ] > Processing Locus CUFF.583_From_ct_1_3302721_õ [* ] > Processing Locus CUFF.593_From_can_0_3270131õ [* ] > Processing Locus CUFF.593_From_can_0_3270131õ [* ] > Processing Locus CUFF.593_From_can_0_3270131õ [* ] > Processing Locus CUFF.595_From_ct_1_3302721_õ [* ] > Processing Locus CUFF.615_From_edi_0_2932438õ [* ] > Processing Locus CUFF.629_From_kn_0_3594465_õ [* ] > Processing Locus CUFF.637_From_kn_0_3626969_õ [* ] > Processing Locus CUFF.649_From_kn_0_3617271_õ [* ] > Processing Locus CUFF.659_From_ler_0_4153595õ [* ] > Processing Locus CUFF.663_From_kn_0_3613403_õ [* ] > Processing Locus CUFF.665_From_hi_0_2939638_õ [** ] > Processing Locus CUFF.666_From_ler_0_4004770õ [** ] > Processing Locus CUFF.671_From_edi_0_2859720õ [** ] > Processing Locus CUFF.677_From_ct_1_3133995_õ [** ] > Processing Locus CUFF.679_From_ler_0_3998410õ [** ] > Processing Locus CUFF.685_From_mt_0_4231054_õ [** ] > Processing Locus CUFF.687_From_mt_0_4230874_õ [** ] > Processing Locus CUFF.689_From_ler_0_4018856õ [** ] > Processing Locus CUFF.695_From_mt_0_4217716_õ [** ] > Processing Locus CUFF.697_From_mt_0_4229662_õ [** ] > Processing Locus CUFF.699_From_no_0_2905273_õ [*** ] > Processing Locus CUFF.701_From_no_0_2951521_õ [*** ] > Processing Locus CUFF.703_From_no_0_2885444_õ [*** ] > Processing Locus CUFF.707_From_no_0_2959683_õ [*** ] > Processing Locus CUFF.725_From_no_0_3116640_õ [*** ] > Processing Locus CUFF.731_From_po_0_3324652_õ [*** ] > Processing Locus CUFF.733_From_no_0_2956652_õ [*** ] > Processing Locus CUFF.735_From_po_0_3293868_õ [*** ] > Processing Locus CUFF.747_From_po_0_3299272_õ [*** ] > Processing Locus CUFF.749_From_oy_0_3162092_õ [**** ] > Processing Locus CUFF.751_From_rsch_4_403485õ [**** ] > Processing Locus CUFF.753_From_oy_0_3121110_õ [**** ] > Processing Locus CUFF.755_From_mt_0_4193196_õ [**** ] > Processing Locus CUFF.757_From_po_0_3372769_õ [**** ] > Processing Locus CUFF.761_From_po_0_3606391_õ [**** ] > Processing Locus CUFF.761_From_po_0_3606391_õ [**** ] > Processing Locus CUFF.763_From_rsch_4_403203õ [**** ] > Processing Locus CUFF.767_From_rsch_4_411814õ [**** ] > Processing Locus CUFF.771_From_po_0_3332479_õ [**** ] > Processing Locus CUFF.773_From_po_0_3606391_õ [**** ] > Processing Locus CUFF.773_From_po_0_3606391_õ [**** ] > Processing Locus CUFF.775_From_rsch_4_409124õ [***** ] > Processing Locus CUFF.779_From_rsch_4_421454õ [***** ] > Processing Locus CUFF.785_From_no_0_3128142_õ [***** ] > Processing Locus CUFF.785_From_no_0_3128142_õ [***** ] > Processing Locus CUFF.791_From_rsch_4_425553õ [***** ] > Processing Locus CUFF.793_From_sf_2_2504999_õ [***** ] > Processing Locus CUFF.795_From_rsch_4_429714õ [***** ] > Processing Locus CUFF.803_From_po_0_3573778_õ [***** ] > Processing Locus CUFF.811_From_sf_2_2459023_õ [***** ] > Processing Locus CUFF.821_From_tsu_0_3175121õ [***** ] > Processing Locus CUFF.823_From_tsu_0_3175121õ [****** ] > Processing Locus CUFF.829_From_tsu_0_3135135õ [****** ] > Processing Locus CUFF.837_From_tsu_0_3215671õ [****** ] > Processing Locus CUFF.837_From_tsu_0_3215671õ [****** ] > Processing Locus CUFF.839_From_sf_2_2680171_õ [****** ] > Processing Locus CUFF.843_From_rsch_4_429219õ [****** ] > Processing Locus CUFF.847_From_tsu_0_3242833õ [****** ] > Processing Locus CUFF.857_From_sf_2_2653966_õ [****** ] > Processing Locus CUFF.859_From_tsu_0_3215737õ [****** ] > Processing Locus CUFF.865_From_wil_2_2892485õ [****** ] > Processing Locus CUFF.869_From_sf_2_2701328_õ [****** ] > Processing Locus CUFF.871_From_rsch_4_426655õ [******* ] > Processing Locus CUFF.873_From_wil_2_3050523õ [******* ] > Processing Locus CUFF.877_From_sf_2_2687786_õ [******* ] > Processing Locus CUFF.877_From_sf_2_2687786_õ [******* ] > Processing Locus CUFF.893_From_ws_0_3190679_õ [******* ] > Processing Locus CUFF.899_From_ws_0_3190963_õ [******* ] > Processing Locus CUFF.905_From_ws_0_3339092_õ [******* ] > Processing Locus CUFF.907_From_ws_0_3182508_õ [******* ] > Processing Locus CUFF.919_From_ws_0_3347582_õ [******* ] > Processing Locus CUFF.935_From_ws_0_3380934_õ [******* ] > Processing Locus CUFF.943_From_zu_0_3075813_õ [******** ] > Processing Locus CUFF.945_From_wu_0_2678387_õ [******** ] > Processing Locus CUFF.947_From_wu_0_2654219_õ [******** ] > Processing Locus CUFF.963_From_zu_0_3092045_õ [******** ] > Processing Locus CUFF.967_From_zu_0_3022629_õ [******** ] > Processing Locus CUFF.969_From_zu_0_3190435_õ [******** ] > Processing Locus CUFF.973_From_zu_0_3242889_õ [******** ] > Processing Locus CUFF.975_From_zu_0_3259399_õ [******** ] > Processing Locus CUFF.977_From_zu_0_3255503_õ [******** ] > Processing Locus CUFF.979_From_zu_0_3278243_õ [********* ] > Processing Locus CUFF.983_From_zu_0_3243571_õ [********* ] > Processing Locus CUFF.983_From_zu_0_3243571_õ [********* ] > Processing Locus CUFF.985_From_zu_0_3280213_õ [********* ] > Processing Locus CUFF.987_From_zu_0_3118546_õ [********* ] > Processing Locus CUFF.991_From_zu_0_3277661_õ [********* ] > Processing Locus CUFF.993_From_zu_0_3082201_õ [********* ] > Processed 101 loci. [*************************] 100% > Map Properties: > Total Map Mass: 6535.69 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [16:29:41] Assembling transcripts and estimating abundances. > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 0% > Processing Locus CUFF.533_From_bur_0_2020452 [ ] 0% > Processing Locus CUFF.535_From_bur_0_1969548 [ ] 1% > Processing Locus CUFF.543_From_can_0_3017860 [ ] 2% > Processing Locus CUFF.553_From_can_0_3223655 [ ] 3% > Processing Locus CUFF.559_From_can_0_3231205 [* ] 4% > Processing Locus CUFF.563_From_bur_0_2020452 [* ] 5% > Processing Locus CUFF.563_From_bur_0_2020452 [* ] 6% > Processing Locus CUFF.567_From_can_0_3258779 [* ] 7% > Processing Locus CUFF.567_From_can_0_3258779 [** ] 8% > Processing Locus CUFF.571_From_can_0_3076940 [** ] 9% > Processing Locus CUFF.575_From_ct_1_3082021_ [** ] 10% > Processing Locus CUFF.583_From_ct_1_3302721_ [** ] 11% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 12% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 13% > Processing Locus CUFF.593_From_can_0_3270131 [*** ] 14% > Processing Locus CUFF.595_From_ct_1_3302721_ [*** ] 15% > Processing Locus CUFF.615_From_edi_0_2932438 [**** ] 16% > Processing Locus CUFF.629_From_kn_0_3594465_ [**** ] 17% > Processing Locus CUFF.637_From_kn_0_3626969_ [**** ] 18% > Processing Locus CUFF.649_From_kn_0_3617271_ [**** ] 19% > Processing Locus CUFF.659_From_ler_0_4153595 [***** ] 20% > Processing Locus CUFF.663_From_kn_0_3613403_ [***** ] 21% > Processing Locus CUFF.665_From_hi_0_2939638_ [***** ] 22% > Processing Locus CUFF.666_From_ler_0_4004770 [***** ] 23% > Processing Locus CUFF.671_From_edi_0_2859720 [****** ] 24% > Processing Locus CUFF.677_From_ct_1_3133995_ [****** ] 25% > Processing Locus CUFF.679_From_ler_0_3998410 [****** ] 26% > Processing Locus CUFF.685_From_mt_0_4231054_ [****** ] 27% > Processing Locus CUFF.687_From_mt_0_4230874_ [******* ] 28% > Processing Locus CUFF.689_From_ler_0_4018856 [******* ] 29% > Processing Locus CUFF.695_From_mt_0_4217716_ [******* ] 30% > Processing Locus CUFF.697_From_mt_0_4229662_ [******* ] 31% > Processing Locus CUFF.699_From_no_0_2905273_ [******** ] 32% > Processing Locus CUFF.701_From_no_0_2951521_ [******** ] 33% > Processing Locus CUFF.703_From_no_0_2885444_ [******** ] 34% > Processing Locus CUFF.707_From_no_0_2959683_ [******** ] 35% > Processing Locus CUFF.725_From_no_0_3116640_ [********* ] 36% > Processing Locus CUFF.731_From_po_0_3324652_ [********* ] 37% > Processing Locus CUFF.733_From_no_0_2956652_ [********* ] 38% > Processing Locus CUFF.735_From_po_0_3293868_ [********* ] 39% > Processing Locus CUFF.747_From_po_0_3299272_ [********** ] 40% > Processing Locus CUFF.749_From_oy_0_3162092_ [********** ] 41% > Processing Locus CUFF.751_From_rsch_4_403485 [********** ] 42% > Processing Locus CUFF.753_From_oy_0_3121110_ [********** ] 43% > Processing Locus CUFF.755_From_mt_0_4193196_ [*********** ] 44% > Processing Locus CUFF.757_From_po_0_3372769_ [*********** ] 45% > Processing Locus CUFF.761_From_po_0_3606391_ [*********** ] 46% > Processing Locus CUFF.761_From_po_0_3606391_ [*********** ] 47% > Processing Locus CUFF.763_From_rsch_4_403203 [************ ] 48% > Processing Locus CUFF.767_From_rsch_4_411814 [************ ] 49% > Processing Locus CUFF.771_From_po_0_3332479_ [************ ] 50% > Processing Locus CUFF.773_From_po_0_3606391_ [************ ] 51% > Processing Locus CUFF.773_From_po_0_3606391_ [************* ] 52% > Processing Locus CUFF.775_From_rsch_4_409124 [************* ] 53% > Processing Locus CUFF.779_From_rsch_4_421454 [************* ] 54% > Processing Locus CUFF.785_From_no_0_3128142_ [************* ] 55% > Processing Locus CUFF.785_From_no_0_3128142_ [************** ] 56% > Processing Locus CUFF.791_From_rsch_4_425553 [************** ] 57% > Processing Locus CUFF.793_From_sf_2_2504999_ [************** ] 58% > Processing Locus CUFF.795_From_rsch_4_429714 [************** ] 59% > Processing Locus CUFF.803_From_po_0_3573778_ [*************** ] 60% > Processing Locus CUFF.811_From_sf_2_2459023_ [*************** ] 61% > Processing Locus CUFF.821_From_tsu_0_3175121 [*************** ] 62% > Processing Locus CUFF.823_From_tsu_0_3175121 [*************** ] 63% > Processing Locus CUFF.829_From_tsu_0_3135135 [**************** ] 64% > Processing Locus CUFF.837_From_tsu_0_3215671 [**************** ] 65% > Processing Locus CUFF.837_From_tsu_0_3215671 [**************** ] 66% > Processing Locus CUFF.839_From_sf_2_2680171_ [**************** ] 67% > Processing Locus CUFF.843_From_rsch_4_429219 [***************** ] 68% > Processing Locus CUFF.847_From_tsu_0_3242833 [***************** ] 69% > Processing Locus CUFF.857_From_sf_2_2653966_ [***************** ] 70% > Processing Locus CUFF.859_From_tsu_0_3215737 [***************** ] 71% > Processing Locus CUFF.865_From_wil_2_2892485 [****************** ] 72% > Processing Locus CUFF.869_From_sf_2_2701328_ [****************** ] 73% > Processing Locus CUFF.871_From_rsch_4_426655 [****************** ] 74% > Processing Locus CUFF.873_From_wil_2_3050523 [****************** ] 75% > Processing Locus CUFF.877_From_sf_2_2687786_ [******************* ] 76% > Processing Locus CUFF.877_From_sf_2_2687786_ [******************* ] 77% > Processing Locus CUFF.893_From_ws_0_3190679_ [******************* ] 78% > Processing Locus CUFF.899_From_ws_0_3190963_ [******************* ] 79% > Processing Locus CUFF.905_From_ws_0_3339092_ [******************** ] 80% > Processing Locus CUFF.907_From_ws_0_3182508_ [******************** ] 81% > Processing Locus CUFF.919_From_ws_0_3347582_ [******************** ] 82% > Processing Locus CUFF.935_From_ws_0_3380934_ [******************** ] 83% > Processing Locus CUFF.943_From_zu_0_3075813_ [********************* ] 84% > Processing Locus CUFF.945_From_wu_0_2678387_ [********************* ] 85% > Processing Locus CUFF.947_From_wu_0_2654219_ [********************* ] 86% > Processing Locus CUFF.963_From_zu_0_3092045_ [********************* ] 87% > Processing Locus CUFF.967_From_zu_0_3022629_ [********************** ] 88% > Processing Locus CUFF.969_From_zu_0_3190435_ [********************** ] 89% > Processing Locus CUFF.973_From_zu_0_3242889_ [********************** ] 90% > Processing Locus CUFF.975_From_zu_0_3259399_ [********************** ] 91% > Processing Locus CUFF.977_From_zu_0_3255503_ [*********************** ] 92% > Processing Locus CUFF.979_From_zu_0_3278243_ [*********************** ] 93% > Processing Locus CUFF.983_From_zu_0_3243571_ [*********************** ] 94% > Processing Locus CUFF.983_From_zu_0_3243571_ [*********************** ] 95% > Processing Locus CUFF.985_From_zu_0_3280213_ [************************ ] 96% > Processing Locus CUFF.987_From_zu_0_3118546_ [************************ ] 97% > Processing Locus CUFF.991_From_zu_0_3277661_ [************************ ] 98% > Processing Locus CUFF.993_From_zu_0_3082201_ [************************ ] 99% > Processed 101 loci. [*************************] 100% [16:29:41] Loading reference annotation and sequence [16:29:41] Learning bias parameters. > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 0% > Processing Locus CUFF.535_From_bur_0_1969548 [ ] 0% > Processing Locus CUFF.559_From_can_0_3231205 [ ] 1% > Processing Locus CUFF.563_From_bur_0_2020452 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 5% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 6% > Processing Locus CUFF.615_From_edi_0_2932438 [* ] 7% > Processing Locus CUFF.629_From_kn_0_3594465_ [** ] 8% > Processing Locus CUFF.649_From_kn_0_3617271_ [** ] 9% > Processing Locus CUFF.659_From_ler_0_4153595 [** ] 10% > Processing Locus CUFF.663_From_kn_0_3613403_ [** ] 11% > Processing Locus CUFF.665_From_hi_0_2939638_ [*** ] 12% > Processing Locus CUFF.671_From_edi_0_2859720 [*** ] 13% > Processing Locus CUFF.677_From_ct_1_3133995_ [*** ] 14% > Processing Locus CUFF.679_From_ler_0_3998410 [*** ] 15% > Processing Locus CUFF.685_From_mt_0_4231054_ [**** ] 16% > Processing Locus CUFF.687_From_mt_0_4230874_ [**** ] 17% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 18% > Processing Locus CUFF.695_From_mt_0_4217716_ [**** ] 19% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 20% > Processing Locus CUFF.699_From_no_0_2905273_ [***** ] 21% > Processing Locus CUFF.701_From_no_0_2951521_ [***** ] 22% > Processing Locus CUFF.703_From_no_0_2885444_ [***** ] 23% > Processing Locus CUFF.725_From_no_0_3116640_ [****** ] 24% > Processing Locus CUFF.731_From_po_0_3324652_ [****** ] 25% > Processing Locus CUFF.733_From_no_0_2956652_ [****** ] 26% > Processing Locus CUFF.747_From_po_0_3299272_ [****** ] 27% > Processing Locus CUFF.751_From_rsch_4_403485 [******* ] 28% > Processing Locus CUFF.753_From_oy_0_3121110_ [******* ] 29% > Processing Locus CUFF.755_From_mt_0_4193196_ [******* ] 30% > Processing Locus CUFF.761_From_po_0_3606391_ [******* ] 31% > Processing Locus CUFF.763_From_rsch_4_403203 [******** ] 32% > Processing Locus CUFF.767_From_rsch_4_411814 [******** ] 33% > Processing Locus CUFF.771_From_po_0_3332479_ [******** ] 34% > Processing Locus CUFF.779_From_rsch_4_421454 [******** ] 35% > Processing Locus CUFF.785_From_no_0_3128142_ [********* ] 36% > Processing Locus CUFF.785_From_no_0_3128142_ [********* ] 37% > Processing Locus CUFF.791_From_rsch_4_425553 [********* ] 38% > Processing Locus CUFF.793_From_sf_2_2504999_ [********* ] 39% > Processing Locus CUFF.803_From_po_0_3573778_ [********** ] 40% > Processing Locus CUFF.811_From_sf_2_2459023_ [********** ] 41% > Processing Locus CUFF.821_From_tsu_0_3175121 [********** ] 42% > Processing Locus CUFF.823_From_tsu_0_3175121 [********** ] 43% > Processing Locus CUFF.839_From_sf_2_2680171_ [*********** ] 44% > Processing Locus CUFF.843_From_rsch_4_429219 [*********** ] 45% > Processing Locus CUFF.847_From_tsu_0_3242833 [*********** ] 46% > Processing Locus CUFF.857_From_sf_2_2653966_ [*********** ] 47% > Processing Locus CUFF.859_From_tsu_0_3215737 [************ ] 48% > Processing Locus CUFF.869_From_sf_2_2701328_ [************ ] 49% > Processing Locus CUFF.871_From_rsch_4_426655 [************ ] 50% > Processing Locus CUFF.877_From_sf_2_2687786_ [************ ] 51% > Processing Locus CUFF.877_From_sf_2_2687786_ [************* ] 52% > Processing Locus CUFF.899_From_ws_0_3190963_ [************* ] 53% > Processing Locus CUFF.907_From_ws_0_3182508_ [************* ] 54% > Processing Locus CUFF.919_From_ws_0_3347582_ [************* ] 55% > Processing Locus CUFF.935_From_ws_0_3380934_ [************** ] 56% > Processing Locus CUFF.945_From_wu_0_2678387_ [************** ] 57% > Processing Locus CUFF.967_From_zu_0_3022629_ [************** ] 58% > Processing Locus CUFF.969_From_zu_0_3190435_ [************** ] 59% > Processing Locus CUFF.973_From_zu_0_3242889_ [*************** ] 60% > Processing Locus CUFF.975_From_zu_0_3259399_ [*************** ] 61% > Processing Locus CUFF.977_From_zu_0_3255503_ [*************** ] 62% > Processing Locus CUFF.983_From_zu_0_3243571_ [*************** ] 63% > Processing Locus CUFF.985_From_zu_0_3280213_ [**************** ] 64% > Processing Locus CUFF.987_From_zu_0_3118546_ [**************** ] 65% > Processing Locus CUFF.991_From_zu_0_3277661_ [**************** ] 66% > Processing Locus CUFF.993_From_zu_0_3082201_ [**************** ] 67% > Processed 69 loci. [*************************] 100% [16:29:41] Assembling transcripts and estimating abundances. > Processing Locus CUFF.529_From_bur_0_1873494 [ ] 0% > Processing Locus CUFF.535_From_bur_0_1969548 [ ] 0% > Processing Locus CUFF.559_From_can_0_3231205 [ ] 1% > Processing Locus CUFF.563_From_bur_0_2020452 [ ] 2% > Processing Locus CUFF.571_From_can_0_3076940 [ ] 3% > Processing Locus CUFF.575_From_ct_1_3082021_ [* ] 4% > Processing Locus CUFF.593_From_can_0_3270131 [* ] 5% > Processing Locus CUFF.595_From_ct_1_3302721_ [* ] 6% > Processing Locus CUFF.615_From_edi_0_2932438 [* ] 7% > Processing Locus CUFF.629_From_kn_0_3594465_ [** ] 8% > Processing Locus CUFF.649_From_kn_0_3617271_ [** ] 9% > Processing Locus CUFF.659_From_ler_0_4153595 [** ] 10% > Processing Locus CUFF.663_From_kn_0_3613403_ [** ] 11% > Processing Locus CUFF.665_From_hi_0_2939638_ [*** ] 12% > Processing Locus CUFF.671_From_edi_0_2859720 [*** ] 13% > Processing Locus CUFF.677_From_ct_1_3133995_ [*** ] 14% > Processing Locus CUFF.679_From_ler_0_3998410 [*** ] 15% > Processing Locus CUFF.685_From_mt_0_4231054_ [**** ] 16% > Processing Locus CUFF.687_From_mt_0_4230874_ [**** ] 17% > Processing Locus CUFF.689_From_ler_0_4018856 [**** ] 18% > Processing Locus CUFF.695_From_mt_0_4217716_ [**** ] 19% > Processing Locus CUFF.697_From_mt_0_4229662_ [***** ] 20% > Processing Locus CUFF.699_From_no_0_2905273_ [***** ] 21% > Processing Locus CUFF.701_From_no_0_2951521_ [***** ] 22% > Processing Locus CUFF.703_From_no_0_2885444_ [***** ] 23% > Processing Locus CUFF.725_From_no_0_3116640_ [****** ] 24% > Processing Locus CUFF.731_From_po_0_3324652_ [****** ] 25% > Processing Locus CUFF.733_From_no_0_2956652_ [****** ] 26% > Processing Locus CUFF.747_From_po_0_3299272_ [****** ] 27% > Processing Locus CUFF.751_From_rsch_4_403485 [******* ] 28% > Processing Locus CUFF.753_From_oy_0_3121110_ [******* ] 29% > Processing Locus CUFF.755_From_mt_0_4193196_ [******* ] 30% > Processing Locus CUFF.761_From_po_0_3606391_ [******* ] 31% > Processing Locus CUFF.763_From_rsch_4_403203 [******** ] 32% > Processing Locus CUFF.767_From_rsch_4_411814 [******** ] 33% > Processing Locus CUFF.771_From_po_0_3332479_ [******** ] 34% > Processing Locus CUFF.779_From_rsch_4_421454 [******** ] 35% > Processing Locus CUFF.785_From_no_0_3128142_ [********* ] 36% > Processing Locus CUFF.785_From_no_0_3128142_ [********* ] 37% > Processing Locus CUFF.791_From_rsch_4_425553 [********* ] 38% > Processing Locus CUFF.793_From_sf_2_2504999_ [********* ] 39% > Processing Locus CUFF.803_From_po_0_3573778_ [********** ] 40% > Processing Locus CUFF.811_From_sf_2_2459023_ [********** ] 41% > Processing Locus CUFF.821_From_tsu_0_3175121 [********** ] 42% > Processing Locus CUFF.823_From_tsu_0_3175121 [********** ] 43% > Processing Locus CUFF.839_From_sf_2_2680171_ [*********** ] 44% > Processing Locus CUFF.843_From_rsch_4_429219 [*********** ] 45% > Processing Locus CUFF.847_From_tsu_0_3242833 [*********** ] 46% > Processing Locus CUFF.857_From_sf_2_2653966_ [*********** ] 47% > Processing Locus CUFF.859_From_tsu_0_3215737 [************ ] 48% > Processing Locus CUFF.869_From_sf_2_2701328_ [************ ] 49% > Processing Locus CUFF.871_From_rsch_4_426655 [************ ] 50% > Processing Locus CUFF.877_From_sf_2_2687786_ [************ ] 51% > Processing Locus CUFF.877_From_sf_2_2687786_ [************* ] 52% > Processing Locus CUFF.899_From_ws_0_3190963_ [************* ] 53% > Processing Locus CUFF.907_From_ws_0_3182508_ [************* ] 54% > Processing Locus CUFF.919_From_ws_0_3347582_ [************* ] 55% > Processing Locus CUFF.935_From_ws_0_3380934_ [************** ] 56% > Processing Locus CUFF.945_From_wu_0_2678387_ [************** ] 57% > Processing Locus CUFF.967_From_zu_0_3022629_ [************** ] 58% > Processing Locus CUFF.969_From_zu_0_3190435_ [************** ] 59% > Processing Locus CUFF.973_From_zu_0_3242889_ [*************** ] 60% > Processing Locus CUFF.975_From_zu_0_3259399_ [*************** ] 61% > Processing Locus CUFF.977_From_zu_0_3255503_ [*************** ] 62% > Processing Locus CUFF.983_From_zu_0_3243571_ [*************** ] 63% > Processing Locus CUFF.985_From_zu_0_3280213_ [**************** ] 64% > Processing Locus CUFF.987_From_zu_0_3118546_ [**************** ] 65% > Processing Locus CUFF.991_From_zu_0_3277661_ [**************** ] 66% > Processing Locus CUFF.993_From_zu_0_3082201_ [**************** ] 67% > Processed 69 loci. [*************************] 100% /Net/fs1/home/xianggan/svncode/novGene//sta_bams.pl -o 0 Bur_0.Tongene.merge.bam Can_0.Tongene.merge.bam Col_0.Tongene.merge.bam Ct_1.Tongene.merge.bam Edi_0.Tongene.merge.bam Hi_0.Tongene.merge.bam Kn_0.Tongene.merge.bam Ler_0.Tongene.merge.bam Mt_0.Tongene.merge.bam No_0.Tongene.merge.bam Oy_0.Tongene.merge.bam Po_0.Tongene.merge.bam Rsch_4.Tongene.merge.bam Sf_2.Tongene.merge.bam Tsu_0.Tongene.merge.bam Wil_2.Tongene.merge.bam Ws_0.Tongene.merge.bam Wu_0.Tongene.merge.bam Zu_0.Tongene.merge.bam