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 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 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 ./Col_0 -n it2.fa Col_0.Toit2.merge.fq reference: it2.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 ./Ct_1 -n it2.fa Ct_1.Toit2.merge.fq reference: it2.fa $RNAGI/rnagi.sh -o ./Bur_0 -n it2.fa Bur_0.Toit2.merge.fq reference: it2.fa $RNAGI/rnagi.sh -o ./Can_0 -n it2.fa Can_0.Toit2.merge.fq reference: it2.fa $RNAGI/rnagi.sh -o ./Edi_0 -n it2.fa Edi_0.Toit2.merge.fq reference: it2.fa Settings: Output files: "it2.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: it2.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: 50485 Using parameters --bmax 37864 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 37864 --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 Split 1, merged 0; 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 Split 1, merged 0; iterating... Avg bucket size: 22437.1 (target: 37863) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 9 Reserving size (37864) 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 7328 (Using difference cover) Sorting block time: 00:00:00 Returning block of 7329 Getting block 2 of 9 Reserving size (37864) 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 6491 (Using difference cover) Sorting block time: 00:00:00 Returning block of 6492 Getting block 3 of 9 Reserving size (37864) 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 37016 (Using difference cover) Sorting block time: 00:00:00 Returning block of 37017 Getting block 4 of 9 Reserving size (37864) 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 9156 (Using difference cover) Sorting block time: 00:00:00 Returning block of 9157 Getting block 5 of 9 Reserving size (37864) 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 28936 (Using difference cover) Sorting block time: 00:00:00 Returning block of 28937 Getting block 6 of 9 Reserving size (37864) 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 36465 (Using difference cover) Sorting block time: 00:00:00 Returning block of 36466 Getting block 7 of 9 Reserving size (37864) 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 32914 (Using difference cover) Sorting block time: 00:00:00 Returning block of 32915 Getting block 8 of 9 Reserving size (37864) 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 30697 (Using difference cover) Sorting block time: 00:00:00 Returning block of 30698 Getting block 9 of 9 Reserving size (37864) 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 12931 (Using difference cover) Sorting block time: 00:00:00 Returning block of 12932 Exited Ebwt loop fchr[A]: 0 fchr[C]: 59995 fchr[G]: 101472 fchr[T]: 142007 fchr[$]: 201942 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4259678 bytes to primary EBWT file: it2.fa.1.ebwt Wrote 25248 bytes to secondary EBWT file: it2.fa.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 201942 bwtLen: 201943 sz: 50486 bwtSz: 50486 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6311 offsSz: 25244 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 451 numSides: 902 numLines: 902 ebwtTotLen: 57728 ebwtTotSz: 57728 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: 50485 Using parameters --bmax 37864 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 37864 --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 2, 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 2; 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: 28848 (target: 37863) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (37864) 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 31448 (Using difference cover) Sorting block time: 00:00:00 Returning block of 31449 Getting block 2 of 7 Reserving size (37864) 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 15612 (Using difference cover) Sorting block time: 00:00:00 Returning block of 15613 Getting block 3 of 7 Reserving size (37864) 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 37481 (Using difference cover) Sorting block time: 00:00:00 Returning block of 37482 Getting block 4 of 7 Reserving size (37864) 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 36658 (Using difference cover) Sorting block time: 00:00:00 Returning block of 36659 Getting block 5 of 7 Reserving size (37864) 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 20803 (Using difference cover) Sorting block time: 00:00:00 Returning block of 20804 Getting block 6 of 7 Reserving size (37864) 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 24552 (Using difference cover) Sorting block time: 00:00:00 Returning block of 24553 Getting block 7 of 7 Reserving size (37864) 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 35382 (Using difference cover) Sorting block time: 00:00:00 Returning block of 35383 Exited Ebwt loop fchr[A]: 0 fchr[C]: 59995 fchr[G]: 101472 fchr[T]: 142007 fchr[$]: 201942 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4259678 bytes to primary EBWT file: it2.fa.rev.1.ebwt Wrote 25248 bytes to secondary EBWT file: it2.fa.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 201942 bwtLen: 201943 sz: 50486 bwtSz: 50486 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6311 offsSz: 25244 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 451 numSides: 902 numLines: 902 ebwtTotLen: 57728 ebwtTotSz: 57728 reverse: 0 Total time for backward call to driver() for mirror index: 00:00:00 tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Col_0 it2.fa ./Col_0/Col_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:06:41 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:06:41 2011] Preparing output location ./Col_0// [Mon Apr 4 14:06:41 2011] Checking for Bowtie index files [Mon Apr 4 14:06:41 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:06:41 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:06:41 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:06:41 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:06:42 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Ct_1 it2.fa ./Ct_1/Ct_1.Toit2.merge.flt_1.fq [Mon Apr 4 14:06:45 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:06:45 2011] Preparing output location ./Ct_1// [Mon Apr 4 14:06:45 2011] Checking for Bowtie index files [Mon Apr 4 14:06:45 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:06:45 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:06:45 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:06:45 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:06:45 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Edi_0 it2.fa ./Edi_0/Edi_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:06:46 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:06:46 2011] Preparing output location ./Edi_0// [Mon Apr 4 14:06:46 2011] Checking for Bowtie index files [Mon Apr 4 14:06:46 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:06:46 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:06:46 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:06:46 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:06:46 2011] Checking reads min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 14:06:48 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:06:50 2011] Joining segment hits tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Can_0 it2.fa ./Can_0/Can_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:06:50 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:06:50 2011] Preparing output location ./Can_0// [Mon Apr 4 14:06:50 2011] Checking for Bowtie index files [Mon Apr 4 14:06:50 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:06:50 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:06:50 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:06:50 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:06:50 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 ./Bur_0 it2.fa ./Bur_0/Bur_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:06:53 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:06:53 2011] Preparing output location ./Bur_0// [Mon Apr 4 14:06:53 2011] Checking for Bowtie index files [Mon Apr 4 14:06:53 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:06:53 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:06:53 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:06:53 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:06:53 2011] Checking reads [Mon Apr 4 14:06:53 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:06:55 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:06:56 2011] Joining segment hits [Mon Apr 4 14:06:57 2011] Mapping reads against it2.fa with Bowtie(2/3) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 14:06:58 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:07:00 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:07:00 2011] Searching for junctions via segment mapping [Mon Apr 4 14:07:04 2011] Joining segment hits [Mon Apr 4 14:07:04 2011] Mapping reads against it2.fa with Bowtie(1/3) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 14:07:06 2011] Mapping reads against it2.fa with Bowtie(2/3) 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 [Mon Apr 4 14:07:08 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:07:08 2011] Retrieving sequences for splices [Mon Apr 4 14:07:08 2011] Indexing splices min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 14:07:08 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:07:09 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:07:10 2011] Mapping reads against segment_juncs with Bowtie $RNAGI/rnagi.sh -o ./Hi_0 -n it2.fa Hi_0.Toit2.merge.fq reference: it2.fa [Mon Apr 4 14:07:11 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:07:11 2011] Searching for junctions via segment mapping [Mon Apr 4 14:07:12 2011] Joining segment hits [Mon Apr 4 14:07:13 2011] Reporting output tracks [Mon Apr 4 14:07:13 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:07:13 2011] Joining segment hits ----------------------------------------------- Run complete [00:00:32 elapsed] cufflinks -p 4 -o ./Col_0 -r it2.fa ./Col_0/accepted_hits.bam [14:07:18] Inspecting reads and determining fragment length distribution. > Processing Locus ct_1_3082021_0:1-125 [ ] 0% > Processing Locus kn_0_3613403_0:0-142 [ ] 0% > Processing Locus ler_0_3998410_0:0-163 [ ] 0% > Processing Locus ler_0_4018856_0:0-186 [ ] 1% > Processing Locus no_0_2885444_0:15-109 [ ] 1% > Processing Locus no_0_2905273_0:9-123 [ ] 2% > Processing Locus no_0_2956652_0:5-178 [ ] 2% > Processing Locus rsch_4_4032032_0:0-89 [ ] 2% > Processing Locus wil_2_2834553_0:0-78 [ ] 3% > Processing Locus wu_0_2678387_0:7-162 [ ] 3% > Processed 10 loci. [*************************] 100% > Map Properties: > Total Map Mass: 111.00 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:07:18] Assembling transcripts and estimating abundances. > Processing Locus ct_1_3082021_0:1-125 [ ] 0% > Processing Locus kn_0_3613403_0:0-142 [** ] 10% > Processing Locus ler_0_3998410_0:0-163 [***** ] 20% > Processing Locus ler_0_4018856_0:0-186 [******* ] 30% > Processing Locus no_0_2885444_0:15-109 [********** ] 40% > Processing Locus no_0_2905273_0:9-123 [************ ] 50% > Processing Locus no_0_2956652_0:5-178 [*************** ] 60% > Processing Locus rsch_4_4032032_0:0-89 [***************** ] 70% > Processing Locus wil_2_2834553_0:0-78 [******************** ] 80% > Processing Locus wu_0_2678387_0:7-162 [********************** ] 90% > Processed 10 loci. [*************************] 100% [14:07:18] Loading reference annotation and sequence No fasta index found for it2.fa. Rebuilding, please wait.. Fasta index rebuilt. [14:07:18] Learning bias parameters. > Processing Locus ct_1_3082021_0:1-125 [ ] 0% > Processing Locus kn_0_3613403_0:0-142 [** ] 10% > Processing Locus ler_0_3998410_0:0-163 [***** ] 20% > Processing Locus ler_0_4018856_0:0-186 [******* ] 30% > Processing Locus no_0_2956652_0:5-178 [********** ] 40% > Processing Locus rsch_4_4032032_0:0-89 [************ ] 50% > Processed 6 loci. [*************************] 100% [14:07:18] Assembling transcripts and estimating abundances. > Processing Locus ct_1_3082021_0:1-125 [ ] 0% > Processing Locus kn_0_3613403_0:0-142 [** ] 10% > Processing Locus ler_0_3998410_0:0-163 [***** ] 20% > Processing Locus ler_0_4018856_0:0-186 [******* ] 30% > Processing Locus no_0_2956652_0:5-178 [********** ] 40% > Processing Locus rsch_4_4032032_0:0-89 [************ ] 50% > Processed 6 loci. [*************************] 100% [Mon Apr 4 14:07:18 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:07:19 2011] Joining segment hits [Mon Apr 4 14:07:21 2011] Mapping reads against it2.fa with Bowtie(2/3) tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Hi_0 it2.fa ./Hi_0/Hi_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:07:23 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:07:23 2011] Preparing output location ./Hi_0// [Mon Apr 4 14:07:23 2011] Checking for Bowtie index files [Mon Apr 4 14:07:23 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:07:23 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:07:23 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:07:23 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:07:24 2011] Checking reads [Mon Apr 4 14:07:24 2011] Retrieving sequences for splices [Mon Apr 4 14:07:24 2011] Indexing splices [Mon Apr 4 14:07:25 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:07:25 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:07:26 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:07:28 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:07:28 2011] Searching for junctions via segment mapping [Mon Apr 4 14:07:28 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:07:30 2011] Joining segment hits [Mon Apr 4 14:07:31 2011] Reporting output tracks [Mon Apr 4 14:07:32 2011] Mapping reads against it2.fa with Bowtie(2/3) ----------------------------------------------- Run complete [00:00:47 elapsed] [Mon Apr 4 14:07:35 2011] Mapping reads against it2.fa with Bowtie(1/3) cufflinks -p 4 -o ./Ct_1 -r it2.fa ./Ct_1/accepted_hits.bam [14:07:36] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:0-86 [ ] 0% > Processing Locus bur_0_1873494_0:4-183 [ ] 0% > Processing Locus can_0_3076940_0:0-129 [ ] 0% > Processing Locus can_0_3122480_0:0-116 [ ] 1% > Processing Locus can_0_3189753_0:1-202 [ ] 1% > Processing Locus can_0_3218459_0:27-297 [ ] 2% > Processing Locus can_0_3218459_0:550-900 [ ] 2% > Processing Locus can_0_3270131_0:20-2269 [ ] 2% > Processing Locus ct_1_3082021_0:6-128 [ ] 2% > Processing Locus ct_1_3125173_0:21-180 [ ] 3% > Processing Locus ct_1_3132277_0:0-175 [ ] 3% > Processing Locus ct_1_3133451_0:21-180 [* ] 4% > Processing Locus ct_1_3133995_0:14-195 [* ] 4% > Processing Locus ct_1_3241157_0:5-760 [* ] 5% > Processing Locus ct_1_3247037_0:227-475 [* ] 5% > Processing Locus ct_1_3302721_0:383-1593 [* ] 5% > Processing Locus edi_0_2859720_0:132-524 [* ] 6% > Processing Locus edi_0_2871668_0:188-523 [* ] 6% > Processing Locus edi_0_2891226_0:502-795 [* ] 7% > Processing Locus edi_0_2891226_0:1009-1087 [* ] 7% > Processing Locus edi_0_2932438_0:37-288 [* ] 7% > Processing Locus hi_0_2795398_0:0-191 [* ] 7% > Processing Locus hi_0_2939638_0:12-639 [** ] 8% > Processing Locus hi_0_2953648_0:897-975 [** ] 8% > Processing Locus hi_0_2961678_0:213-1508 [** ] 9% > Processing Locus kn_0_3594465_0:13-159 [** ] 9% > Processing Locus kn_0_3613403_0:9-130 [** ] 10% > Processing Locus ler_0_3998410_0:11-163 [** ] 10% > Processing Locus ler_0_4018856_0:6-182 [** ] 10% > Processing Locus ler_0_4224097_0:847-1752 [** ] 11% > Processing Locus ler_0_4225073_0:196-696 [** ] 11% > Processing Locus mt_0_4217716_0:8-175 [*** ] 12% > Processing Locus mt_0_4229662_0:1-196 [*** ] 12% > Processing Locus mt_0_4230874_0:34-188 [*** ] 13% > Processing Locus mt_0_4231054_0:3-81 [*** ] 13% > Processing Locus mt_0_4528444_1:307-385 [*** ] 13% > Processing Locus mt_0_4528444_1:552-1245 [*** ] 13% > Processing Locus no_0_2885444_0:9-105 [*** ] 14% > Processing Locus no_0_2905273_0:13-121 [*** ] 14% > Processing Locus no_0_2934639_0:40-124 [*** ] 15% > Processing Locus no_0_2956652_0:17-172 [*** ] 15% > Processing Locus no_0_3128142_0:1740-2956 [*** ] 15% > Processing Locus oy_0_3001818_0:33-154 [**** ] 16% > Processing Locus oy_0_3121110_0:50-535 [**** ] 16% > Processing Locus po_0_3299272_0:4-119 [**** ] 17% > Processing Locus po_0_3306688_0:15-122 [**** ] 17% > Processing Locus po_0_3324652_0:6-130 [**** ] 18% > Processing Locus po_0_3330421_0:4-135 [**** ] 18% > Processing Locus po_0_3332479_0:0-136 [**** ] 18% > Processing Locus po_0_3340213_0:2-137 [**** ] 19% > Processing Locus po_0_3382155_0:0-128 [**** ] 19% > Processing Locus po_0_3573778_0:349-1257 [***** ] 20% > Processing Locus rsch_4_4032032_0:0-85 [***** ] 20% > Processing Locus rsch_4_4055167_0:0-107 [***** ] 21% > Processing Locus rsch_4_4219071_0:91-362 [***** ] 21% > Processing Locus rsch_4_4266550_0:6-1142 [***** ] 21% > Processing Locus rsch_4_4277288_0:0-1368 [***** ] 22% > Processing Locus sf_2_2682779_0:647-779 [***** ] 22% > Processing Locus sf_2_2682779_0:913-991 [***** ] 22% > Processing Locus sf_2_2682779_0:1277-1355 [***** ] 22% > Processing Locus sf_2_2687786_0:2-2191 [***** ] 23% > Processing Locus tsu_0_3208747_0:9-401 [***** ] 23% > Processing Locus wil_2_2834553_0:0-95 [***** ] 23% > Processing Locus wil_2_2925323_0:0-195 [****** ] 24% > Processing Locus wil_2_3077447_0:647-1007 [****** ] 24% > Processing Locus ws_0_3190963_0:52-130 [****** ] 25% > Processing Locus ws_0_3326342_0:39-362 [****** ] 25% > Processing Locus ws_0_3340488_0:176-1139 [****** ] 26% > Processing Locus ws_0_3347582_0:314-686 [****** ] 26% > Processing Locus ws_0_3347582_0:792-870 [****** ] 26% > Processing Locus ws_0_3347582_0:1188-1358 [****** ] 26% > Processing Locus ws_0_3371988_0:0-250 [****** ] 26% > Processing Locus ws_0_3371988_0:1663-1741 [****** ] 26% > Processing Locus ws_0_3373604_0:1607-2762 [****** ] 27% > Processing Locus ws_0_3380934_0:3-190 [****** ] 27% > Processing Locus ws_0_3381390_0:8-1730 [******* ] 28% > Processing Locus wu_0_2654219_0:39-142 [******* ] 28% > Processing Locus wu_0_2678387_0:38-128 [******* ] 28% > Processing Locus zu_0_3243571_0:55-799 [******* ] 29% > Processing Locus zu_0_3259399_1:90-318 [******* ] 29% > Processed 80 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5535.87 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:07:36] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:0-86 [ ] 0% > Processing Locus bur_0_1873494_0:4-183 [ ] 1% > Processing Locus can_0_3076940_0:0-129 [ ] 2% > Processing Locus can_0_3122480_0:0-116 [ ] 3% > Processing Locus can_0_3189753_0:1-202 [* ] 5% > Processing Locus can_0_3218459_0:27-297 [* ] 6% > Processing Locus can_0_3218459_0:550-900 [* ] 7% > Processing Locus can_0_3270131_0:20-2269 [** ] 8% > Processing Locus ct_1_3082021_0:6-128 [** ] 10% > Processing Locus ct_1_3125173_0:21-180 [** ] 11% > Processing Locus ct_1_3132277_0:0-175 [*** ] 12% > Processing Locus ct_1_3133451_0:21-180 [*** ] 13% > Processing Locus ct_1_3133995_0:14-195 [*** ] 15% > Processing Locus ct_1_3241157_0:5-760 [**** ] 16% > Processing Locus ct_1_3247037_0:227-475 [**** ] 17% > Processing Locus ct_1_3302721_0:383-1593 [**** ] 18% > Processing Locus edi_0_2859720_0:132-524 [***** ] 20% > Processing Locus edi_0_2871668_0:188-523 [***** ] 21% > Processing Locus edi_0_2891226_0:502-795 [***** ] 22% > Processing Locus edi_0_2891226_0:1009-1087 [***** ] 23% > Processing Locus edi_0_2932438_0:37-288 [****** ] 25% > Processing Locus hi_0_2795398_0:0-191 [****** ] 26% > Processing Locus hi_0_2939638_0:12-639 [****** ] 27% > Processing Locus hi_0_2953648_0:897-975 [******* ] 28% > Processing Locus hi_0_2961678_0:213-1508 [******* ] 30% > Processing Locus kn_0_3594465_0:13-159 [******* ] 31% > Processing Locus kn_0_3613403_0:9-130 [******** ] 32% > Processing Locus ler_0_3998410_0:11-163 [******** ] 33% > Processing Locus ler_0_4018856_0:6-182 [******** ] 35% > Processing Locus ler_0_4224097_0:847-1752 [********* ] 36% > Processing Locus ler_0_4225073_0:196-696 [********* ] 37% > Processing Locus mt_0_4217716_0:8-175 [********* ] 38% > Processing Locus mt_0_4229662_0:1-196 [********** ] 40% > Processing Locus mt_0_4230874_0:34-188 [********** ] 41% > Processing Locus mt_0_4231054_0:3-81 [********** ] 42% > Processing Locus mt_0_4528444_1:307-385 [********** ] 43% > Processing Locus mt_0_4528444_1:552-1245 [*********** ] 45% > Processing Locus no_0_2885444_0:9-105 [*********** ] 46% > Processing Locus no_0_2905273_0:13-121 [*********** ] 47% > Processing Locus no_0_2934639_0:40-124 [************ ] 48% > Processing Locus no_0_2956652_0:17-172 [************ ] 50% > Processing Locus no_0_3128142_0:1740-2956 [************ ] 51% > Processing Locus oy_0_3001818_0:33-154 [************* ] 52% > Processing Locus oy_0_3121110_0:50-535 [************* ] 53% > Processing Locus po_0_3299272_0:4-119 [************* ] 55% > Processing Locus po_0_3306688_0:15-122 [************** ] 56% > Processing Locus po_0_3324652_0:6-130 [************** ] 57% > Processing Locus po_0_3330421_0:4-135 [************** ] 58% > Processing Locus po_0_3332479_0:0-136 [*************** ] 60% > Processing Locus po_0_3340213_0:2-137 [*************** ] 61% > Processing Locus po_0_3382155_0:0-128 [*************** ] 62% > Processing Locus po_0_3573778_0:349-1257 [*************** ] 63% > Processing Locus rsch_4_4032032_0:0-85 [**************** ] 65% > Processing Locus rsch_4_4055167_0:0-107 [**************** ] 66% > Processing Locus rsch_4_4219071_0:91-362 [**************** ] 67% > Processing Locus rsch_4_4266550_0:6-1142 [***************** ] 68% > Processing Locus rsch_4_4277288_0:0-1368 [***************** ] 70% > Processing Locus sf_2_2682779_0:647-779 [***************** ] 71% > Processing Locus sf_2_2682779_0:913-991 [****************** ] 72% > Processing Locus sf_2_2682779_0:1277-1355 [****************** ] 73% > Processing Locus sf_2_2687786_0:2-2191 [****************** ] 75% > Processing Locus tsu_0_3208747_0:9-401 [******************* ] 76% > Processing Locus wil_2_2834553_0:0-95 [******************* ] 77% > Processing Locus wil_2_2925323_0:0-195 [******************* ] 78% > Processing Locus wil_2_3077447_0:647-1007 [******************** ] 80% > Processing Locus ws_0_3190963_0:52-130 [******************** ] 81% > Processing Locus ws_0_3326342_0:39-362 [******************** ] 82% > Processing Locus ws_0_3340488_0:176-1139 [******************** ] 83% > Processing Locus ws_0_3347582_0:314-686 [********************* ] 85% > Processing Locus ws_0_3347582_0:792-870 [********************* ] 86% > Processing Locus ws_0_3347582_0:1188-1358 [********************* ] 87% > Processing Locus ws_0_3371988_0:0-250 [********************** ] 88% > Processing Locus ws_0_3371988_0:1663-1741 [********************** ] 90% > Processing Locus ws_0_3373604_0:1607-2762 [********************** ] 91% > Processing Locus ws_0_3380934_0:3-190 [*********************** ] 92% > Processing Locus ws_0_3381390_0:8-1730 [*********************** ] 93% > Processing Locus wu_0_2654219_0:39-142 [*********************** ] 95% > Processing Locus wu_0_2678387_0:38-128 [************************ ] 96% > Processing Locus zu_0_3243571_0:55-799 [************************ ] 97% > Processing Locus zu_0_3259399_1:90-318 [************************ ] 98% > Processed 80 loci. [*************************] 100% [14:07:36] Loading reference annotation and sequence [14:07:36] Learning bias parameters. > Processing Locus can_0_3076940_0:0-129 [ ] 0% > Processing Locus can_0_3122480_0:0-116 [ ] 1% > Processing Locus can_0_3189753_0:1-202 [ ] 2% > Processing Locus can_0_3218459_0:27-297 [ ] 3% > Processing Locus can_0_3218459_0:550-900 [* ] 5% > Processing Locus can_0_3270131_0:20-2269 [* ] 6% > Processing Locus ct_1_3082021_0:6-128 [* ] 7% > Processing Locus ct_1_3125173_0:21-180 [** ] 8% > Processing Locus ct_1_3132277_0:0-175 [** ] 10% > Processing Locus ct_1_3133451_0:21-180 [** ] 11% > Processing Locus ct_1_3133995_0:14-195 [*** ] 12% > Processing Locus ct_1_3241157_0:5-760 [*** ] 13% > Processing Locus ct_1_3302721_0:383-966 [*** ] 15% > Processing Locus ct_1_3302721_0:1121-1593 [**** ] 16% > Processing Locus edi_0_2859720_0:132-524 [**** ] 17% > Processing Locus edi_0_2871668_0:188-523 [**** ] 18% > Processing Locus edi_0_2932438_0:37-288 [***** ] 20% > Processing Locus hi_0_2795398_0:0-191 [***** ] 21% > Processing Locus hi_0_2939638_0:12-639 [***** ] 22% > Processing Locus hi_0_2961678_0:213-1508 [***** ] 23% > Processing Locus kn_0_3594465_0:13-159 [****** ] 25% > Processing Locus ler_0_4018856_0:6-182 [****** ] 26% > Processing Locus ler_0_4224097_0:847-1752 [****** ] 27% > Processing Locus mt_0_4217716_0:8-175 [******* ] 28% > Processing Locus mt_0_4229662_0:1-196 [******* ] 30% > Processing Locus mt_0_4230874_0:34-188 [******* ] 31% > Processing Locus mt_0_4528444_1:552-1245 [******** ] 32% > Processing Locus no_0_3128142_0:1740-2956 [******** ] 33% > Processing Locus oy_0_3001818_0:33-154 [******** ] 35% > Processing Locus oy_0_3121110_0:50-535 [********* ] 36% > Processing Locus po_0_3299272_0:4-119 [********* ] 37% > Processing Locus po_0_3306688_0:15-122 [********* ] 38% > Processing Locus po_0_3324652_0:6-130 [********** ] 40% > Processing Locus po_0_3330421_0:4-135 [********** ] 41% > Processing Locus po_0_3332479_0:0-136 [********** ] 42% > Processing Locus po_0_3382155_0:0-128 [********** ] 43% > Processing Locus po_0_3573778_0:349-1257 [*********** ] 45% > Processing Locus rsch_4_4032032_0:0-85 [*********** ] 46% > Processing Locus rsch_4_4055167_0:0-107 [*********** ] 47% > Processing Locus rsch_4_4266550_0:6-1142 [************ ] 48% > Processing Locus rsch_4_4277288_0:0-1368 [************ ] 50% > Processing Locus sf_2_2687786_0:2-2191 [************ ] 51% > Processing Locus tsu_0_3208747_0:9-401 [************* ] 52% > Processing Locus wil_2_2925323_0:0-195 [************* ] 53% > Processing Locus ws_0_3340488_0:176-1139 [************* ] 55% > Processing Locus ws_0_3347582_0:314-686 [************** ] 56% > Processing Locus ws_0_3371988_0:0-250 [************** ] 57% > Processing Locus ws_0_3373604_0:1607-2762 [************** ] 58% > Processing Locus ws_0_3380934_0:3-190 [*************** ] 60% > Processing Locus ws_0_3381390_0:8-1730 [*************** ] 61% > Processing Locus zu_0_3243571_0:55-799 [*************** ] 62% > Processing Locus zu_0_3259399_1:90-318 [*************** ] 63% > Processed 52 loci. [*************************] 100% [14:07:36] Assembling transcripts and estimating abundances. > Processing Locus can_0_3076940_0:0-129 [ ] 0% > Processing Locus can_0_3122480_0:0-116 [ ] 1% > Processing Locus can_0_3189753_0:1-202 [ ] 2% > Processing Locus can_0_3218459_0:27-297 [ ] 3% > Processing Locus can_0_3218459_0:550-900 [* ] 5% > Processing Locus can_0_3270131_0:20-2269 [* ] 6% > Processing Locus ct_1_3082021_0:6-128 [* ] 7% > Processing Locus ct_1_3125173_0:21-180 [** ] 8% > Processing Locus ct_1_3132277_0:0-175 [** ] 10% > Processing Locus ct_1_3133451_0:21-180 [** ] 11% > Processing Locus ct_1_3133995_0:14-195 [*** ] 12% > Processing Locus ct_1_3241157_0:5-760 [*** ] 13% > Processing Locus ct_1_3302721_0:383-966 [*** ] 15% > Processing Locus ct_1_3302721_0:1121-1593 [**** ] 16% > Processing Locus edi_0_2859720_0:132-524 [**** ] 17% > Processing Locus edi_0_2871668_0:188-523 [**** ] 18% > Processing Locus edi_0_2932438_0:37-288 [***** ] 20% > Processing Locus hi_0_2795398_0:0-191 [***** ] 21% > Processing Locus hi_0_2939638_0:12-639 [***** ] 22% > Processing Locus hi_0_2961678_0:213-1508 [***** ] 23% > Processing Locus kn_0_3594465_0:13-159 [****** ] 25% > Processing Locus ler_0_4018856_0:6-182 [****** ] 26% > Processing Locus ler_0_4224097_0:847-1752 [****** ] 27% > Processing Locus mt_0_4217716_0:8-175 [******* ] 28% > Processing Locus mt_0_4229662_0:1-196 [******* ] 30% > Processing Locus mt_0_4230874_0:34-188 [******* ] 31% > Processing Locus mt_0_4528444_1:552-1245 [******** ] 32% > Processing Locus no_0_3128142_0:1740-2956 [******** ] 33% > Processing Locus oy_0_3001818_0:33-154 [******** ] 35% > Processing Locus oy_0_3121110_0:50-535 [********* ] 36% > Processing Locus po_0_3299272_0:4-119 [********* ] 37% > Processing Locus po_0_3306688_0:15-122 [********* ] 38% > Processing Locus po_0_3324652_0:6-130 [********** ] 40% > Processing Locus po_0_3330421_0:4-135 [********** ] 41% > Processing Locus po_0_3332479_0:0-136 [********** ] 42% > Processing Locus po_0_3382155_0:0-128 [********** ] 43% > Processing Locus po_0_3573778_0:349-1257 [*********** ] 45% > Processing Locus rsch_4_4032032_0:0-85 [*********** ] 46% > Processing Locus rsch_4_4055167_0:0-107 [*********** ] 47% > Processing Locus rsch_4_4266550_0:6-1142 [************ ] 48% > Processing Locus rsch_4_4277288_0:0-1368 [************ ] 50% > Processing Locus sf_2_2687786_0:2-2191 [************ ] 51% > Processing Locus tsu_0_3208747_0:9-401 [************* ] 52% > Processing Locus wil_2_2925323_0:0-195 [************* ] 53% > Processing Locus ws_0_3340488_0:176-1139 [************* ] 55% > Processing Locus ws_0_3347582_0:314-686 [************** ] 56% > Processing Locus ws_0_3371988_0:0-250 [************** ] 57% > Processing Locus ws_0_3373604_0:1607-2762 [************** ] 58% > Processing Locus ws_0_3380934_0:3-190 [*************** ] 60% > Processing Locus ws_0_3381390_0:8-1730 [*************** ] 61% > Processing Locus zu_0_3243571_0:55-799 [*************** ] 62% > Processing Locus zu_0_3259399_1:90-318 [*************** ] 63% > Processed 52 loci. [*************************] 100% [Mon Apr 4 14:07:36 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:07:40 2011] Mapping reads against it2.fa with Bowtie(2/3) min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 14:07:40 2011] Searching for junctions via segment mapping [Mon Apr 4 14:07:43 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:07:45 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:07:47 2011] Joining segment hits [Mon Apr 4 14:07:48 2011] Retrieving sequences for splices [Mon Apr 4 14:07:48 2011] Indexing splices [Mon Apr 4 14:07:48 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:07:49 2011] Searching for junctions via segment mapping [Mon Apr 4 14:07:50 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:07:53 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:07:55 2011] Joining segment hits [Mon Apr 4 14:07:56 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:11 elapsed] [Mon Apr 4 14:07:58 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:08:02 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:08:02 2011] Retrieving sequences for splices [Mon Apr 4 14:08:02 2011] Indexing splices [Mon Apr 4 14:08:02 2011] Mapping reads against segment_juncs with Bowtie cufflinks -p 4 -o ./Edi_0 -r it2.fa ./Edi_0/accepted_hits.bam [14:08:03] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:7-87 [ ] 0% > Processing Locus can_0_3076940_0:8-142 [ ] 0% > Processing Locus can_0_3093852_0:0-126 [ ] 0% > Processing Locus can_0_3122480_0:5-167 [ ] 1% > Processing Locus can_0_3258779_0:48-639 [ ] 1% > Processing Locus can_0_3270131_0:66-977 [ ] 2% > Processing Locus can_0_3270131_0:1119-2270 [ ] 2% > Processing Locus ct_1_3082021_0:0-129 [ ] 2% > Processing Locus ct_1_3132277_0:65-174 [ ] 2% > Processing Locus ct_1_3302721_0:1261-1339 [ ] 3% > Processing Locus edi_0_2723255_0:2-138 [ ] 3% > Processing Locus edi_0_2744702_0:0-156 [* ] 4% > Processing Locus edi_0_2759827_0:4-172 [* ] 4% > Processing Locus edi_0_2859720_0:146-523 [* ] 5% > Processing Locus edi_0_2871668_0:39-534 [* ] 5% > Processing Locus edi_0_2888586_0:7-1052 [* ] 5% > Processing Locus edi_0_2889434_0:4-203 [* ] 6% > Processing Locus edi_0_2889434_0:316-915 [* ] 6% > Processing Locus edi_0_2921730_0:620-1183 [* ] 6% > Processing Locus hi_0_2755116_0:2-84 [* ] 7% > Processing Locus hi_0_2778596_0:14-168 [* ] 7% > Processing Locus hi_0_2916184_0:301-379 [* ] 7% > Processing Locus hi_0_2939638_0:93-642 [** ] 8% > Processing Locus hi_0_2953648_0:212-290 [** ] 8% > Processing Locus hi_0_2961678_0:86-1510 [** ] 9% > Processing Locus kn_0_3594465_0:3-154 [** ] 9% > Processing Locus kn_0_3605300_0:1-161 [** ] 10% > Processing Locus kn_0_3613403_0:0-176 [** ] 10% > Processing Locus kn_0_3617271_0:9-177 [** ] 10% > Processing Locus kn_0_3626969_0:6-189 [** ] 11% > Processing Locus kn_0_3799876_0:73-1492 [** ] 11% > Processing Locus ler_0_3998410_0:1-163 [*** ] 12% > Processing Locus ler_0_4004770_0:65-143 [*** ] 12% > Processing Locus ler_0_4018856_0:1-182 [*** ] 13% > Processing Locus mt_0_4193196_0:0-166 [*** ] 13% > Processing Locus mt_0_4217716_0:4-176 [*** ] 13% > Processing Locus mt_0_4230874_0:42-186 [*** ] 14% > Processing Locus mt_0_4231054_0:0-83 [*** ] 14% > Processing Locus mt_0_4528444_1:555-1196 [*** ] 15% > Processing Locus no_0_2885444_0:2-107 [*** ] 15% > Processing Locus no_0_2905273_0:8-120 [*** ] 15% > Processing Locus no_0_2951521_0:0-151 [**** ] 16% > Processing Locus no_0_2956652_0:2-178 [**** ] 16% > Processing Locus no_0_2959683_0:0-179 [**** ] 17% > Processing Locus no_0_3088052_0:0-953 [**** ] 17% > Processing Locus no_0_3120392_0:231-309 [**** ] 18% > Processing Locus no_0_3120392_0:448-595 [**** ] 18% > Processing Locus no_0_3120392_0:785-863 [**** ] 18% > Processing Locus no_0_3120392_0:1649-1727 [**** ] 18% > Processing Locus no_0_3120392_0:1924-2002 [**** ] 18% > Processing Locus no_0_3120392_0:2149-2523 [**** ] 18% > Processing Locus oy_0_2965192_0:18-123 [**** ] 18% > Processing Locus oy_0_3148368_0:1020-1098 [**** ] 18% > Processing Locus po_0_3330421_0:0-131 [**** ] 19% > Processing Locus rsch_4_4032032_0:0-89 [**** ] 19% > Processing Locus rsch_4_4055167_0:0-107 [***** ] 20% > Processing Locus rsch_4_4085063_0:2-128 [***** ] 20% > Processing Locus rsch_4_4091241_0:11-135 [***** ] 21% > Processing Locus rsch_4_4107621_0:2-155 [***** ] 21% > Processing Locus rsch_4_4110791_0:2-160 [***** ] 21% > Processing Locus rsch_4_4118145_0:5-170 [***** ] 22% > Processing Locus rsch_4_4214541_0:1-234 [***** ] 22% > Processing Locus rsch_4_4219071_0:184-412 [***** ] 23% > Processing Locus rsch_4_4255532_0:0-285 [***** ] 23% > Processing Locus rsch_4_4266550_0:303-381 [***** ] 23% > Processing Locus rsch_4_4277288_0:0-1369 [****** ] 24% > Processing Locus rsch_4_4292194_1:0-832 [****** ] 24% > Processing Locus rsch_4_4292194_1:969-1119 [****** ] 24% > Processing Locus rsch_4_4297142_0:43-291 [****** ] 25% > Processing Locus sf_2_2459023_0:7-110 [****** ] 25% > Processing Locus sf_2_2532172_0:7-175 [****** ] 26% > Processing Locus sf_2_2680171_0:2-1151 [****** ] 26% > Processing Locus sf_2_2687786_0:11-2198 [****** ] 26% > Processing Locus tsu_0_3036945_0:38-143 [****** ] 27% > Processing Locus wil_2_2834553_0:0-82 [****** ] 27% > Processing Locus wil_2_2915899_0:46-172 [******* ] 28% > Processing Locus wil_2_2925323_0:53-190 [******* ] 28% > Processing Locus wil_2_3050523_0:68-264 [******* ] 28% > Processing Locus wil_2_3090237_0:261-495 [******* ] 29% > Processing Locus wil_2_3092619_0:1187-1265 [******* ] 29% > Processing Locus ws_0_3182508_0:4-177 [******* ] 30% > Processing Locus ws_0_3190679_0:31-168 [******* ] 30% > Processing Locus ws_0_3326342_0:90-412 [******* ] 31% > Processing Locus ws_0_3340488_0:200-1139 [******* ] 31% > Processing Locus ws_0_3373604_0:1593-2783 [******* ] 31% > Processing Locus ws_0_3380934_0:1-211 [******** ] 32% > Processing Locus wu_0_2654219_0:5-124 [******** ] 32% > Processing Locus wu_0_2655481_0:3-148 [******** ] 33% > Processing Locus wu_0_2678387_0:7-179 [******** ] 33% > Processing Locus zu_0_3022629_0:4-82 [******** ] 34% > Processing Locus zu_0_3082201_0:1-148 [******** ] 34% > Processing Locus zu_0_3190435_0:119-248 [******** ] 34% > Processing Locus zu_0_3255169_0:98-1118 [******** ] 35% > Processing Locus zu_0_3255503_0:217-295 [******** ] 35% > Processing Locus zu_0_3255503_0:1140-1390 [******** ] 35% > Processing Locus zu_0_3260131_0:167-401 [********* ] 36% > Processing Locus zu_0_3277661_0:240-910 [********* ] 36% > Processed 97 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5628.60 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:08:03] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:7-87 [ ] 0% > Processing Locus can_0_3076940_0:8-142 [ ] 1% > Processing Locus can_0_3093852_0:0-126 [ ] 2% > Processing Locus can_0_3122480_0:5-167 [ ] 3% > Processing Locus can_0_3258779_0:48-639 [* ] 4% > Processing Locus can_0_3270131_0:66-977 [* ] 5% > Processing Locus can_0_3270131_0:1119-2270 [* ] 6% > Processing Locus ct_1_3082021_0:0-129 [* ] 7% > Processing Locus ct_1_3132277_0:65-174 [** ] 8% > Processing Locus ct_1_3302721_0:1261-1339 [** ] 9% > Processing Locus edi_0_2723255_0:2-138 [** ] 10% > Processing Locus edi_0_2744702_0:0-156 [** ] 11% > Processing Locus edi_0_2759827_0:4-172 [*** ] 12% > Processing Locus edi_0_2859720_0:146-523 [*** ] 13% > Processing Locus edi_0_2871668_0:39-534 [*** ] 14% > Processing Locus edi_0_2888586_0:7-1052 [*** ] 15% > Processing Locus edi_0_2889434_0:4-203 [**** ] 16% > Processing Locus edi_0_2889434_0:316-915 [**** ] 17% > Processing Locus edi_0_2921730_0:620-1183 [**** ] 18% > Processing Locus hi_0_2755116_0:2-84 [**** ] 19% > Processing Locus hi_0_2778596_0:14-168 [***** ] 20% > Processing Locus hi_0_2916184_0:301-379 [***** ] 21% > Processing Locus hi_0_2939638_0:93-642 [***** ] 22% > Processing Locus hi_0_2953648_0:212-290 [***** ] 23% > Processing Locus hi_0_2961678_0:86-1510 [****** ] 24% > Processing Locus kn_0_3594465_0:3-154 [****** ] 25% > Processing Locus kn_0_3605300_0:1-161 [****** ] 26% > Processing Locus kn_0_3613403_0:0-176 [****** ] 27% > Processing Locus kn_0_3617271_0:9-177 [******* ] 28% > Processing Locus kn_0_3626969_0:6-189 [******* ] 29% > Processing Locus kn_0_3799876_0:73-1492 [******* ] 30% > Processing Locus ler_0_3998410_0:1-163 [******* ] 31% > Processing Locus ler_0_4004770_0:65-143 [******** ] 32% > Processing Locus ler_0_4018856_0:1-182 [******** ] 34% > Processing Locus mt_0_4193196_0:0-166 [******** ] 35% > Processing Locus mt_0_4217716_0:4-176 [********* ] 36% > Processing Locus mt_0_4230874_0:42-186 [********* ] 37% > Processing Locus mt_0_4231054_0:0-83 [********* ] 38% > Processing Locus mt_0_4528444_1:555-1196 [********* ] 39% > Processing Locus no_0_2885444_0:2-107 [********** ] 40% > Processing Locus no_0_2905273_0:8-120 [********** ] 41% > Processing Locus no_0_2951521_0:0-151 [********** ] 42% > Processing Locus no_0_2956652_0:2-178 [********** ] 43% > Processing Locus no_0_2959683_0:0-179 [*********** ] 44% > Processing Locus no_0_3088052_0:0-953 [*********** ] 45% > Processing Locus no_0_3120392_0:231-309 [*********** ] 46% > Processing Locus no_0_3120392_0:448-595 [*********** ] 47% > Processing Locus no_0_3120392_0:785-863 [************ ] 48% > Processing Locus no_0_3120392_0:1649-1727 [************ ] 49% > Processing Locus no_0_3120392_0:1924-2002 [************ ] 50% > Processing Locus no_0_3120392_0:2149-2523 [************ ] 51% > Processing Locus oy_0_2965192_0:18-123 [************* ] 52% > Processing Locus oy_0_3148368_0:1020-1098 [************* ] 53% > Processing Locus po_0_3330421_0:0-131 [************* ] 54% > Processing Locus rsch_4_4032032_0:0-89 [************* ] 55% > Processing Locus rsch_4_4055167_0:0-107 [************** ] 56% > Processing Locus rsch_4_4085063_0:2-128 [************** ] 57% > Processing Locus rsch_4_4091241_0:11-135 [************** ] 58% > Processing Locus rsch_4_4107621_0:2-155 [************** ] 59% > Processing Locus rsch_4_4110791_0:2-160 [*************** ] 60% > Processing Locus rsch_4_4118145_0:5-170 [*************** ] 61% > Processing Locus rsch_4_4214541_0:1-234 [*************** ] 62% > Processing Locus rsch_4_4219071_0:184-412 [*************** ] 63% > Processing Locus rsch_4_4255532_0:0-285 [**************** ] 64% > Processing Locus rsch_4_4266550_0:303-381 [**************** ] 65% > Processing Locus rsch_4_4277288_0:0-1369 [**************** ] 67% > Processing Locus rsch_4_4292194_1:0-832 [***************** ] 68% > Processing Locus rsch_4_4292194_1:969-1119 [***************** ] 69% > Processing Locus rsch_4_4297142_0:43-291 [***************** ] 70% > Processing Locus sf_2_2459023_0:7-110 [***************** ] 71% > Processing Locus sf_2_2532172_0:7-175 [****************** ] 72% > Processing Locus sf_2_2680171_0:2-1151 [****************** ] 73% > Processing Locus sf_2_2687786_0:11-2198 [****************** ] 74% > Processing Locus tsu_0_3036945_0:38-143 [****************** ] 75% > Processing Locus wil_2_2834553_0:0-82 [******************* ] 76% > Processing Locus wil_2_2915899_0:46-172 [******************* ] 77% > Processing Locus wil_2_2925323_0:53-190 [******************* ] 78% > Processing Locus wil_2_3050523_0:68-264 [******************* ] 79% > Processing Locus wil_2_3090237_0:261-495 [******************** ] 80% > Processing Locus wil_2_3092619_0:1187-1265 [******************** ] 81% > Processing Locus ws_0_3182508_0:4-177 [******************** ] 82% > Processing Locus ws_0_3190679_0:31-168 [******************** ] 83% > Processing Locus ws_0_3326342_0:90-412 [********************* ] 84% > Processing Locus ws_0_3340488_0:200-1139 [********************* ] 85% > Processing Locus ws_0_3373604_0:1593-2783 [********************* ] 86% > Processing Locus ws_0_3380934_0:1-211 [********************* ] 87% > Processing Locus wu_0_2654219_0:5-124 [********************** ] 88% > Processing Locus wu_0_2655481_0:3-148 [********************** ] 89% > Processing Locus wu_0_2678387_0:7-179 [********************** ] 90% > Processing Locus zu_0_3022629_0:4-82 [********************** ] 91% > Processing Locus zu_0_3082201_0:1-148 [*********************** ] 92% > Processing Locus zu_0_3190435_0:119-248 [*********************** ] 93% > Processing Locus zu_0_3255169_0:98-1118 [*********************** ] 94% > Processing Locus zu_0_3255503_0:217-295 [*********************** ] 95% > Processing Locus zu_0_3255503_0:1140-1390 [************************ ] 96% > Processing Locus zu_0_3260131_0:167-401 [************************ ] 97% > Processing Locus zu_0_3277661_0:240-910 [************************ ] 98% > Processed 97 loci. [*************************] 100% [14:08:03] Loading reference annotation and sequence [14:08:03] Learning bias parameters. > Processing Locus can_0_3076940_0:8-142 [ ] 0% > Processing Locus can_0_3122480_0:5-167 [ ] 1% > Processing Locus can_0_3258779_0:48-639 [ ] 2% > Processing Locus can_0_3270131_0:66-977 [ ] 3% > Processing Locus can_0_3270131_0:1119-2270 [* ] 4% > Processing Locus ct_1_3082021_0:0-129 [* ] 5% > Processing Locus ct_1_3132277_0:65-174 [* ] 6% > Processing Locus edi_0_2723255_0:2-138 [* ] 7% > Processing Locus edi_0_2744702_0:0-156 [** ] 8% > Processing Locus edi_0_2759827_0:4-172 [** ] 9% > Processing Locus edi_0_2859720_0:146-523 [** ] 10% > Processing Locus edi_0_2871668_0:39-534 [** ] 11% > Processing Locus edi_0_2888586_0:7-1052 [*** ] 12% > Processing Locus edi_0_2889434_0:4-203 [*** ] 13% > Processing Locus edi_0_2889434_0:316-915 [*** ] 14% > Processing Locus edi_0_2921730_0:620-1183 [*** ] 15% > Processing Locus hi_0_2778596_0:14-168 [**** ] 16% > Processing Locus hi_0_2939638_0:93-642 [**** ] 17% > Processing Locus hi_0_2961678_0:86-1510 [**** ] 18% > Processing Locus kn_0_3594465_0:3-154 [**** ] 19% > Processing Locus kn_0_3605300_0:1-161 [***** ] 20% > Processing Locus kn_0_3613403_0:0-176 [***** ] 21% > Processing Locus kn_0_3617271_0:9-177 [***** ] 22% > Processing Locus kn_0_3626969_0:6-189 [***** ] 23% > Processing Locus kn_0_3799876_0:73-1492 [****** ] 24% > Processing Locus ler_0_3998410_0:1-163 [****** ] 25% > Processing Locus ler_0_4018856_0:1-182 [****** ] 26% > Processing Locus mt_0_4193196_0:0-166 [****** ] 27% > Processing Locus mt_0_4217716_0:4-176 [******* ] 28% > Processing Locus mt_0_4230874_0:42-186 [******* ] 29% > Processing Locus mt_0_4231054_0:0-83 [******* ] 30% > Processing Locus mt_0_4528444_1:555-1196 [******* ] 31% > Processing Locus no_0_2885444_0:2-107 [******** ] 32% > Processing Locus no_0_2905273_0:8-120 [******** ] 34% > Processing Locus no_0_2951521_0:0-151 [******** ] 35% > Processing Locus no_0_2956652_0:2-178 [********* ] 36% > Processing Locus no_0_2959683_0:0-179 [********* ] 37% > Processing Locus no_0_3088052_0:0-953 [********* ] 38% > Processing Locus oy_0_2965192_0:18-123 [********* ] 39% > Processing Locus po_0_3330421_0:0-131 [********** ] 40% > Processing Locus rsch_4_4032032_0:0-89 [********** ] 41% > Processing Locus rsch_4_4055167_0:0-107 [********** ] 42% > Processing Locus rsch_4_4085063_0:2-128 [********** ] 43% > Processing Locus rsch_4_4107621_0:2-155 [*********** ] 44% > Processing Locus rsch_4_4118145_0:5-170 [*********** ] 45% > Processing Locus rsch_4_4214541_0:1-234 [*********** ] 46% > Processing Locus rsch_4_4255532_0:0-285 [*********** ] 47% > Processing Locus rsch_4_4277288_0:0-1369 [************ ] 48% > Processing Locus rsch_4_4292194_1:0-832 [************ ] 49% > Processing Locus rsch_4_4297142_0:43-291 [************ ] 50% > Processing Locus sf_2_2459023_0:7-110 [************ ] 51% > Processing Locus sf_2_2532172_0:7-175 [************* ] 52% > Processing Locus sf_2_2680171_0:2-1151 [************* ] 53% > Processing Locus sf_2_2687786_0:11-2198 [************* ] 54% > Processing Locus wil_2_2925323_0:53-190 [************* ] 55% > Processing Locus wil_2_3050523_0:68-264 [************** ] 56% > Processing Locus ws_0_3340488_0:200-1139 [************** ] 57% > Processing Locus ws_0_3373604_0:1593-2783 [************** ] 58% > Processing Locus ws_0_3380934_0:1-211 [************** ] 59% > Processing Locus wu_0_2654219_0:5-124 [*************** ] 60% > Processing Locus wu_0_2655481_0:3-148 [*************** ] 61% > Processing Locus wu_0_2678387_0:7-179 [*************** ] 62% > Processing Locus zu_0_3082201_0:1-148 [*************** ] 63% > Processing Locus zu_0_3255169_0:98-1118 [**************** ] 64% > Processing Locus zu_0_3255503_0:1140-1390 [**************** ] 65% > Processing Locus zu_0_3277661_0:240-910 [**************** ] 67% > Processed 66 loci. [*************************] 100% [14:08:03] Assembling transcripts and estimating abundances. > Processing Locus can_0_3076940_0:8-142 [ ] 0% > Processing Locus can_0_3122480_0:5-167 [ ] 1% > Processing Locus can_0_3258779_0:48-639 [ ] 2% > Processing Locus can_0_3270131_0:66-977 [ ] 3% > Processing Locus can_0_3270131_0:1119-2270 [* ] 4% > Processing Locus ct_1_3082021_0:0-129 [* ] 5% > Processing Locus ct_1_3132277_0:65-174 [* ] 6% > Processing Locus edi_0_2723255_0:2-138 [* ] 7% > Processing Locus edi_0_2744702_0:0-156 [** ] 8% > Processing Locus edi_0_2759827_0:4-172 [** ] 9% > Processing Locus edi_0_2859720_0:146-523 [** ] 10% > Processing Locus edi_0_2871668_0:39-534 [** ] 11% > Processing Locus edi_0_2888586_0:7-1052 [*** ] 12% > Processing Locus edi_0_2889434_0:4-203 [*** ] 13% > Processing Locus edi_0_2889434_0:316-915 [*** ] 14% > Processing Locus edi_0_2921730_0:620-1183 [*** ] 15% > Processing Locus hi_0_2778596_0:14-168 [**** ] 16% > Processing Locus hi_0_2939638_0:93-642 [**** ] 17% > Processing Locus hi_0_2961678_0:86-1510 [**** ] 18% > Processing Locus kn_0_3594465_0:3-154 [**** ] 19% > Processing Locus kn_0_3605300_0:1-161 [***** ] 20% > Processing Locus kn_0_3613403_0:0-176 [***** ] 21% > Processing Locus kn_0_3617271_0:9-177 [***** ] 22% > Processing Locus kn_0_3626969_0:6-189 [***** ] 23% > Processing Locus kn_0_3799876_0:73-1492 [****** ] 24% > Processing Locus ler_0_3998410_0:1-163 [****** ] 25% > Processing Locus ler_0_4018856_0:1-182 [****** ] 26% > Processing Locus mt_0_4193196_0:0-166 [****** ] 27% > Processing Locus mt_0_4217716_0:4-176 [******* ] 28% > Processing Locus mt_0_4230874_0:42-186 [******* ] 29% > Processing Locus mt_0_4231054_0:0-83 [******* ] 30% > Processing Locus mt_0_4528444_1:555-1196 [******* ] 31% > Processing Locus no_0_2885444_0:2-107 [******** ] 32% > Processing Locus no_0_2905273_0:8-120 [******** ] 34% > Processing Locus no_0_2951521_0:0-151 [******** ] 35% > Processing Locus no_0_2956652_0:2-178 [********* ] 36% > Processing Locus no_0_2959683_0:0-179 [********* ] 37% > Processing Locus no_0_3088052_0:0-953 [********* ] 38% > Processing Locus oy_0_2965192_0:18-123 [********* ] 39% > Processing Locus po_0_3330421_0:0-131 [********** ] 40% > Processing Locus rsch_4_4032032_0:0-89 [********** ] 41% > Processing Locus rsch_4_4055167_0:0-107 [********** ] 42% > Processing Locus rsch_4_4085063_0:2-128 [********** ] 43% > Processing Locus rsch_4_4107621_0:2-155 [*********** ] 44% > Processing Locus rsch_4_4118145_0:5-170 [*********** ] 45% > Processing Locus rsch_4_4214541_0:1-234 [*********** ] 46% > Processing Locus rsch_4_4255532_0:0-285 [*********** ] 47% > Processing Locus rsch_4_4277288_0:0-1369 [************ ] 48% > Processing Locus rsch_4_4292194_1:0-832 [************ ] 49% > Processing Locus rsch_4_4297142_0:43-291 [************ ] 50% > Processing Locus sf_2_2459023_0:7-110 [************ ] 51% > Processing Locus sf_2_2532172_0:7-175 [************* ] 52% > Processing Locus sf_2_2680171_0:2-1151 [************* ] 53% > Processing Locus sf_2_2687786_0:11-2198 [************* ] 54% > Processing Locus wil_2_2925323_0:53-190 [************* ] 55% > Processing Locus wil_2_3050523_0:68-264 [************** ] 56% > Processing Locus ws_0_3340488_0:200-1139 [************** ] 57% > Processing Locus ws_0_3373604_0:1593-2783 [************** ] 58% > Processing Locus ws_0_3380934_0:1-211 [************** ] 59% > Processing Locus wu_0_2654219_0:5-124 [*************** ] 60% > Processing Locus wu_0_2655481_0:3-148 [*************** ] 61% > Processing Locus wu_0_2678387_0:7-179 [*************** ] 62% > Processing Locus zu_0_3082201_0:1-148 [*************** ] 63% > Processing Locus zu_0_3255169_0:98-1118 [**************** ] 64% > Processing Locus zu_0_3255503_0:1140-1390 [**************** ] 65% > Processing Locus zu_0_3277661_0:240-910 [**************** ] 67% > Processed 66 loci. [*************************] 100% [Mon Apr 4 14:08:05 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:08:06 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:08:09 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:08:09 2011] Searching for junctions via segment mapping [Mon Apr 4 14:08:10 2011] Retrieving sequences for splices [Mon Apr 4 14:08:10 2011] Indexing splices [Mon Apr 4 14:08:10 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:08:12 2011] Joining segment hits [Mon Apr 4 14:08:13 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:08:14 2011] Reporting output tracks [Mon Apr 4 14:08:16 2011] Mapping reads against segment_juncs with Bowtie ----------------------------------------------- Run complete [00:01:25 elapsed] [Mon Apr 4 14:08:19 2011] Joining segment hits [Mon Apr 4 14:08:20 2011] Reporting output tracks cufflinks -p 4 -o ./Can_0 -r it2.fa ./Can_0/accepted_hits.bam [14:08:21] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1856286_0:68-152 [ ] 0% > Processing Locus bur_0_1863298_0:31-139 [ ] 0% > Processing Locus bur_0_1868430_0:38-120 [ ] 0% > Processing Locus bur_0_1967596_0:83-161 [ ] 1% > Processing Locus bur_0_1969548_0:29-669 [ ] 1% > Processing Locus bur_0_1999718_0:231-309 [ ] 2% > Processing Locus bur_0_2025286_0:13-2844 [ ] 2% > Processing Locus can_0_3017860_0:0-111 [ ] 2% > Processing Locus can_0_3059433_0:0-138 [ ] 3% > Processing Locus can_0_3076940_0:2-133 [ ] 3% > Processing Locus can_0_3093852_0:0-191 [* ] 4% > Processing Locus can_0_3122480_0:0-176 [* ] 4% > Processing Locus can_0_3216099_0:13-818 [* ] 5% > Processing Locus can_0_3217045_0:6-721 [* ] 5% > Processing Locus can_0_3218459_0:22-900 [* ] 5% > Processing Locus can_0_3223655_0:150-693 [* ] 6% > Processing Locus can_0_3231205_0:12-864 [* ] 6% > Processing Locus can_0_3233581_0:22-456 [* ] 7% > Processing Locus can_0_3234869_1:35-842 [* ] 7% > Processing Locus can_0_3239881_0:3-1064 [* ] 7% > Processing Locus can_0_3257137_1:71-306 [** ] 8% > Processing Locus can_0_3258779_0:39-812 [** ] 8% > Processing Locus can_0_3263637_0:604-877 [** ] 9% > Processing Locus can_0_3270131_0:24-2264 [** ] 9% > Processing Locus ct_1_3082021_0:1-126 [** ] 10% > Processing Locus ct_1_3132277_0:77-175 [** ] 10% > Processing Locus ct_1_3133995_0:0-78 [** ] 10% > Processing Locus ct_1_3241157_0:4-753 [** ] 11% > Processing Locus ct_1_3247037_0:255-553 [** ] 11% > Processing Locus ct_1_3277323_0:47-1266 [*** ] 12% > Processing Locus ct_1_3302721_0:1261-1339 [*** ] 12% > Processing Locus edi_0_2723255_0:4-138 [*** ] 13% > Processing Locus edi_0_2859720_0:143-525 [*** ] 13% > Processing Locus edi_0_2871668_0:41-534 [*** ] 13% > Processing Locus edi_0_2888586_0:24-1049 [*** ] 14% > Processing Locus edi_0_2921730_0:767-875 [*** ] 14% > Processing Locus edi_0_2934714_0:17-454 [*** ] 15% > Processing Locus edi_0_2934714_0:586-857 [*** ] 15% > Processing Locus hi_0_2755116_0:7-86 [*** ] 15% > Processing Locus hi_0_2773206_0:35-113 [*** ] 15% > Processing Locus hi_0_2778596_0:0-166 [**** ] 16% > Processing Locus hi_0_2939638_0:26-633 [**** ] 16% > Processing Locus hi_0_2961678_0:258-398 [**** ] 17% > Processing Locus kn_0_3594465_0:5-156 [**** ] 17% > Processing Locus kn_0_3613403_0:0-129 [**** ] 18% > Processing Locus kn_0_3617271_0:1-177 [**** ] 18% > Processing Locus kn_0_3626969_0:0-191 [**** ] 18% > Processing Locus kn_0_3751597_0:157-235 [**** ] 19% > Processing Locus ler_0_3998410_0:1-164 [**** ] 19% > Processing Locus ler_0_4004770_0:4-171 [***** ] 20% > Processing Locus ler_0_4018856_0:1-185 [***** ] 20% > Processing Locus mt_0_4193196_0:3-166 [***** ] 21% > Processing Locus mt_0_4217716_0:1-185 [***** ] 21% > Processing Locus mt_0_4229662_0:1-196 [***** ] 21% > Processing Locus mt_0_4231054_0:118-198 [***** ] 22% > Processing Locus mt_0_4528444_1:312-390 [***** ] 22% > Processing Locus mt_0_4528444_1:553-1230 [***** ] 22% > Processing Locus no_0_2885444_0:5-109 [***** ] 23% > Processing Locus no_0_2905273_0:7-122 [***** ] 23% > Processing Locus no_0_2951521_0:0-154 [***** ] 23% > Processing Locus no_0_2956652_0:3-177 [****** ] 24% > Processing Locus no_0_2959683_0:0-182 [****** ] 24% > Processing Locus no_0_3116640_0:476-1873 [****** ] 25% > Processing Locus no_0_3128142_0:78-400 [****** ] 25% > Processing Locus no_0_3128142_0:502-747 [****** ] 25% > Processing Locus no_0_3128142_0:1624-2934 [****** ] 25% > Processing Locus oy_0_3001818_0:51-156 [****** ] 26% > Processing Locus oy_0_3148368_0:21-1309 [****** ] 26% > Processing Locus oy_0_3162092_0:1565-1643 [****** ] 26% > Processing Locus po_0_3299272_0:0-119 [****** ] 27% > Processing Locus po_0_3330421_0:0-131 [****** ] 27% > Processing Locus po_0_3332479_0:0-134 [******* ] 28% > Processing Locus po_0_3340213_0:3-139 [******* ] 28% > Processing Locus po_0_3382155_0:2-146 [******* ] 28% > Processing Locus po_0_3393401_0:0-152 [******* ] 29% > Processing Locus rsch_4_4032032_0:0-89 [******* ] 29% > Processing Locus rsch_4_4034850_0:0-102 [******* ] 30% > Processing Locus rsch_4_4055167_0:0-110 [******* ] 30% > Processing Locus rsch_4_4085063_0:2-125 [******* ] 31% > Processing Locus rsch_4_4091241_0:0-139 [******* ] 31% > Processing Locus rsch_4_4107621_0:8-153 [******* ] 31% > Processing Locus rsch_4_4110791_0:1-158 [******** ] 32% > Processing Locus rsch_4_4118145_0:5-170 [******** ] 32% > Processing Locus rsch_4_4122727_0:23-176 [******** ] 33% > Processing Locus rsch_4_4214541_0:1-234 [******** ] 33% > Processing Locus rsch_4_4219071_0:100-412 [******** ] 34% > Processing Locus rsch_4_4255532_0:3-285 [******** ] 34% > Processing Locus rsch_4_4292194_1:0-829 [******** ] 34% > Processing Locus rsch_4_4292194_1:937-1123 [******** ] 34% > Processing Locus rsch_4_4297142_0:37-304 [******** ] 35% > Processing Locus sf_2_2459023_0:1-110 [******** ] 35% > Processing Locus sf_2_2486157_0:6-118 [********* ] 36% > Processing Locus sf_2_2532172_0:6-180 [********* ] 36% > Processing Locus sf_2_2680171_0:0-1135 [********* ] 36% > Processing Locus sf_2_2682779_0:582-1442 [********* ] 37% > Processing Locus sf_2_2687774_0:495-1429 [********* ] 37% > Processing Locus sf_2_2687786_0:2075-2153 [********* ] 38% > Processing Locus tsu_0_3036945_0:0-150 [********* ] 38% > Processing Locus tsu_0_3135135_0:2-212 [********* ] 39% > Processing Locus tsu_0_3215821_0:285-1120 [********* ] 39% > Processing Locus tsu_0_3229935_0:21-1251 [********* ] 39% > Processing Locus wil_2_2834553_0:0-104 [********** ] 40% > Processing Locus wil_2_2892485_0:23-138 [********** ] 40% > Processing Locus wil_2_2915899_0:11-179 [********** ] 41% > Processing Locus wil_2_2925323_0:55-133 [********** ] 41% > Processing Locus wil_2_3050523_0:25-272 [********** ] 42% > Processing Locus wil_2_3052273_0:37-1108 [********** ] 42% > Processing Locus wil_2_3066229_0:242-543 [********** ] 42% > Processing Locus wil_2_3090237_0:265-494 [********** ] 43% > Processing Locus wil_2_3092619_0:469-1394 [********** ] 43% > Processing Locus ws_0_3182508_0:4-174 [*********** ] 44% > Processing Locus ws_0_3190679_0:29-194 [*********** ] 44% > Processing Locus ws_0_3326342_0:35-412 [*********** ] 44% > Processing Locus ws_0_3340488_0:200-1139 [*********** ] 45% > Processing Locus ws_0_3372048_0:21-988 [*********** ] 45% > Processing Locus ws_0_3372048_0:1126-1251 [*********** ] 45% > Processing Locus ws_0_3380934_0:36-203 [*********** ] 46% > Processing Locus ws_0_3381390_0:2-1683 [*********** ] 46% > Processing Locus wu_0_2654219_0:0-78 [*********** ] 47% > Processing Locus wu_0_2678387_0:6-168 [*********** ] 47% > Processing Locus wu_0_2837848_0:40-2520 [*********** ] 47% > Processing Locus zu_0_3022629_0:0-113 [************ ] 48% > Processing Locus zu_0_3075813_0:0-105 [************ ] 48% > Processing Locus zu_0_3082201_0:1-149 [************ ] 49% > Processing Locus zu_0_3091101_0:4-157 [************ ] 49% > Processing Locus zu_0_3092045_0:9-87 [************ ] 50% > Processing Locus zu_0_3118546_0:4-168 [************ ] 50% > Processing Locus zu_0_3119698_0:71-193 [************ ] 50% > Processing Locus zu_0_3238769_0:19-193 [************ ] 51% > Processing Locus zu_0_3238769_0:341-419 [************ ] 51% > Processing Locus zu_0_3242889_0:2-384 [************ ] 51% > Processing Locus zu_0_3255169_0:253-688 [************* ] 52% > Processing Locus zu_0_3255169_0:909-1111 [************* ] 52% > Processing Locus zu_0_3255503_0:1066-1385 [************* ] 52% > Processing Locus zu_0_3260131_0:171-400 [************* ] 52% > Processing Locus zu_0_3277661_0:232-911 [************* ] 53% > Processing Locus zu_0_3278243_0:0-107 [************* ] 53% > Processed 137 loci. [*************************] 100% > Map Properties: > Total Map Mass: 11122.91 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:08:21] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1856286_0:68-152 [ ] 0% > Processing Locus bur_0_1863298_0:31-139 [ ] 0% > Processing Locus bur_0_1868430_0:38-120 [ ] 1% > Processing Locus bur_0_1967596_0:83-161 [ ] 2% > Processing Locus bur_0_1969548_0:29-669 [ ] 2% > Processing Locus bur_0_1999718_0:231-309 [ ] 3% > Processing Locus bur_0_2025286_0:13-2844 [* ] 4% > Processing Locus can_0_3017860_0:0-111 [* ] 5% > Processing Locus can_0_3059433_0:0-138 [* ] 5% > Processing Locus can_0_3076940_0:2-133 [* ] 6% > Processing Locus can_0_3093852_0:0-191 [* ] 7% > Processing Locus can_0_3122480_0:0-176 [** ] 8% > Processing Locus can_0_3216099_0:13-818 [** ] 8% > Processing Locus can_0_3217045_0:6-721 [** ] 9% > Processing Locus can_0_3218459_0:22-900 [** ] 10% > Processing Locus can_0_3223655_0:150-693 [** ] 10% > Processing Locus can_0_3231205_0:12-864 [** ] 11% > Processing Locus can_0_3233581_0:22-456 [*** ] 12% > Processing Locus can_0_3234869_1:35-842 [*** ] 13% > Processing Locus can_0_3239881_0:3-1064 [*** ] 13% > Processing Locus can_0_3257137_1:71-306 [*** ] 14% > Processing Locus can_0_3258779_0:39-812 [*** ] 15% > Processing Locus can_0_3263637_0:604-877 [**** ] 16% > Processing Locus can_0_3270131_0:24-2264 [**** ] 16% > Processing Locus ct_1_3082021_0:1-126 [**** ] 17% > Processing Locus ct_1_3132277_0:77-175 [**** ] 18% > Processing Locus ct_1_3133995_0:0-78 [**** ] 18% > Processing Locus ct_1_3241157_0:4-753 [**** ] 19% > Processing Locus ct_1_3247037_0:255-553 [***** ] 20% > Processing Locus ct_1_3277323_0:47-1266 [***** ] 21% > Processing Locus ct_1_3302721_0:1261-1339 [***** ] 21% > Processing Locus edi_0_2723255_0:4-138 [***** ] 22% > Processing Locus edi_0_2859720_0:143-525 [***** ] 23% > Processing Locus edi_0_2871668_0:41-534 [****** ] 24% > Processing Locus edi_0_2888586_0:24-1049 [****** ] 24% > Processing Locus edi_0_2921730_0:767-875 [****** ] 25% > Processing Locus edi_0_2934714_0:17-454 [****** ] 26% > Processing Locus edi_0_2934714_0:586-857 [****** ] 27% > Processing Locus hi_0_2755116_0:7-86 [****** ] 27% > Processing Locus hi_0_2773206_0:35-113 [******* ] 28% > Processing Locus hi_0_2778596_0:0-166 [******* ] 29% > Processing Locus hi_0_2939638_0:26-633 [******* ] 29% > Processing Locus hi_0_2961678_0:258-398 [******* ] 30% > Processing Locus kn_0_3594465_0:5-156 [******* ] 31% > Processing Locus kn_0_3613403_0:0-129 [******** ] 32% > Processing Locus kn_0_3617271_0:1-177 [******** ] 32% > Processing Locus kn_0_3626969_0:0-191 [******** ] 33% > Processing Locus kn_0_3751597_0:157-235 [******** ] 34% > Processing Locus ler_0_3998410_0:1-164 [******** ] 35% > Processing Locus ler_0_4004770_0:4-171 [******** ] 35% > Processing Locus ler_0_4018856_0:1-185 [********* ] 36% > Processing Locus mt_0_4193196_0:3-166 [********* ] 37% > Processing Locus mt_0_4217716_0:1-185 [********* ] 37% > Processing Locus mt_0_4229662_0:1-196 [********* ] 38% > Processing Locus mt_0_4231054_0:118-198 [********* ] 39% > Processing Locus mt_0_4528444_1:312-390 [********** ] 40% > Processing Locus mt_0_4528444_1:553-1230 [********** ] 40% > Processing Locus no_0_2885444_0:5-109 [********** ] 41% > Processing Locus no_0_2905273_0:7-122 [********** ] 42% > Processing Locus no_0_2951521_0:0-154 [********** ] 43% > Processing Locus no_0_2956652_0:3-177 [********** ] 43% > Processing Locus no_0_2959683_0:0-182 [*********** ] 44% > Processing Locus no_0_3116640_0:476-1873 [*********** ] 45% > Processing Locus no_0_3128142_0:78-400 [*********** ] 45% > Processing Locus no_0_3128142_0:502-747 [*********** ] 46% > Processing Locus no_0_3128142_0:1624-2934 [*********** ] 47% > Processing Locus oy_0_3001818_0:51-156 [************ ] 48% > Processing Locus oy_0_3148368_0:21-1309 [************ ] 48% > Processing Locus oy_0_3162092_0:1565-1643 [************ ] 49% > Processing Locus po_0_3299272_0:0-119 [************ ] 50% > Processing Locus po_0_3330421_0:0-131 [************ ] 51% > Processing Locus po_0_3332479_0:0-134 [************ ] 51% > Processing Locus po_0_3340213_0:3-139 [************* ] 52% > Processing Locus po_0_3382155_0:2-146 [************* ] 53% > Processing Locus po_0_3393401_0:0-152 [************* ] 54% > Processing Locus rsch_4_4032032_0:0-89 [************* ] 54% > Processing Locus rsch_4_4034850_0:0-102 [************* ] 55% > Processing Locus rsch_4_4055167_0:0-110 [************** ] 56% > Processing Locus rsch_4_4085063_0:2-125 [************** ] 56% > Processing Locus rsch_4_4091241_0:0-139 [************** ] 57% > Processing Locus rsch_4_4107621_0:8-153 [************** ] 58% > Processing Locus rsch_4_4110791_0:1-158 [************** ] 59% > Processing Locus rsch_4_4118145_0:5-170 [************** ] 59% > Processing Locus rsch_4_4122727_0:23-176 [*************** ] 60% > Processing Locus rsch_4_4214541_0:1-234 [*************** ] 61% > Processing Locus rsch_4_4219071_0:100-412 [*************** ] 62% > Processing Locus rsch_4_4255532_0:3-285 [*************** ] 62% > Processing Locus rsch_4_4292194_1:0-829 [*************** ] 63% > Processing Locus rsch_4_4292194_1:937-1123 [**************** ] 64% > Processing Locus rsch_4_4297142_0:37-304 [**************** ] 64% > Processing Locus sf_2_2459023_0:1-110 [**************** ] 65% > Processing Locus sf_2_2486157_0:6-118 [**************** ] 66% > Processing Locus sf_2_2532172_0:6-180 [**************** ] 67% > Processing Locus sf_2_2680171_0:0-1135 [**************** ] 67% > Processing Locus sf_2_2682779_0:582-1442 [***************** ] 68% > Processing Locus sf_2_2687774_0:495-1429 [***************** ] 69% > Processing Locus sf_2_2687786_0:2075-2153 [***************** ] 70% > Processing Locus tsu_0_3036945_0:0-150 [***************** ] 70% > Processing Locus tsu_0_3135135_0:2-212 [***************** ] 71% > Processing Locus tsu_0_3215821_0:285-1120 [****************** ] 72% > Processing Locus tsu_0_3229935_0:21-1251 [****************** ] 72% > Processing Locus wil_2_2834553_0:0-104 [****************** ] 73% > Processing Locus wil_2_2892485_0:23-138 [****************** ] 74% > Processing Locus wil_2_2915899_0:11-179 [****************** ] 75% > Processing Locus wil_2_2925323_0:55-133 [****************** ] 75% > Processing Locus wil_2_3050523_0:25-272 [******************* ] 76% > Processing Locus wil_2_3052273_0:37-1108 [******************* ] 77% > Processing Locus wil_2_3066229_0:242-543 [******************* ] 78% > Processing Locus wil_2_3090237_0:265-494 [******************* ] 78% > Processing Locus wil_2_3092619_0:469-1394 [******************* ] 79% > Processing Locus ws_0_3182508_0:4-174 [******************** ] 80% > Processing Locus ws_0_3190679_0:29-194 [******************** ] 81% > Processing Locus ws_0_3326342_0:35-412 [******************** ] 81% > Processing Locus ws_0_3340488_0:200-1139 [******************** ] 82% > Processing Locus ws_0_3372048_0:21-988 [******************** ] 83% > Processing Locus ws_0_3372048_0:1126-1251 [******************** ] 83% > Processing Locus ws_0_3380934_0:36-203 [********************* ] 84% > Processing Locus ws_0_3381390_0:2-1683 [********************* ] 85% > Processing Locus wu_0_2654219_0:0-78 [********************* ] 86% > Processing Locus wu_0_2678387_0:6-168 [********************* ] 86% > Processing Locus wu_0_2837848_0:40-2520 [********************* ] 87% > Processing Locus zu_0_3022629_0:0-113 [********************** ] 88% > Processing Locus zu_0_3075813_0:0-105 [********************** ] 89% > Processing Locus zu_0_3082201_0:1-149 [********************** ] 89% > Processing Locus zu_0_3091101_0:4-157 [********************** ] 90% > Processing Locus zu_0_3092045_0:9-87 [********************** ] 91% > Processing Locus zu_0_3118546_0:4-168 [********************** ] 91% > Processing Locus zu_0_3119698_0:71-193 [*********************** ] 92% > Processing Locus zu_0_3238769_0:19-193 [*********************** ] 93% > Processing Locus zu_0_3238769_0:341-419 [*********************** ] 94% > Processing Locus zu_0_3242889_0:2-384 [*********************** ] 94% > Processing Locus zu_0_3255169_0:253-688 [*********************** ] 95% > Processing Locus zu_0_3255169_0:909-1111 [************************ ] 96% > Processing Locus zu_0_3255503_0:1066-1385 [************************ ] 97% > Processing Locus zu_0_3260131_0:171-400 [************************ ] 97% > Processing Locus zu_0_3277661_0:232-911 [************************ ] 98% > Processing Locus zu_0_3278243_0:0-107 [************************ ] 99% > Processed 137 loci. [*************************] 100% [14:08:21] Loading reference annotation and sequence [14:08:21] Learning bias parameters. > Processing Locus bur_0_1863298_0:31-139 [ ] 0% > Processing Locus bur_0_1969548_0:29-669 [ ] 0% > Processing Locus bur_0_2025286_0:13-2844 [ ] 1% > Processing Locus can_0_3017860_0:0-111 [ ] 2% > Processing Locus can_0_3059433_0:0-138 [ ] 2% > Processing Locus can_0_3076940_0:2-133 [ ] 3% > Processing Locus can_0_3122480_0:0-176 [* ] 4% > Processing Locus can_0_3216099_0:13-818 [* ] 5% > Processing Locus can_0_3217045_0:6-721 [* ] 5% > Processing Locus can_0_3218459_0:22-900 [* ] 6% > Processing Locus can_0_3223655_0:150-693 [* ] 7% > Processing Locus can_0_3231205_0:12-864 [** ] 8% > Processing Locus can_0_3233581_0:22-456 [** ] 8% > Processing Locus can_0_3234869_1:35-842 [** ] 9% > Processing Locus can_0_3239881_0:3-1064 [** ] 10% > Processing Locus can_0_3257137_1:71-306 [** ] 10% > Processing Locus can_0_3258779_0:39-812 [** ] 11% > Processing Locus can_0_3263637_0:604-877 [*** ] 12% > Processing Locus can_0_3270131_0:24-2264 [*** ] 13% > Processing Locus ct_1_3082021_0:1-126 [*** ] 13% > Processing Locus ct_1_3132277_0:77-175 [*** ] 14% > Processing Locus ct_1_3241157_0:4-753 [*** ] 15% > Processing Locus ct_1_3277323_0:47-1266 [**** ] 16% > Processing Locus edi_0_2723255_0:4-138 [**** ] 16% > Processing Locus edi_0_2859720_0:143-525 [**** ] 17% > Processing Locus edi_0_2871668_0:41-534 [**** ] 18% > Processing Locus edi_0_2888586_0:24-1049 [**** ] 18% > Processing Locus hi_0_2755116_0:7-86 [**** ] 19% > Processing Locus hi_0_2778596_0:0-166 [***** ] 20% > Processing Locus hi_0_2939638_0:26-633 [***** ] 21% > Processing Locus kn_0_3594465_0:5-156 [***** ] 21% > Processing Locus kn_0_3613403_0:0-129 [***** ] 22% > Processing Locus kn_0_3617271_0:1-177 [***** ] 23% > Processing Locus kn_0_3626969_0:0-191 [****** ] 24% > Processing Locus ler_0_3998410_0:1-164 [****** ] 24% > Processing Locus ler_0_4004770_0:4-171 [****** ] 25% > Processing Locus ler_0_4018856_0:1-185 [****** ] 26% > Processing Locus mt_0_4193196_0:3-166 [****** ] 27% > Processing Locus mt_0_4217716_0:1-185 [****** ] 27% > Processing Locus mt_0_4229662_0:1-196 [******* ] 28% > Processing Locus mt_0_4528444_1:553-1230 [******* ] 29% > Processing Locus no_0_2885444_0:5-109 [******* ] 29% > Processing Locus no_0_2905273_0:7-122 [******* ] 30% > Processing Locus no_0_2956652_0:3-177 [******* ] 31% > Processing Locus no_0_2959683_0:0-182 [******** ] 32% > Processing Locus no_0_3116640_0:476-1873 [******** ] 32% > Processing Locus no_0_3128142_0:78-400 [******** ] 33% > Processing Locus no_0_3128142_0:502-747 [******** ] 34% > Processing Locus no_0_3128142_0:1624-2934 [******** ] 35% > Processing Locus oy_0_3001818_0:51-156 [******** ] 35% > Processing Locus po_0_3299272_0:0-119 [********* ] 36% > Processing Locus po_0_3330421_0:0-131 [********* ] 37% > Processing Locus po_0_3332479_0:0-134 [********* ] 37% > Processing Locus rsch_4_4032032_0:0-89 [********* ] 38% > Processing Locus rsch_4_4034850_0:0-102 [********* ] 39% > Processing Locus rsch_4_4055167_0:0-110 [********** ] 40% > Processing Locus rsch_4_4085063_0:2-125 [********** ] 40% > Processing Locus rsch_4_4091241_0:0-139 [********** ] 41% > Processing Locus rsch_4_4107621_0:8-153 [********** ] 42% > Processing Locus rsch_4_4118145_0:5-170 [********** ] 43% > Processing Locus rsch_4_4214541_0:1-234 [********** ] 43% > Processing Locus rsch_4_4255532_0:3-285 [*********** ] 44% > Processing Locus rsch_4_4292194_1:0-829 [*********** ] 45% > Processing Locus rsch_4_4292194_1:937-1123 [*********** ] 45% > Processing Locus rsch_4_4297142_0:37-304 [*********** ] 46% > Processing Locus sf_2_2459023_0:1-110 [*********** ] 47% > Processing Locus sf_2_2486157_0:6-118 [************ ] 48% > Processing Locus sf_2_2532172_0:6-180 [************ ] 48% > Processing Locus sf_2_2680171_0:0-1135 [************ ] 49% > Processing Locus sf_2_2682779_0:582-1442 [************ ] 50% > Processing Locus sf_2_2687774_0:495-1429 [************ ] 51% > Processing Locus tsu_0_3036945_0:0-150 [************ ] 51% > Processing Locus tsu_0_3135135_0:2-212 [************* ] 52% > Processing Locus tsu_0_3215821_0:285-1120 [************* ] 53% > Processing Locus wil_2_2834553_0:0-104 [************* ] 54% > Processing Locus wil_2_2892485_0:23-138 [************* ] 54% > Processing Locus wil_2_2915899_0:11-179 [************* ] 55% > Processing Locus wil_2_3050523_0:25-272 [************** ] 56% > Processing Locus wil_2_3052273_0:37-1108 [************** ] 56% > Processing Locus ws_0_3182508_0:4-174 [************** ] 57% > Processing Locus ws_0_3340488_0:200-1139 [************** ] 58% > Processing Locus ws_0_3381390_0:2-1683 [************** ] 59% > Processing Locus wu_0_2678387_0:6-168 [************** ] 59% > Processing Locus wu_0_2837848_0:40-2520 [*************** ] 60% > Processing Locus zu_0_3022629_0:0-113 [*************** ] 61% > Processing Locus zu_0_3075813_0:0-105 [*************** ] 62% > Processing Locus zu_0_3082201_0:1-149 [*************** ] 62% > Processing Locus zu_0_3118546_0:4-168 [*************** ] 63% > Processing Locus zu_0_3242889_0:2-384 [**************** ] 64% > Processing Locus zu_0_3255169_0:253-688 [**************** ] 64% > Processing Locus zu_0_3255169_0:909-1111 [**************** ] 65% > Processing Locus zu_0_3255503_0:1066-1385 [**************** ] 66% > Processing Locus zu_0_3277661_0:232-911 [**************** ] 67% > Processing Locus zu_0_3278243_0:0-107 [**************** ] 67% > Processed 94 loci. [*************************] 100% [14:08:21] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1863298_0:31-139 [ ] 0% > Processing Locus bur_0_1969548_0:29-669 [ ] 0% > Processing Locus bur_0_2025286_0:13-2844 [ ] 1% > Processing Locus can_0_3017860_0:0-111 [ ] 2% > Processing Locus can_0_3059433_0:0-138 [ ] 2% > Processing Locus can_0_3076940_0:2-133 [ ] 3% > Processing Locus can_0_3122480_0:0-176 [* ] 4% > Processing Locus can_0_3216099_0:13-818 [* ] 5% > Processing Locus can_0_3217045_0:6-721 [* ] 5% > Processing Locus can_0_3218459_0:22-900 [* ] 6% > Processing Locus can_0_3223655_0:150-693 [* ] 7% > Processing Locus can_0_3231205_0:12-864 [** ] 8% > Processing Locus can_0_3233581_0:22-456 [** ] 8% > Processing Locus can_0_3234869_1:35-842 [** ] 9% > Processing Locus can_0_3239881_0:3-1064 [** ] 10% > Processing Locus can_0_3257137_1:71-306 [** ] 10% > Processing Locus can_0_3258779_0:39-812 [** ] 11% > Processing Locus can_0_3263637_0:604-877 [*** ] 12% > Processing Locus can_0_3270131_0:24-2264 [*** ] 13% > Processing Locus ct_1_3082021_0:1-126 [*** ] 13% > Processing Locus ct_1_3132277_0:77-175 [*** ] 14% > Processing Locus ct_1_3241157_0:4-753 [*** ] 15% > Processing Locus ct_1_3277323_0:47-1266 [**** ] 16% > Processing Locus edi_0_2723255_0:4-138 [**** ] 16% > Processing Locus edi_0_2859720_0:143-525 [**** ] 17% > Processing Locus edi_0_2871668_0:41-534 [**** ] 18% > Processing Locus edi_0_2888586_0:24-1049 [**** ] 18% > Processing Locus hi_0_2755116_0:7-86 [**** ] 19% > Processing Locus hi_0_2778596_0:0-166 [***** ] 20% > Processing Locus hi_0_2939638_0:26-633 [***** ] 21% > Processing Locus kn_0_3594465_0:5-156 [***** ] 21% > Processing Locus kn_0_3613403_0:0-129 [***** ] 22% > Processing Locus kn_0_3617271_0:1-177 [***** ] 23% > Processing Locus kn_0_3626969_0:0-191 [****** ] 24% > Processing Locus ler_0_3998410_0:1-164 [****** ] 24% > Processing Locus ler_0_4004770_0:4-171 [****** ] 25% > Processing Locus ler_0_4018856_0:1-185 [****** ] 26% > Processing Locus mt_0_4193196_0:3-166 [****** ] 27% > Processing Locus mt_0_4217716_0:1-185 [****** ] 27% > Processing Locus mt_0_4229662_0:1-196 [******* ] 28% > Processing Locus mt_0_4528444_1:553-1230 [******* ] 29% > Processing Locus no_0_2885444_0:5-109 [******* ] 29% > Processing Locus no_0_2905273_0:7-122 [******* ] 30% > Processing Locus no_0_2956652_0:3-177 [******* ] 31% > Processing Locus no_0_2959683_0:0-182 [******** ] 32% > Processing Locus no_0_3116640_0:476-1873 [******** ] 32% > Processing Locus no_0_3128142_0:78-400 [******** ] 33% > Processing Locus no_0_3128142_0:502-747 [******** ] 34% > Processing Locus no_0_3128142_0:1624-2934 [******** ] 35% > Processing Locus oy_0_3001818_0:51-156 [******** ] 35% > Processing Locus po_0_3299272_0:0-119 [********* ] 36% > Processing Locus po_0_3330421_0:0-131 [********* ] 37% > Processing Locus po_0_3332479_0:0-134 [********* ] 37% > Processing Locus rsch_4_4032032_0:0-89 [********* ] 38% > Processing Locus rsch_4_4034850_0:0-102 [********* ] 39% > Processing Locus rsch_4_4055167_0:0-110 [********** ] 40% > Processing Locus rsch_4_4085063_0:2-125 [********** ] 40% > Processing Locus rsch_4_4091241_0:0-139 [********** ] 41% > Processing Locus rsch_4_4107621_0:8-153 [********** ] 42% > Processing Locus rsch_4_4118145_0:5-170 [********** ] 43% > Processing Locus rsch_4_4214541_0:1-234 [********** ] 43% > Processing Locus rsch_4_4255532_0:3-285 [*********** ] 44% > Processing Locus rsch_4_4292194_1:0-829 [*********** ] 45% > Processing Locus rsch_4_4292194_1:937-1123 [*********** ] 45% > Processing Locus rsch_4_4297142_0:37-304 [*********** ] 46% > Processing Locus sf_2_2459023_0:1-110 [*********** ] 47% > Processing Locus sf_2_2486157_0:6-118 [************ ] 48% > Processing Locus sf_2_2532172_0:6-180 [************ ] 48% > Processing Locus sf_2_2680171_0:0-1135 [************ ] 49% > Processing Locus sf_2_2682779_0:582-1442 [************ ] 50% > Processing Locus sf_2_2687774_0:495-1429 [************ ] 51% > Processing Locus tsu_0_3036945_0:0-150 [************ ] 51% > Processing Locus tsu_0_3135135_0:2-212 [************* ] 52% > Processing Locus tsu_0_3215821_0:285-1120 [************* ] 53% > Processing Locus wil_2_2834553_0:0-104 [************* ] 54% > Processing Locus wil_2_2892485_0:23-138 [************* ] 54% > Processing Locus wil_2_2915899_0:11-179 [************* ] 55% > Processing Locus wil_2_3050523_0:25-272 [************** ] 56% > Processing Locus wil_2_3052273_0:37-1108 [************** ] 56% > Processing Locus ws_0_3182508_0:4-174 [************** ] 57% > Processing Locus ws_0_3340488_0:200-1139 [************** ] 58% > Processing Locus ws_0_3381390_0:2-1683 [************** ] 59% > Processing Locus wu_0_2678387_0:6-168 [************** ] 59% > Processing Locus wu_0_2837848_0:40-2520 [*************** ] 60% > Processing Locus zu_0_3022629_0:0-113 [*************** ] 61% > Processing Locus zu_0_3075813_0:0-105 [*************** ] 62% > Processing Locus zu_0_3082201_0:1-149 [*************** ] 62% > Processing Locus zu_0_3118546_0:4-168 [*************** ] 63% > Processing Locus zu_0_3242889_0:2-384 [**************** ] 64% > Processing Locus zu_0_3255169_0:253-688 [**************** ] 64% > Processing Locus zu_0_3255169_0:909-1111 [**************** ] 65% > Processing Locus zu_0_3255503_0:1066-1385 [**************** ] 66% > Processing Locus zu_0_3277661_0:232-911 [**************** ] 67% > Processing Locus zu_0_3278243_0:0-107 [**************** ] 67% > Processed 94 loci. [*************************] 100% ----------------------------------------------- Run complete [00:01:29 elapsed] [Mon Apr 4 14:08:25 2011] Retrieving sequences for splices [Mon Apr 4 14:08:25 2011] Indexing splices [Mon Apr 4 14:08:26 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:08:28 2011] Mapping reads against segment_juncs with Bowtie cufflinks -p 4 -o ./Bur_0 -r it2.fa ./Bur_0/accepted_hits.bam [14:08:28] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:0-113 [ ] 0% > Processing Locus bur_0_1856286_0:5-162 [ ] 0% > Processing Locus bur_0_1863298_0:48-153 [ ] 0% > Processing Locus bur_0_1868430_0:31-135 [ ] 1% > Processing Locus bur_0_1873494_0:14-187 [ ] 1% > Processing Locus bur_0_1967596_0:8-428 [ ] 2% > Processing Locus bur_0_1969548_0:1-680 [ ] 2% > Processing Locus bur_0_1999718_0:2-901 [ ] 2% > Processing Locus bur_0_2020452_0:0-1309 [ ] 3% > Processing Locus bur_0_2020452_0:1445-1523 [ ] 3% > Processing Locus bur_0_2020452_0:1906-2243 [ ] 3% > Processing Locus bur_0_2021834_0:82-918 [ ] 3% > Processing Locus bur_0_2025286_0:4-2231 [* ] 4% > Processing Locus bur_0_2025286_0:2333-2819 [* ] 4% > Processing Locus can_0_3076940_0:1-133 [* ] 4% > Processing Locus can_0_3233581_0:65-459 [* ] 5% > Processing Locus can_0_3234869_1:53-880 [* ] 5% > Processing Locus can_0_3263637_0:608-880 [* ] 5% > Processing Locus can_0_3270131_0:20-2318 [* ] 6% > Processing Locus ct_1_3082021_0:1-129 [* ] 6% > Processing Locus ct_1_3125173_0:21-170 [* ] 7% > Processing Locus ct_1_3132277_0:0-175 [* ] 7% > Processing Locus ct_1_3133995_0:1-195 [* ] 7% > Processing Locus ct_1_3247037_0:421-499 [** ] 8% > Processing Locus ct_1_3277323_0:34-1218 [** ] 8% > Processing Locus ct_1_3302721_0:1261-1339 [** ] 9% > Processing Locus edi_0_2859720_0:151-518 [** ] 9% > Processing Locus edi_0_2891226_0:54-1147 [** ] 10% > Processing Locus edi_0_2918156_0:501-579 [** ] 10% > Processing Locus edi_0_2921730_0:598-1183 [** ] 10% > Processing Locus edi_0_2932438_0:31-289 [** ] 11% > Processing Locus hi_0_2773206_0:0-158 [** ] 11% > Processing Locus hi_0_2778596_0:7-168 [*** ] 12% > Processing Locus hi_0_2939638_0:8-643 [*** ] 12% > Processing Locus hi_0_2961678_0:80-1508 [*** ] 13% > Processing Locus kn_0_3605300_0:1-168 [*** ] 13% > Processing Locus kn_0_3613403_0:1-165 [*** ] 13% > Processing Locus kn_0_3751597_0:3-547 [*** ] 14% > Processing Locus ler_0_3998410_0:4-164 [*** ] 14% > Processing Locus ler_0_4018856_0:1-186 [*** ] 15% > Processing Locus mt_0_4193196_0:0-166 [*** ] 15% > Processing Locus mt_0_4217716_0:5-186 [*** ] 15% > Processing Locus mt_0_4230874_0:32-193 [**** ] 16% > Processing Locus mt_0_4231054_0:0-190 [**** ] 16% > Processing Locus mt_0_4528444_1:1086-1164 [**** ] 17% > Processing Locus no_0_2885444_0:4-110 [**** ] 17% > Processing Locus no_0_2905273_0:15-121 [**** ] 18% > Processing Locus no_0_2936769_0:2-152 [**** ] 18% > Processing Locus no_0_2956652_0:0-177 [**** ] 18% > Processing Locus no_0_3116640_0:418-1883 [**** ] 19% > Processing Locus no_0_3120392_0:1107-2792 [**** ] 19% > Processing Locus no_0_3128142_0:18-1385 [***** ] 20% > Processing Locus no_0_3128142_0:1586-2954 [***** ] 20% > Processing Locus oy_0_2965192_0:44-125 [***** ] 20% > Processing Locus oy_0_3001818_0:46-155 [***** ] 21% > Processing Locus oy_0_3121110_0:53-535 [***** ] 21% > Processing Locus oy_0_3148368_0:647-725 [***** ] 21% > Processing Locus po_0_3324652_0:0-127 [***** ] 22% > Processing Locus po_0_3382155_0:1-145 [***** ] 22% > Processing Locus po_0_3573778_0:343-1280 [***** ] 23% > Processing Locus po_0_3606391_0:854-1829 [***** ] 23% > Processing Locus po_0_3606391_0:2012-2883 [***** ] 23% > Processing Locus po_0_3606391_1:42-936 [***** ] 23% > Processing Locus rsch_4_4032032_0:0-89 [****** ] 24% > Processing Locus rsch_4_4055167_0:0-107 [****** ] 24% > Processing Locus rsch_4_4219071_0:12-435 [****** ] 25% > Processing Locus rsch_4_4275442_0:15-623 [****** ] 25% > Processing Locus sf_2_2459023_0:2-110 [****** ] 26% > Processing Locus sf_2_2524453_0:0-167 [****** ] 26% > Processing Locus sf_2_2662232_0:12-116 [****** ] 26% > Processing Locus sf_2_2680171_0:122-284 [****** ] 27% > Processing Locus sf_2_2687786_0:2014-2092 [****** ] 27% > Processing Locus sf_2_2700286_0:77-185 [******* ] 28% > Processing Locus sf_2_2700286_0:330-2484 [******* ] 28% > Processing Locus tsu_0_3215821_0:189-1175 [******* ] 28% > Processing Locus tsu_0_3242833_1:42-120 [******* ] 28% > Processing Locus wil_2_2834553_0:0-82 [******* ] 29% > Processing Locus wil_2_2925323_0:53-195 [******* ] 29% > Processing Locus wil_2_3050523_0:17-270 [******* ] 30% > Processing Locus wil_2_3092619_0:814-892 [******* ] 30% > Processing Locus ws_0_3182508_0:11-177 [******* ] 31% > Processing Locus ws_0_3326342_0:12-411 [******* ] 31% > Processing Locus ws_0_3340488_0:180-258 [******* ] 31% > Processing Locus ws_0_3347582_0:114-1373 [******** ] 32% > Processing Locus ws_0_3371988_0:0-124 [******** ] 32% > Processing Locus ws_0_3372048_0:349-427 [******** ] 33% > Processing Locus ws_0_3381390_0:4-1707 [******** ] 33% > Processing Locus ws_0_3382500_0:383-580 [******** ] 34% > Processing Locus ws_0_3382500_0:1816-1894 [******** ] 34% > Processing Locus ws_0_3382500_0:2236-2314 [******** ] 34% > Processing Locus ws_0_3382500_0:2539-2617 [******** ] 34% > Processing Locus ws_0_3382500_0:3198-3276 [******** ] 34% > Processing Locus ws_0_3382500_0:3628-3706 [******** ] 34% > Processing Locus wu_0_2654219_0:0-135 [******** ] 34% > Processing Locus wu_0_2678387_0:0-176 [******** ] 34% > Processing Locus zu_0_3022629_0:3-82 [******** ] 35% > Processing Locus zu_0_3082201_0:1-148 [******** ] 35% > Processing Locus zu_0_3092045_0:2-158 [********* ] 36% > Processing Locus zu_0_3118546_0:3-164 [********* ] 36% > Processing Locus zu_0_3238769_0:7-452 [********* ] 36% > Processing Locus zu_0_3243571_0:92-170 [********* ] 37% > Processing Locus zu_0_3243571_0:301-795 [********* ] 37% > Processing Locus zu_0_3259399_1:88-320 [********* ] 37% > Processing Locus zu_0_3280213_0:562-640 [********* ] 38% > Processing Locus zu_0_3280213_0:998-1151 [********* ] 38% > Processing Locus zu_0_3280213_0:1378-1887 [********* ] 38% > Processing Locus zu_0_3280213_0:1995-2083 [********* ] 38% > Processing Locus zu_0_3289907_1:3779-3857 [********* ] 38% > Processed 108 loci. [*************************] 100% > Map Properties: > Total Map Mass: 10311.86 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:08:28] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:0-113 [ ] 0% > Processing Locus bur_0_1856286_0:5-162 [ ] 0% > Processing Locus bur_0_1863298_0:48-153 [ ] 1% > Processing Locus bur_0_1868430_0:31-135 [ ] 2% > Processing Locus bur_0_1873494_0:14-187 [ ] 3% > Processing Locus bur_0_1967596_0:8-428 [* ] 4% > Processing Locus bur_0_1969548_0:1-680 [* ] 5% > Processing Locus bur_0_1999718_0:2-901 [* ] 6% > Processing Locus bur_0_2020452_0:0-1309 [* ] 7% > Processing Locus bur_0_2020452_0:1445-1523 [** ] 8% > Processing Locus bur_0_2020452_0:1906-2243 [** ] 9% > Processing Locus bur_0_2021834_0:82-918 [** ] 10% > Processing Locus bur_0_2025286_0:4-2231 [** ] 11% > Processing Locus bur_0_2025286_0:2333-2819 [*** ] 12% > Processing Locus can_0_3076940_0:1-133 [*** ] 12% > Processing Locus can_0_3233581_0:65-459 [*** ] 13% > Processing Locus can_0_3234869_1:53-880 [*** ] 14% > Processing Locus can_0_3263637_0:608-880 [*** ] 15% > Processing Locus can_0_3270131_0:20-2318 [**** ] 16% > Processing Locus ct_1_3082021_0:1-129 [**** ] 17% > Processing Locus ct_1_3125173_0:21-170 [**** ] 18% > Processing Locus ct_1_3132277_0:0-175 [**** ] 19% > Processing Locus ct_1_3133995_0:1-195 [***** ] 20% > Processing Locus ct_1_3247037_0:421-499 [***** ] 21% > Processing Locus ct_1_3277323_0:34-1218 [***** ] 22% > Processing Locus ct_1_3302721_0:1261-1339 [***** ] 23% > Processing Locus edi_0_2859720_0:151-518 [****** ] 24% > Processing Locus edi_0_2891226_0:54-1147 [****** ] 25% > Processing Locus edi_0_2918156_0:501-579 [****** ] 25% > Processing Locus edi_0_2921730_0:598-1183 [****** ] 26% > Processing Locus edi_0_2932438_0:31-289 [****** ] 27% > Processing Locus hi_0_2773206_0:0-158 [******* ] 28% > Processing Locus hi_0_2778596_0:7-168 [******* ] 29% > Processing Locus hi_0_2939638_0:8-643 [******* ] 30% > Processing Locus hi_0_2961678_0:80-1508 [******* ] 31% > Processing Locus kn_0_3605300_0:1-168 [******** ] 32% > Processing Locus kn_0_3613403_0:1-165 [******** ] 33% > Processing Locus kn_0_3751597_0:3-547 [******** ] 34% > Processing Locus ler_0_3998410_0:4-164 [******** ] 35% > Processing Locus ler_0_4018856_0:1-186 [********* ] 36% > Processing Locus mt_0_4193196_0:0-166 [********* ] 37% > Processing Locus mt_0_4217716_0:5-186 [********* ] 37% > Processing Locus mt_0_4230874_0:32-193 [********* ] 38% > Processing Locus mt_0_4231054_0:0-190 [********* ] 39% > Processing Locus mt_0_4528444_1:1086-1164 [********** ] 40% > Processing Locus no_0_2885444_0:4-110 [********** ] 41% > Processing Locus no_0_2905273_0:15-121 [********** ] 42% > Processing Locus no_0_2936769_0:2-152 [********** ] 43% > Processing Locus no_0_2956652_0:0-177 [*********** ] 44% > Processing Locus no_0_3116640_0:418-1883 [*********** ] 45% > Processing Locus no_0_3120392_0:1107-2792 [*********** ] 46% > Processing Locus no_0_3128142_0:18-1385 [*********** ] 47% > Processing Locus no_0_3128142_0:1586-2954 [************ ] 48% > Processing Locus oy_0_2965192_0:44-125 [************ ] 49% > Processing Locus oy_0_3001818_0:46-155 [************ ] 50% > Processing Locus oy_0_3121110_0:53-535 [************ ] 50% > Processing Locus oy_0_3148368_0:647-725 [************ ] 51% > Processing Locus po_0_3324652_0:0-127 [************* ] 52% > Processing Locus po_0_3382155_0:1-145 [************* ] 53% > Processing Locus po_0_3573778_0:343-1280 [************* ] 54% > Processing Locus po_0_3606391_0:854-1829 [************* ] 55% > Processing Locus po_0_3606391_0:2012-2883 [************** ] 56% > Processing Locus po_0_3606391_1:42-936 [************** ] 57% > Processing Locus rsch_4_4032032_0:0-89 [************** ] 58% > Processing Locus rsch_4_4055167_0:0-107 [************** ] 59% > Processing Locus rsch_4_4219071_0:12-435 [*************** ] 60% > Processing Locus rsch_4_4275442_0:15-623 [*************** ] 61% > Processing Locus sf_2_2459023_0:2-110 [*************** ] 62% > Processing Locus sf_2_2524453_0:0-167 [*************** ] 62% > Processing Locus sf_2_2662232_0:12-116 [*************** ] 63% > Processing Locus sf_2_2680171_0:122-284 [**************** ] 64% > Processing Locus sf_2_2687786_0:2014-2092 [**************** ] 65% > Processing Locus sf_2_2700286_0:77-185 [**************** ] 66% > Processing Locus sf_2_2700286_0:330-2484 [**************** ] 67% > Processing Locus tsu_0_3215821_0:189-1175 [***************** ] 68% > Processing Locus tsu_0_3242833_1:42-120 [***************** ] 69% > Processing Locus wil_2_2834553_0:0-82 [***************** ] 70% > Processing Locus wil_2_2925323_0:53-195 [***************** ] 71% > Processing Locus wil_2_3050523_0:17-270 [****************** ] 72% > Processing Locus wil_2_3092619_0:814-892 [****************** ] 73% > Processing Locus ws_0_3182508_0:11-177 [****************** ] 74% > Processing Locus ws_0_3326342_0:12-411 [****************** ] 75% > Processing Locus ws_0_3340488_0:180-258 [****************** ] 75% > Processing Locus ws_0_3347582_0:114-1373 [******************* ] 76% > Processing Locus ws_0_3371988_0:0-124 [******************* ] 77% > Processing Locus ws_0_3372048_0:349-427 [******************* ] 78% > Processing Locus ws_0_3381390_0:4-1707 [******************* ] 79% > Processing Locus ws_0_3382500_0:383-580 [******************** ] 80% > Processing Locus ws_0_3382500_0:1816-1894 [******************** ] 81% > Processing Locus ws_0_3382500_0:2236-2314 [******************** ] 82% > Processing Locus ws_0_3382500_0:2539-2617 [******************** ] 83% > Processing Locus ws_0_3382500_0:3198-3276 [********************* ] 84% > Processing Locus ws_0_3382500_0:3628-3706 [********************* ] 85% > Processing Locus wu_0_2654219_0:0-135 [********************* ] 86% > Processing Locus wu_0_2678387_0:0-176 [********************* ] 87% > Processing Locus zu_0_3022629_0:3-82 [********************* ] 87% > Processing Locus zu_0_3082201_0:1-148 [********************** ] 88% > Processing Locus zu_0_3092045_0:2-158 [********************** ] 89% > Processing Locus zu_0_3118546_0:3-164 [********************** ] 90% > Processing Locus zu_0_3238769_0:7-452 [********************** ] 91% > Processing Locus zu_0_3243571_0:92-170 [*********************** ] 92% > Processing Locus zu_0_3243571_0:301-795 [*********************** ] 93% > Processing Locus zu_0_3259399_1:88-320 [*********************** ] 94% > Processing Locus zu_0_3280213_0:562-640 [*********************** ] 95% > Processing Locus zu_0_3280213_0:998-1151 [************************ ] 96% > Processing Locus zu_0_3280213_0:1378-1887 [************************ ] 97% > Processing Locus zu_0_3280213_0:1995-2083 [************************ ] 98% > Processing Locus zu_0_3289907_1:3779-3857 [************************ ] 99% > Processed 108 loci. [*************************] 100% [14:08:28] Loading reference annotation and sequence [14:08:28] Learning bias parameters. > Processing Locus bur_0_1804399_0:0-113 [ ] 0% > Processing Locus bur_0_1856286_0:5-162 [ ] 0% > Processing Locus bur_0_1863298_0:48-153 [ ] 1% > Processing Locus bur_0_1868430_0:31-135 [ ] 2% > Processing Locus bur_0_1873494_0:14-187 [ ] 3% > Processing Locus bur_0_1967596_0:8-428 [* ] 4% > Processing Locus bur_0_1969548_0:1-680 [* ] 5% > Processing Locus bur_0_1999718_0:2-901 [* ] 6% > Processing Locus bur_0_2020452_0:0-1309 [* ] 7% > Processing Locus bur_0_2021834_0:82-918 [** ] 8% > Processing Locus bur_0_2025286_0:4-2231 [** ] 9% > Processing Locus bur_0_2025286_0:2333-2801 [** ] 10% > Processing Locus can_0_3076940_0:1-133 [** ] 11% > Processing Locus can_0_3234869_1:53-880 [*** ] 12% > Processing Locus can_0_3263637_0:608-880 [*** ] 12% > Processing Locus can_0_3270131_0:20-2318 [*** ] 13% > Processing Locus ct_1_3082021_0:1-129 [*** ] 14% > Processing Locus ct_1_3125173_0:21-170 [*** ] 15% > Processing Locus ct_1_3132277_0:0-175 [**** ] 16% > Processing Locus ct_1_3133995_0:1-195 [**** ] 17% > Processing Locus ct_1_3277323_0:34-1218 [**** ] 18% > Processing Locus edi_0_2859720_0:151-518 [**** ] 19% > Processing Locus edi_0_2891226_0:54-1147 [***** ] 20% > Processing Locus edi_0_2921730_0:598-1183 [***** ] 21% > Processing Locus edi_0_2932438_0:31-289 [***** ] 22% > Processing Locus hi_0_2773206_0:0-158 [***** ] 23% > Processing Locus hi_0_2778596_0:7-168 [****** ] 24% > Processing Locus hi_0_2939638_0:8-643 [****** ] 25% > Processing Locus hi_0_2961678_0:109-1508 [****** ] 25% > Processing Locus kn_0_3605300_0:1-168 [****** ] 26% > Processing Locus kn_0_3613403_0:1-165 [****** ] 27% > Processing Locus kn_0_3751597_0:3-547 [******* ] 28% > Processing Locus ler_0_3998410_0:4-164 [******* ] 29% > Processing Locus ler_0_4018856_0:1-186 [******* ] 30% > Processing Locus mt_0_4193196_0:0-166 [******* ] 31% > Processing Locus mt_0_4217716_0:5-186 [******** ] 32% > Processing Locus mt_0_4230874_0:32-193 [******** ] 33% > Processing Locus mt_0_4231054_0:0-190 [******** ] 34% > Processing Locus no_0_2885444_0:4-110 [******** ] 35% > Processing Locus no_0_2905273_0:15-121 [********* ] 36% > Processing Locus no_0_2936769_0:2-152 [********* ] 37% > Processing Locus no_0_2956652_0:0-177 [********* ] 37% > Processing Locus no_0_3116640_0:418-1883 [********* ] 38% > Processing Locus no_0_3120392_0:1107-2792 [********* ] 39% > Processing Locus no_0_3128142_0:18-1385 [********** ] 40% > Processing Locus no_0_3128142_0:1586-2954 [********** ] 41% > Processing Locus oy_0_3001818_0:46-155 [********** ] 42% > Processing Locus oy_0_3121110_0:53-535 [********** ] 43% > Processing Locus po_0_3324652_0:0-127 [*********** ] 44% > Processing Locus po_0_3573778_0:343-1280 [*********** ] 45% > Processing Locus po_0_3606391_0:854-1829 [*********** ] 46% > Processing Locus po_0_3606391_0:2012-2883 [*********** ] 47% > Processing Locus po_0_3606391_1:42-936 [************ ] 48% > Processing Locus rsch_4_4032032_0:0-89 [************ ] 49% > Processing Locus rsch_4_4055167_0:0-107 [************ ] 50% > Processing Locus rsch_4_4219071_0:12-435 [************ ] 50% > Processing Locus rsch_4_4275442_0:15-623 [************ ] 51% > Processing Locus sf_2_2459023_0:2-110 [************* ] 52% > Processing Locus sf_2_2524453_0:0-167 [************* ] 53% > Processing Locus sf_2_2662232_0:12-116 [************* ] 54% > Processing Locus sf_2_2700286_0:330-2484 [************* ] 55% > Processing Locus tsu_0_3215821_0:189-1175 [************** ] 56% > Processing Locus wil_2_2925323_0:53-195 [************** ] 57% > Processing Locus wil_2_3050523_0:17-270 [************** ] 58% > Processing Locus ws_0_3347582_0:114-1373 [************** ] 59% > Processing Locus ws_0_3371988_0:0-124 [*************** ] 60% > Processing Locus ws_0_3381390_0:4-1707 [*************** ] 61% > Processing Locus wu_0_2654219_0:0-135 [*************** ] 62% > Processing Locus wu_0_2678387_0:0-176 [*************** ] 62% > Processing Locus zu_0_3022629_0:3-82 [*************** ] 63% > Processing Locus zu_0_3082201_0:1-148 [**************** ] 64% > Processing Locus zu_0_3092045_0:2-158 [**************** ] 65% > Processing Locus zu_0_3118546_0:3-164 [**************** ] 66% > Processing Locus zu_0_3238769_0:7-452 [**************** ] 67% > Processing Locus zu_0_3243571_0:301-795 [***************** ] 68% > Processing Locus zu_0_3259399_1:88-320 [***************** ] 69% > Processed 76 loci. [*************************] 100% [14:08:28] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:0-113 [ ] 0% > Processing Locus bur_0_1856286_0:5-162 [ ] 0% > Processing Locus bur_0_1863298_0:48-153 [ ] 1% > Processing Locus bur_0_1868430_0:31-135 [ ] 2% > Processing Locus bur_0_1873494_0:14-187 [ ] 3% > Processing Locus bur_0_1967596_0:8-428 [* ] 4% > Processing Locus bur_0_1969548_0:1-680 [* ] 5% > Processing Locus bur_0_1999718_0:2-901 [* ] 6% > Processing Locus bur_0_2020452_0:0-1309 [* ] 7% > Processing Locus bur_0_2021834_0:82-918 [** ] 8% > Processing Locus bur_0_2025286_0:4-2231 [** ] 9% > Processing Locus bur_0_2025286_0:2333-2801 [** ] 10% > Processing Locus can_0_3076940_0:1-133 [** ] 11% > Processing Locus can_0_3234869_1:53-880 [*** ] 12% > Processing Locus can_0_3263637_0:608-880 [*** ] 12% > Processing Locus can_0_3270131_0:20-2318 [*** ] 13% > Processing Locus ct_1_3082021_0:1-129 [*** ] 14% > Processing Locus ct_1_3125173_0:21-170 [*** ] 15% > Processing Locus ct_1_3132277_0:0-175 [**** ] 16% > Processing Locus ct_1_3133995_0:1-195 [**** ] 17% > Processing Locus ct_1_3277323_0:34-1218 [**** ] 18% > Processing Locus edi_0_2859720_0:151-518 [**** ] 19% > Processing Locus edi_0_2891226_0:54-1147 [***** ] 20% > Processing Locus edi_0_2921730_0:598-1183 [***** ] 21% > Processing Locus edi_0_2932438_0:31-289 [***** ] 22% > Processing Locus hi_0_2773206_0:0-158 [***** ] 23% > Processing Locus hi_0_2778596_0:7-168 [****** ] 24% > Processing Locus hi_0_2939638_0:8-643 [****** ] 25% > Processing Locus hi_0_2961678_0:109-1508 [****** ] 25% > Processing Locus kn_0_3605300_0:1-168 [****** ] 26% > Processing Locus kn_0_3613403_0:1-165 [****** ] 27% > Processing Locus kn_0_3751597_0:3-547 [******* ] 28% > Processing Locus ler_0_3998410_0:4-164 [******* ] 29% > Processing Locus ler_0_4018856_0:1-186 [******* ] 30% > Processing Locus mt_0_4193196_0:0-166 [******* ] 31% > Processing Locus mt_0_4217716_0:5-186 [******** ] 32% > Processing Locus mt_0_4230874_0:32-193 [******** ] 33% > Processing Locus mt_0_4231054_0:0-190 [******** ] 34% > Processing Locus no_0_2885444_0:4-110 [******** ] 35% > Processing Locus no_0_2905273_0:15-121 [********* ] 36% > Processing Locus no_0_2936769_0:2-152 [********* ] 37% > Processing Locus no_0_2956652_0:0-177 [********* ] 37% > Processing Locus no_0_3116640_0:418-1883 [********* ] 38% > Processing Locus no_0_3120392_0:1107-2792 [********* ] 39% > Processing Locus no_0_3128142_0:18-1385 [********** ] 40% > Processing Locus no_0_3128142_0:1586-2954 [********** ] 41% > Processing Locus oy_0_3001818_0:46-155 [********** ] 42% > Processing Locus oy_0_3121110_0:53-535 [********** ] 43% > Processing Locus po_0_3324652_0:0-127 [*********** ] 44% > Processing Locus po_0_3573778_0:343-1280 [*********** ] 45% > Processing Locus po_0_3606391_0:854-1829 [*********** ] 46% > Processing Locus po_0_3606391_0:2012-2883 [*********** ] 47% > Processing Locus po_0_3606391_1:42-936 [************ ] 48% > Processing Locus rsch_4_4032032_0:0-89 [************ ] 49% > Processing Locus rsch_4_4055167_0:0-107 [************ ] 50% > Processing Locus rsch_4_4219071_0:12-435 [************ ] 50% > Processing Locus rsch_4_4275442_0:15-623 [************ ] 51% > Processing Locus sf_2_2459023_0:2-110 [************* ] 52% > Processing Locus sf_2_2524453_0:0-167 [************* ] 53% > Processing Locus sf_2_2662232_0:12-116 [************* ] 54% > Processing Locus sf_2_2700286_0:330-2484 [************* ] 55% > Processing Locus tsu_0_3215821_0:189-1175 [************** ] 56% > Processing Locus wil_2_2925323_0:53-195 [************** ] 57% > Processing Locus wil_2_3050523_0:17-270 [************** ] 58% > Processing Locus ws_0_3347582_0:114-1373 [************** ] 59% > Processing Locus ws_0_3371988_0:0-124 [*************** ] 60% > Processing Locus ws_0_3381390_0:4-1707 [*************** ] 61% > Processing Locus wu_0_2654219_0:0-135 [*************** ] 62% > Processing Locus wu_0_2678387_0:0-176 [*************** ] 62% > Processing Locus zu_0_3022629_0:3-82 [*************** ] 63% > Processing Locus zu_0_3082201_0:1-148 [**************** ] 64% > Processing Locus zu_0_3092045_0:2-158 [**************** ] 65% > Processing Locus zu_0_3118546_0:3-164 [**************** ] 66% > Processing Locus zu_0_3238769_0:7-452 [**************** ] 67% > Processing Locus zu_0_3243571_0:301-795 [***************** ] 68% > Processing Locus zu_0_3259399_1:88-320 [***************** ] 69% > Processed 76 loci. [*************************] 100% [Mon Apr 4 14:08:29 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:08:31 2011] Joining segment hits [Mon Apr 4 14:08:33 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:11 elapsed] cufflinks -p 4 -o ./Hi_0 -r it2.fa ./Hi_0/accepted_hits.bam [14:08:39] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:2-108 [ ] 0% > Processing Locus bur_0_1863298_0:47-137 [ ] 0% > Processing Locus bur_0_1873494_0:39-188 [ ] 0% > Processing Locus bur_0_2025286_0:17-2826 [ ] 1% > Processing Locus can_0_3076940_0:0-134 [ ] 1% > Processing Locus can_0_3122480_0:4-149 [ ] 2% > Processing Locus can_0_3189753_0:15-203 [ ] 2% > Processing Locus can_0_3218459_0:15-896 [ ] 2% > Processing Locus can_0_3223655_0:439-517 [ ] 3% > Processing Locus can_0_3270131_0:447-957 [ ] 3% > Processing Locus can_0_3270131_0:1174-1252 [ ] 3% > Processing Locus can_0_3270131_0:1510-1588 [ ] 3% > Processing Locus can_0_3270131_0:1750-1963 [ ] 3% > Processing Locus can_0_3270131_0:2264-2342 [ ] 3% > Processing Locus ct_1_3082021_0:6-129 [* ] 4% > Processing Locus ct_1_3132277_0:48-126 [* ] 4% > Processing Locus edi_0_2744702_0:15-93 [* ] 5% > Processing Locus edi_0_2859720_0:14-525 [* ] 5% > Processing Locus hi_0_2755116_0:1-81 [* ] 5% > Processing Locus hi_0_2773206_0:10-131 [* ] 6% > Processing Locus hi_0_2778596_0:18-154 [* ] 6% > Processing Locus hi_0_2795398_0:0-176 [* ] 7% > Processing Locus hi_0_2916184_0:2-528 [* ] 7% > Processing Locus hi_0_2939638_0:104-643 [* ] 7% > Processing Locus hi_0_2953648_0:0-1320 [** ] 8% > Processing Locus hi_0_2959094_0:2-678 [** ] 8% > Processing Locus hi_0_2961678_0:215-1508 [** ] 9% > Processing Locus kn_0_3605300_0:1-168 [** ] 9% > Processing Locus kn_0_3613403_0:1-167 [** ] 10% > Processing Locus kn_0_3751597_0:453-531 [** ] 10% > Processing Locus kn_0_3799876_0:25-1489 [** ] 10% > Processing Locus ler_0_3998410_0:0-164 [** ] 11% > Processing Locus ler_0_4004770_0:65-143 [** ] 11% > Processing Locus ler_0_4018856_0:1-189 [*** ] 12% > Processing Locus mt_0_4193196_0:14-165 [*** ] 12% > Processing Locus mt_0_4213448_0:10-158 [*** ] 13% > Processing Locus mt_0_4217716_0:0-186 [*** ] 13% > Processing Locus mt_0_4229662_0:9-197 [*** ] 13% > Processing Locus mt_0_4230874_0:105-183 [*** ] 14% > Processing Locus mt_0_4231054_0:3-193 [*** ] 14% > Processing Locus mt_0_4399784_0:23-222 [*** ] 15% > Processing Locus mt_0_4528444_1:406-1231 [*** ] 15% > Processing Locus no_0_2885444_0:7-108 [*** ] 15% > Processing Locus no_0_2905273_0:8-123 [**** ] 16% > Processing Locus no_0_2934639_0:32-124 [**** ] 16% > Processing Locus no_0_2936769_0:1-138 [**** ] 17% > Processing Locus no_0_2956652_0:5-169 [**** ] 17% > Processing Locus no_0_3088052_0:793-871 [**** ] 18% > Processing Locus no_0_3116640_0:384-1890 [**** ] 18% > Processing Locus no_0_3128142_0:6-1306 [**** ] 18% > Processing Locus no_0_3128142_0:1433-1511 [**** ] 18% > Processing Locus no_0_3128142_0:1671-2225 [**** ] 18% > Processing Locus no_0_3128142_0:2476-2933 [**** ] 18% > Processing Locus oy_0_3148368_0:37-115 [**** ] 19% > Processing Locus oy_0_3148368_0:308-692 [**** ] 19% > Processing Locus po_0_3330421_0:1-134 [**** ] 19% > Processing Locus po_0_3393401_0:44-122 [***** ] 20% > Processing Locus rsch_4_4032032_0:0-92 [***** ] 20% > Processing Locus rsch_4_4055167_0:2-109 [***** ] 21% > Processing Locus rsch_4_4110791_0:5-155 [***** ] 21% > Processing Locus rsch_4_4266550_0:4-1150 [***** ] 21% > Processing Locus rsch_4_4275442_0:15-611 [***** ] 22% > Processing Locus rsch_4_4297142_0:111-302 [***** ] 22% > Processing Locus sf_2_2488391_0:0-129 [***** ] 23% > Processing Locus sf_2_2504999_0:4-145 [***** ] 23% > Processing Locus sf_2_2524453_0:1-168 [***** ] 23% > Processing Locus sf_2_2653966_0:0-695 [****** ] 24% > Processing Locus sf_2_2680171_0:0-1100 [****** ] 24% > Processing Locus sf_2_2682779_0:602-991 [****** ] 25% > Processing Locus sf_2_2682779_0:1152-1230 [****** ] 25% > Processing Locus sf_2_2687774_0:596-1400 [****** ] 25% > Processing Locus sf_2_2687786_0:61-830 [****** ] 26% > Processing Locus sf_2_2687786_0:948-2177 [****** ] 26% > Processing Locus wil_2_2834553_0:0-104 [****** ] 26% > Processing Locus wil_2_2906137_0:6-148 [****** ] 26% > Processing Locus wil_2_2925323_0:13-193 [****** ] 27% > Processing Locus wil_2_2945095_0:3-205 [****** ] 27% > Processing Locus wil_2_3052273_0:41-982 [******* ] 28% > Processing Locus wil_2_3077447_0:562-1097 [******* ] 28% > Processing Locus wil_2_3090237_0:252-494 [******* ] 28% > Processing Locus wil_2_3092619_0:205-283 [******* ] 29% > Processing Locus wil_2_3092619_0:477-859 [******* ] 29% > Processing Locus ws_0_3182508_0:0-183 [******* ] 29% > Processing Locus ws_0_3190679_0:42-184 [******* ] 30% > Processing Locus ws_0_3190963_0:14-178 [******* ] 30% > Processing Locus ws_0_3298283_0:8-531 [******* ] 31% > Processing Locus ws_0_3340488_0:138-1139 [******* ] 31% > Processing Locus ws_0_3347582_0:228-917 [******* ] 31% > Processing Locus ws_0_3347582_0:1031-1358 [******* ] 31% > Processing Locus ws_0_3365892_0:14-2027 [******** ] 32% > Processing Locus ws_0_3371988_0:0-143 [******** ] 32% > Processing Locus ws_0_3380934_0:3-218 [******** ] 33% > Processing Locus wu_0_2654219_0:40-143 [******** ] 33% > Processing Locus wu_0_2655481_0:1-148 [******** ] 34% > Processing Locus wu_0_2678387_0:6-170 [******** ] 34% > Processing Locus zu_0_3092045_0:6-87 [******** ] 34% > Processing Locus zu_0_3118546_0:4-166 [******** ] 35% > Processing Locus zu_0_3190435_0:156-234 [******** ] 35% > Processing Locus zu_0_3243571_0:111-189 [********* ] 36% > Processing Locus zu_0_3243571_0:301-771 [********* ] 36% > Processing Locus zu_0_3260131_0:158-400 [********* ] 36% > Processing Locus zu_0_3278243_0:15-97 [********* ] 36% > Processed 102 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5961.71 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:08:39] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:2-108 [ ] 0% > Processing Locus bur_0_1863298_0:47-137 [ ] 0% > Processing Locus bur_0_1873494_0:39-188 [ ] 1% > Processing Locus bur_0_2025286_0:17-2826 [ ] 2% > Processing Locus can_0_3076940_0:0-134 [ ] 3% > Processing Locus can_0_3122480_0:4-149 [* ] 4% > Processing Locus can_0_3189753_0:15-203 [* ] 5% > Processing Locus can_0_3218459_0:15-896 [* ] 6% > Processing Locus can_0_3223655_0:439-517 [* ] 7% > Processing Locus can_0_3270131_0:447-957 [** ] 8% > Processing Locus can_0_3270131_0:1174-1252 [** ] 9% > Processing Locus can_0_3270131_0:1510-1588 [** ] 10% > Processing Locus can_0_3270131_0:1750-1963 [** ] 11% > Processing Locus can_0_3270131_0:2264-2342 [*** ] 12% > Processing Locus ct_1_3082021_0:6-129 [*** ] 13% > Processing Locus ct_1_3132277_0:48-126 [*** ] 14% > Processing Locus edi_0_2744702_0:15-93 [*** ] 15% > Processing Locus edi_0_2859720_0:14-525 [**** ] 16% > Processing Locus hi_0_2755116_0:1-81 [**** ] 17% > Processing Locus hi_0_2773206_0:10-131 [**** ] 18% > Processing Locus hi_0_2778596_0:18-154 [**** ] 19% > Processing Locus hi_0_2795398_0:0-176 [***** ] 20% > Processing Locus hi_0_2916184_0:2-528 [***** ] 21% > Processing Locus hi_0_2939638_0:104-643 [***** ] 22% > Processing Locus hi_0_2953648_0:0-1320 [***** ] 23% > Processing Locus hi_0_2959094_0:2-678 [****** ] 24% > Processing Locus hi_0_2961678_0:215-1508 [****** ] 25% > Processing Locus kn_0_3605300_0:1-168 [****** ] 26% > Processing Locus kn_0_3613403_0:1-167 [****** ] 27% > Processing Locus kn_0_3751597_0:453-531 [******* ] 28% > Processing Locus kn_0_3799876_0:25-1489 [******* ] 29% > Processing Locus ler_0_3998410_0:0-164 [******* ] 30% > Processing Locus ler_0_4004770_0:65-143 [******* ] 31% > Processing Locus ler_0_4018856_0:1-189 [******** ] 32% > Processing Locus mt_0_4193196_0:14-165 [******** ] 33% > Processing Locus mt_0_4213448_0:10-158 [******** ] 34% > Processing Locus mt_0_4217716_0:0-186 [******** ] 35% > Processing Locus mt_0_4229662_0:9-197 [********* ] 36% > Processing Locus mt_0_4230874_0:105-183 [********* ] 37% > Processing Locus mt_0_4231054_0:3-193 [********* ] 38% > Processing Locus mt_0_4399784_0:23-222 [********* ] 39% > Processing Locus mt_0_4528444_1:406-1231 [********** ] 40% > Processing Locus no_0_2885444_0:7-108 [********** ] 41% > Processing Locus no_0_2905273_0:8-123 [********** ] 42% > Processing Locus no_0_2934639_0:32-124 [********** ] 43% > Processing Locus no_0_2936769_0:1-138 [*********** ] 44% > Processing Locus no_0_2956652_0:5-169 [*********** ] 45% > Processing Locus no_0_3088052_0:793-871 [*********** ] 46% > Processing Locus no_0_3116640_0:384-1890 [*********** ] 47% > Processing Locus no_0_3128142_0:6-1306 [************ ] 48% > Processing Locus no_0_3128142_0:1433-1511 [************ ] 49% > Processing Locus no_0_3128142_0:1671-2225 [************ ] 50% > Processing Locus no_0_3128142_0:2476-2933 [************ ] 50% > Processing Locus oy_0_3148368_0:37-115 [************ ] 51% > Processing Locus oy_0_3148368_0:308-692 [************* ] 52% > Processing Locus po_0_3330421_0:1-134 [************* ] 53% > Processing Locus po_0_3393401_0:44-122 [************* ] 54% > Processing Locus rsch_4_4032032_0:0-92 [************* ] 55% > Processing Locus rsch_4_4055167_0:2-109 [************** ] 56% > Processing Locus rsch_4_4110791_0:5-155 [************** ] 57% > Processing Locus rsch_4_4266550_0:4-1150 [************** ] 58% > Processing Locus rsch_4_4275442_0:15-611 [************** ] 59% > Processing Locus rsch_4_4297142_0:111-302 [*************** ] 60% > Processing Locus sf_2_2488391_0:0-129 [*************** ] 61% > Processing Locus sf_2_2504999_0:4-145 [*************** ] 62% > Processing Locus sf_2_2524453_0:1-168 [*************** ] 63% > Processing Locus sf_2_2653966_0:0-695 [**************** ] 64% > Processing Locus sf_2_2680171_0:0-1100 [**************** ] 65% > Processing Locus sf_2_2682779_0:602-991 [**************** ] 66% > Processing Locus sf_2_2682779_0:1152-1230 [**************** ] 67% > Processing Locus sf_2_2687774_0:596-1400 [***************** ] 68% > Processing Locus sf_2_2687786_0:61-830 [***************** ] 69% > Processing Locus sf_2_2687786_0:948-2177 [***************** ] 70% > Processing Locus wil_2_2834553_0:0-104 [***************** ] 71% > Processing Locus wil_2_2906137_0:6-148 [****************** ] 72% > Processing Locus wil_2_2925323_0:13-193 [****************** ] 73% > Processing Locus wil_2_2945095_0:3-205 [****************** ] 74% > Processing Locus wil_2_3052273_0:41-982 [****************** ] 75% > Processing Locus wil_2_3077447_0:562-1097 [******************* ] 76% > Processing Locus wil_2_3090237_0:252-494 [******************* ] 77% > Processing Locus wil_2_3092619_0:205-283 [******************* ] 78% > Processing Locus wil_2_3092619_0:477-859 [******************* ] 79% > Processing Locus ws_0_3182508_0:0-183 [******************** ] 80% > Processing Locus ws_0_3190679_0:42-184 [******************** ] 81% > Processing Locus ws_0_3190963_0:14-178 [******************** ] 82% > Processing Locus ws_0_3298283_0:8-531 [******************** ] 83% > Processing Locus ws_0_3340488_0:138-1139 [********************* ] 84% > Processing Locus ws_0_3347582_0:228-917 [********************* ] 85% > Processing Locus ws_0_3347582_0:1031-1358 [********************* ] 86% > Processing Locus ws_0_3365892_0:14-2027 [********************* ] 87% > Processing Locus ws_0_3371988_0:0-143 [********************** ] 88% > Processing Locus ws_0_3380934_0:3-218 [********************** ] 89% > Processing Locus wu_0_2654219_0:40-143 [********************** ] 90% > Processing Locus wu_0_2655481_0:1-148 [********************** ] 91% > Processing Locus wu_0_2678387_0:6-170 [*********************** ] 92% > Processing Locus zu_0_3092045_0:6-87 [*********************** ] 93% > Processing Locus zu_0_3118546_0:4-166 [*********************** ] 94% > Processing Locus zu_0_3190435_0:156-234 [*********************** ] 95% > Processing Locus zu_0_3243571_0:111-189 [************************ ] 96% > Processing Locus zu_0_3243571_0:301-771 [************************ ] 97% > Processing Locus zu_0_3260131_0:158-400 [************************ ] 98% > Processing Locus zu_0_3278243_0:15-97 [************************ ] 99% > Processed 102 loci. [*************************] 100% [14:08:39] Loading reference annotation and sequence [14:08:39] Learning bias parameters. > Processing Locus bur_0_1804399_0:2-108 [ ] 0% > Processing Locus bur_0_1873494_0:39-188 [ ] 0% > Processing Locus bur_0_2025286_0:17-223 [ ] 1% > Processing Locus bur_0_2025286_0:275-2826 [ ] 2% > Processing Locus can_0_3076940_0:0-134 [ ] 3% > Processing Locus can_0_3122480_0:4-149 [* ] 4% > Processing Locus can_0_3189753_0:15-203 [* ] 5% > Processing Locus can_0_3218459_0:15-896 [* ] 6% > Processing Locus ct_1_3082021_0:6-129 [* ] 7% > Processing Locus edi_0_2859720_0:14-525 [** ] 8% > Processing Locus hi_0_2778596_0:18-154 [** ] 9% > Processing Locus hi_0_2795398_0:0-176 [** ] 10% > Processing Locus hi_0_2916184_0:2-528 [** ] 11% > Processing Locus hi_0_2953648_0:0-1320 [*** ] 12% > Processing Locus hi_0_2959094_0:2-678 [*** ] 13% > Processing Locus hi_0_2961678_0:215-1508 [*** ] 14% > Processing Locus kn_0_3605300_0:1-168 [*** ] 15% > Processing Locus kn_0_3613403_0:1-167 [**** ] 16% > Processing Locus kn_0_3799876_0:25-1489 [**** ] 17% > Processing Locus ler_0_3998410_0:0-164 [**** ] 18% > Processing Locus ler_0_4018856_0:1-189 [**** ] 19% > Processing Locus mt_0_4193196_0:14-165 [***** ] 20% > Processing Locus mt_0_4213448_0:10-158 [***** ] 21% > Processing Locus mt_0_4217716_0:0-186 [***** ] 22% > Processing Locus mt_0_4229662_0:9-197 [***** ] 23% > Processing Locus mt_0_4231054_0:3-193 [****** ] 24% > Processing Locus mt_0_4399784_0:23-222 [****** ] 25% > Processing Locus mt_0_4528444_1:406-1231 [****** ] 26% > Processing Locus no_0_2885444_0:7-108 [****** ] 27% > Processing Locus no_0_2905273_0:8-123 [******* ] 28% > Processing Locus no_0_2936769_0:1-138 [******* ] 29% > Processing Locus no_0_2956652_0:5-169 [******* ] 30% > Processing Locus no_0_3116640_0:384-1890 [******* ] 31% > Processing Locus no_0_3128142_0:6-1306 [******** ] 32% > Processing Locus no_0_3128142_0:1671-2225 [******** ] 33% > Processing Locus no_0_3128142_0:2476-2933 [******** ] 34% > Processing Locus po_0_3330421_0:1-134 [******** ] 35% > Processing Locus rsch_4_4032032_0:0-92 [********* ] 36% > Processing Locus rsch_4_4055167_0:2-109 [********* ] 37% > Processing Locus rsch_4_4110791_0:5-155 [********* ] 38% > Processing Locus rsch_4_4266550_0:4-1150 [********* ] 39% > Processing Locus rsch_4_4275442_0:15-611 [********** ] 40% > Processing Locus rsch_4_4297142_0:111-302 [********** ] 41% > Processing Locus sf_2_2488391_0:0-129 [********** ] 42% > Processing Locus sf_2_2504999_0:4-145 [********** ] 43% > Processing Locus sf_2_2524453_0:1-168 [*********** ] 44% > Processing Locus sf_2_2653966_0:0-695 [*********** ] 45% > Processing Locus sf_2_2680171_0:0-1100 [*********** ] 46% > Processing Locus sf_2_2687774_0:596-1400 [*********** ] 47% > Processing Locus sf_2_2687786_0:61-830 [************ ] 48% > Processing Locus sf_2_2687786_0:948-2177 [************ ] 49% > Processing Locus wil_2_2834553_0:0-104 [************ ] 50% > Processing Locus wil_2_2906137_0:6-148 [************ ] 50% > Processing Locus wil_2_2925323_0:13-193 [************ ] 51% > Processing Locus wil_2_2945095_0:3-205 [************* ] 52% > Processing Locus wil_2_3052273_0:41-982 [************* ] 53% > Processing Locus wil_2_3077447_0:562-1097 [************* ] 54% > Processing Locus ws_0_3182508_0:0-183 [************* ] 55% > Processing Locus ws_0_3190963_0:14-178 [************** ] 56% > Processing Locus ws_0_3298283_0:8-531 [************** ] 57% > Processing Locus ws_0_3340488_0:138-1139 [************** ] 58% > Processing Locus ws_0_3347582_0:228-917 [************** ] 59% > Processing Locus ws_0_3365892_0:14-2027 [*************** ] 60% > Processing Locus ws_0_3371988_0:0-143 [*************** ] 61% > Processing Locus ws_0_3380934_0:3-218 [*************** ] 62% > Processing Locus wu_0_2654219_0:40-143 [*************** ] 63% > Processing Locus wu_0_2655481_0:1-148 [**************** ] 64% > Processing Locus wu_0_2678387_0:6-170 [**************** ] 65% > Processing Locus zu_0_3118546_0:4-166 [**************** ] 66% > Processing Locus zu_0_3243571_0:301-771 [**************** ] 67% > Processed 70 loci. [*************************] 100% [14:08:39] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:2-108 [ ] 0% > Processing Locus bur_0_1873494_0:39-188 [ ] 0% > Processing Locus bur_0_2025286_0:17-223 [ ] 1% > Processing Locus bur_0_2025286_0:275-2826 [ ] 2% > Processing Locus can_0_3076940_0:0-134 [ ] 3% > Processing Locus can_0_3122480_0:4-149 [* ] 4% > Processing Locus can_0_3189753_0:15-203 [* ] 5% > Processing Locus can_0_3218459_0:15-896 [* ] 6% > Processing Locus ct_1_3082021_0:6-129 [* ] 7% > Processing Locus edi_0_2859720_0:14-525 [** ] 8% > Processing Locus hi_0_2778596_0:18-154 [** ] 9% > Processing Locus hi_0_2795398_0:0-176 [** ] 10% > Processing Locus hi_0_2916184_0:2-528 [** ] 11% > Processing Locus hi_0_2953648_0:0-1320 [*** ] 12% > Processing Locus hi_0_2959094_0:2-678 [*** ] 13% > Processing Locus hi_0_2961678_0:215-1508 [*** ] 14% > Processing Locus kn_0_3605300_0:1-168 [*** ] 15% > Processing Locus kn_0_3613403_0:1-167 [**** ] 16% > Processing Locus kn_0_3799876_0:25-1489 [**** ] 17% > Processing Locus ler_0_3998410_0:0-164 [**** ] 18% > Processing Locus ler_0_4018856_0:1-189 [**** ] 19% > Processing Locus mt_0_4193196_0:14-165 [***** ] 20% > Processing Locus mt_0_4213448_0:10-158 [***** ] 21% > Processing Locus mt_0_4217716_0:0-186 [***** ] 22% > Processing Locus mt_0_4229662_0:9-197 [***** ] 23% > Processing Locus mt_0_4231054_0:3-193 [****** ] 24% > Processing Locus mt_0_4399784_0:23-222 [****** ] 25% > Processing Locus mt_0_4528444_1:406-1231 [****** ] 26% > Processing Locus no_0_2885444_0:7-108 [****** ] 27% > Processing Locus no_0_2905273_0:8-123 [******* ] 28% > Processing Locus no_0_2936769_0:1-138 [******* ] 29% > Processing Locus no_0_2956652_0:5-169 [******* ] 30% > Processing Locus no_0_3116640_0:384-1890 [******* ] 31% > Processing Locus no_0_3128142_0:6-1306 [******** ] 32% > Processing Locus no_0_3128142_0:1671-2225 [******** ] 33% > Processing Locus no_0_3128142_0:2476-2933 [******** ] 34% > Processing Locus po_0_3330421_0:1-134 [******** ] 35% > Processing Locus rsch_4_4032032_0:0-92 [********* ] 36% > Processing Locus rsch_4_4055167_0:2-109 [********* ] 37% > Processing Locus rsch_4_4110791_0:5-155 [********* ] 38% > Processing Locus rsch_4_4266550_0:4-1150 [********* ] 39% > Processing Locus rsch_4_4275442_0:15-611 [********** ] 40% > Processing Locus rsch_4_4297142_0:111-302 [********** ] 41% > Processing Locus sf_2_2488391_0:0-129 [********** ] 42% > Processing Locus sf_2_2504999_0:4-145 [********** ] 43% > Processing Locus sf_2_2524453_0:1-168 [*********** ] 44% > Processing Locus sf_2_2653966_0:0-695 [*********** ] 45% > Processing Locus sf_2_2680171_0:0-1100 [*********** ] 46% > Processing Locus sf_2_2687774_0:596-1400 [*********** ] 47% > Processing Locus sf_2_2687786_0:61-830 [************ ] 48% > Processing Locus sf_2_2687786_0:948-2177 [************ ] 49% > Processing Locus wil_2_2834553_0:0-104 [************ ] 50% > Processing Locus wil_2_2906137_0:6-148 [************ ] 50% > Processing Locus wil_2_2925323_0:13-193 [************ ] 51% > Processing Locus wil_2_2945095_0:3-205 [************* ] 52% > Processing Locus wil_2_3052273_0:41-982 [************* ] 53% > Processing Locus wil_2_3077447_0:562-1097 [************* ] 54% > Processing Locus ws_0_3182508_0:0-183 [************* ] 55% > Processing Locus ws_0_3190963_0:14-178 [************** ] 56% > Processing Locus ws_0_3298283_0:8-531 [************** ] 57% > Processing Locus ws_0_3340488_0:138-1139 [************** ] 58% > Processing Locus ws_0_3347582_0:228-917 [************** ] 59% > Processing Locus ws_0_3365892_0:14-2027 [*************** ] 60% > Processing Locus ws_0_3371988_0:0-143 [*************** ] 61% > Processing Locus ws_0_3380934_0:3-218 [*************** ] 62% > Processing Locus wu_0_2654219_0:40-143 [*************** ] 63% > Processing Locus wu_0_2655481_0:1-148 [**************** ] 64% > Processing Locus wu_0_2678387_0:6-170 [**************** ] 65% > Processing Locus zu_0_3118546_0:4-166 [**************** ] 66% > Processing Locus zu_0_3243571_0:301-771 [**************** ] 67% > Processed 70 loci. [*************************] 100% 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 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 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 $RNAGI/rnagi.sh -o ./Kn_0 -n it2.fa Kn_0.Toit2.merge.fq reference: it2.fa $RNAGI/rnagi.sh -o ./Ler_0 -n it2.fa Ler_0.Toit2.merge.fq reference: it2.fa $RNAGI/rnagi.sh -o ./No_0 -n it2.fa No_0.Toit2.merge.fq reference: it2.fa $RNAGI/rnagi.sh -o ./Mt_0 -n it2.fa Mt_0.Toit2.merge.fq reference: it2.fa tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Ler_0 it2.fa ./Ler_0/Ler_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:09:17 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:09:17 2011] Preparing output location ./Ler_0// [Mon Apr 4 14:09:17 2011] Checking for Bowtie index files [Mon Apr 4 14:09:17 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:09:17 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:09:17 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:09:17 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:09:17 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Kn_0 it2.fa ./Kn_0/Kn_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:09:18 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:09:18 2011] Preparing output location ./Kn_0// [Mon Apr 4 14:09:18 2011] Checking for Bowtie index files [Mon Apr 4 14:09:18 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:09:18 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:09:18 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:09:18 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:09:18 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./No_0 it2.fa ./No_0/No_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:09:23 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:09:23 2011] Preparing output location ./No_0// [Mon Apr 4 14:09:23 2011] Checking for Bowtie index files [Mon Apr 4 14:09:23 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:09:23 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:09:23 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:09:23 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:09:23 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Mt_0 it2.fa ./Mt_0/Mt_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:09:28 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:09:28 2011] Preparing output location ./Mt_0// [Mon Apr 4 14:09:28 2011] Checking for Bowtie index files [Mon Apr 4 14:09:28 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:09:28 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:09:28 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:09:28 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:09:28 2011] Checking reads 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 14:09:31 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:09:34 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:09:34 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:09:36 2011] Joining segment hits 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 [Mon Apr 4 14:09:39 2011] Joining segment hits [Mon Apr 4 14:09:39 2011] Joining segment hits min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) $RNAGI/rnagi.sh -o ./Oy_0 -n it2.fa Oy_0.Toit2.merge.fq reference: it2.fa [Mon Apr 4 14:09:45 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:09:48 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:09:49 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:09:51 2011] Joining segment hits [Mon Apr 4 14:09:52 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:09:53 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:09:53 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:09:55 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:09:58 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:09:58 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:10:00 2011] Searching for junctions via segment mapping [Mon Apr 4 14:10:03 2011] Searching for junctions via segment mapping [Mon Apr 4 14:10:03 2011] Mapping reads against it2.fa with Bowtie(3/3) tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Oy_0 it2.fa ./Oy_0/Oy_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:10:06 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:10:06 2011] Preparing output location ./Oy_0// [Mon Apr 4 14:10:06 2011] Checking for Bowtie index files [Mon Apr 4 14:10:06 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:10:06 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:10:06 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:10:06 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:10:06 2011] Checking reads [Mon Apr 4 14:10:07 2011] Searching for junctions via segment mapping [Mon Apr 4 14:10:08 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:10:12 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:10:16 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:10:17 2011] Retrieving sequences for splices [Mon Apr 4 14:10:17 2011] Indexing splices [Mon Apr 4 14:10:17 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 14:10:19 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:10:21 2011] Searching for junctions via segment mapping [Mon Apr 4 14:10:21 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:10:21 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:10:23 2011] Joining segment hits [Mon Apr 4 14:10:25 2011] Retrieving sequences for splices [Mon Apr 4 14:10:25 2011] Indexing splices [Mon Apr 4 14:10:25 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:10:25 2011] Reporting output tracks [Mon Apr 4 14:10:26 2011] Joining segment hits ----------------------------------------------- Run complete [00:01:04 elapsed] [Mon Apr 4 14:10:28 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:10:30 2011] Retrieving sequences for splices [Mon Apr 4 14:10:30 2011] Indexing splices [Mon Apr 4 14:10:30 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:10:30 2011] Mapping reads against segment_juncs with Bowtie cufflinks -p 4 -o ./No_0 -r it2.fa ./No_0/accepted_hits.bam [14:10:32] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:24-113 [ ] 0% > Processing Locus bur_0_1863298_0:23-141 [ ] 0% > Processing Locus bur_0_1873494_0:38-188 [ ] 0% > Processing Locus bur_0_2025286_0:7-2576 [ ] 1% > Processing Locus bur_0_2025286_0:2736-2816 [ ] 1% > Processing Locus bur_0_2032354_0:1224-1604 [ ] 1% > Processing Locus can_0_3076940_0:8-137 [ ] 2% > Processing Locus can_0_3189753_0:0-205 [ ] 2% > Processing Locus can_0_3218459_0:23-398 [ ] 2% > Processing Locus can_0_3218459_0:549-899 [ ] 2% > Processing Locus can_0_3223655_0:140-288 [ ] 3% > Processing Locus can_0_3223655_0:478-556 [ ] 3% > Processing Locus can_0_3231205_0:3-885 [ ] 3% > Processing Locus can_0_3233581_0:48-439 [* ] 4% > Processing Locus can_0_3270131_0:2-95 [* ] 4% > Processing Locus can_0_3270131_0:295-861 [* ] 4% > Processing Locus can_0_3270131_0:1208-2036 [* ] 4% > Processing Locus ct_1_3082021_0:1-124 [* ] 5% > Processing Locus ct_1_3132277_0:1-168 [* ] 5% > Processing Locus ct_1_3133451_0:63-141 [* ] 5% > Processing Locus ct_1_3133995_0:110-188 [* ] 6% > Processing Locus ct_1_3247037_0:331-500 [* ] 6% > Processing Locus edi_0_2859720_0:126-525 [* ] 7% > Processing Locus edi_0_2871668_0:11-532 [* ] 7% > Processing Locus edi_0_2934714_0:2619-2697 [* ] 7% > Processing Locus edi_0_2934714_0:5248-5326 [* ] 7% > Processing Locus hi_0_2755116_0:1-86 [** ] 8% > Processing Locus hi_0_2778596_0:3-168 [** ] 8% > Processing Locus hi_0_2795398_0:2-191 [** ] 9% > Processing Locus kn_0_3605300_0:2-168 [** ] 9% > Processing Locus kn_0_3613403_0:9-173 [** ] 10% > Processing Locus kn_0_3617271_0:24-102 [** ] 10% > Processing Locus kn_0_3626969_0:8-86 [** ] 10% > Processing Locus kn_0_3819922_1:1787-1865 [** ] 11% > Processing Locus ler_0_3998132_0:56-141 [** ] 11% > Processing Locus ler_0_3998410_0:5-163 [*** ] 12% > Processing Locus ler_0_4004770_0:35-164 [*** ] 12% > Processing Locus ler_0_4018856_0:3-175 [*** ] 13% > Processing Locus ler_0_4224097_0:729-928 [*** ] 13% > Processing Locus ler_0_4224097_0:1029-1674 [*** ] 13% > Processing Locus mt_0_4217716_0:0-186 [*** ] 13% > Processing Locus mt_0_4229662_0:8-111 [*** ] 14% > Processing Locus mt_0_4230874_0:40-188 [*** ] 14% > Processing Locus mt_0_4231054_0:0-198 [*** ] 15% > Processing Locus mt_0_4528444_1:1049-1127 [*** ] 15% > Processing Locus no_0_2885444_0:17-110 [*** ] 15% > Processing Locus no_0_2905273_0:0-121 [**** ] 16% > Processing Locus no_0_2934639_0:25-128 [**** ] 16% > Processing Locus no_0_2936769_0:1-149 [**** ] 17% > Processing Locus no_0_2956652_0:9-177 [**** ] 17% > Processing Locus no_0_3113578_1:743-821 [**** ] 18% > Processing Locus no_0_3116320_0:62-2164 [**** ] 18% > Processing Locus no_0_3116640_0:168-1875 [**** ] 18% > Processing Locus no_0_3120392_0:671-749 [**** ] 19% > Processing Locus no_0_3120392_0:960-1038 [**** ] 19% > Processing Locus no_0_3120392_0:1395-1473 [**** ] 19% > Processing Locus no_0_3120392_0:1773-1894 [**** ] 19% > Processing Locus no_0_3120392_0:2281-2359 [**** ] 19% > Processing Locus no_0_3120392_0:2479-2739 [**** ] 19% > Processing Locus no_0_3128142_0:10-909 [**** ] 19% > Processing Locus no_0_3128142_0:1024-1102 [**** ] 19% > Processing Locus no_0_3128142_0:1255-1388 [**** ] 19% > Processing Locus no_0_3128142_0:1532-2939 [**** ] 19% > Processing Locus oy_0_2965192_0:26-104 [***** ] 20% > Processing Locus oy_0_3001818_0:56-154 [***** ] 20% > Processing Locus oy_0_3121110_0:51-558 [***** ] 21% > Processing Locus oy_0_3148368_0:666-785 [***** ] 21% > Processing Locus oy_0_3148368_0:1084-1162 [***** ] 21% > Processing Locus po_0_3306688_0:18-123 [***** ] 21% > Processing Locus po_0_3330421_0:1-135 [***** ] 22% > Processing Locus po_0_3332479_0:0-135 [***** ] 22% > Processing Locus po_0_3372769_0:0-149 [***** ] 23% > Processing Locus po_0_3382155_0:2-133 [***** ] 23% > Processing Locus po_0_3393401_0:32-152 [***** ] 23% > Processing Locus po_0_3573778_0:336-1283 [****** ] 24% > Processing Locus rsch_4_4032032_0:4-85 [****** ] 24% > Processing Locus rsch_4_4055167_0:0-107 [****** ] 25% > Processing Locus rsch_4_4219071_0:53-430 [****** ] 25% > Processing Locus rsch_4_4266550_0:9-1148 [****** ] 26% > Processing Locus rsch_4_4297142_0:30-295 [****** ] 26% > Processing Locus sf_2_2459023_0:3-110 [****** ] 26% > Processing Locus sf_2_2486157_0:1-118 [****** ] 27% > Processing Locus sf_2_2524453_0:1-169 [****** ] 27% > Processing Locus sf_2_2532172_0:11-171 [******* ] 28% > Processing Locus sf_2_2682779_0:583-1235 [******* ] 28% > Processing Locus sf_2_2682779_0:1474-1552 [******* ] 28% > Processing Locus tsu_0_3222297_0:11-467 [******* ] 28% > Processing Locus tsu_0_3243273_0:4000-4078 [******* ] 29% > Processing Locus wil_2_2925323_0:0-104 [******* ] 29% > Processing Locus wil_2_3050523_0:8-274 [******* ] 30% > Processing Locus wil_2_3079625_0:308-443 [******* ] 30% > Processing Locus wil_2_3092619_0:833-952 [******* ] 31% > Processing Locus wil_2_3092619_0:1251-1329 [******* ] 31% > Processing Locus ws_0_3182508_0:10-178 [******* ] 31% > Processing Locus ws_0_3190679_0:24-196 [******* ] 31% > Processing Locus ws_0_3326342_0:223-409 [******** ] 32% > Processing Locus ws_0_3349444_1:575-653 [******** ] 32% > Processing Locus ws_0_3371988_0:1-222 [******** ] 33% > Processing Locus ws_0_3371988_0:1215-1293 [******** ] 33% > Processing Locus ws_0_3371988_0:2215-2306 [******** ] 33% > Processing Locus ws_0_3380934_0:2-211 [******** ] 33% > Processing Locus ws_0_3381390_0:0-1697 [******** ] 34% > Processing Locus wu_0_2654219_0:0-149 [******** ] 34% > Processing Locus wu_0_2678387_0:6-170 [******** ] 34% > Processing Locus zu_0_3022629_0:0-112 [******** ] 35% > Processing Locus zu_0_3082201_0:1-148 [******** ] 35% > Processing Locus zu_0_3118546_0:7-165 [********* ] 36% > Processing Locus zu_0_3190435_0:31-276 [********* ] 36% > Processing Locus zu_0_3242889_0:85-163 [********* ] 36% > Processing Locus zu_0_3259399_1:53-318 [********* ] 37% > Processing Locus zu_0_3278243_0:0-120 [********* ] 37% > Processing Locus zu_0_3289907_1:444-827 [********* ] 38% > Processed 112 loci. [*************************] 100% > Map Properties: > Total Map Mass: 4569.91 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:10:32] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:24-113 [ ] 0% > Processing Locus bur_0_1863298_0:23-141 [ ] 0% > Processing Locus bur_0_1873494_0:38-188 [ ] 1% > Processing Locus bur_0_2025286_0:7-2576 [ ] 2% > Processing Locus bur_0_2025286_0:2736-2816 [ ] 3% > Processing Locus bur_0_2032354_0:1224-1604 [* ] 4% > Processing Locus can_0_3076940_0:8-137 [* ] 5% > Processing Locus can_0_3189753_0:0-205 [* ] 6% > Processing Locus can_0_3218459_0:23-398 [* ] 7% > Processing Locus can_0_3218459_0:549-899 [** ] 8% > Processing Locus can_0_3223655_0:140-288 [** ] 8% > Processing Locus can_0_3223655_0:478-556 [** ] 9% > Processing Locus can_0_3231205_0:3-885 [** ] 10% > Processing Locus can_0_3233581_0:48-439 [** ] 11% > Processing Locus can_0_3270131_0:2-95 [*** ] 12% > Processing Locus can_0_3270131_0:295-861 [*** ] 13% > Processing Locus can_0_3270131_0:1208-2036 [*** ] 14% > Processing Locus ct_1_3082021_0:1-124 [*** ] 15% > Processing Locus ct_1_3132277_0:1-168 [**** ] 16% > Processing Locus ct_1_3133451_0:63-141 [**** ] 16% > Processing Locus ct_1_3133995_0:110-188 [**** ] 17% > Processing Locus ct_1_3247037_0:331-500 [**** ] 18% > Processing Locus edi_0_2859720_0:126-525 [**** ] 19% > Processing Locus edi_0_2871668_0:11-532 [***** ] 20% > Processing Locus edi_0_2934714_0:2619-2697 [***** ] 21% > Processing Locus edi_0_2934714_0:5248-5326 [***** ] 22% > Processing Locus hi_0_2755116_0:1-86 [***** ] 23% > Processing Locus hi_0_2778596_0:3-168 [****** ] 24% > Processing Locus hi_0_2795398_0:2-191 [****** ] 25% > Processing Locus kn_0_3605300_0:2-168 [****** ] 25% > Processing Locus kn_0_3613403_0:9-173 [****** ] 26% > Processing Locus kn_0_3617271_0:24-102 [****** ] 27% > Processing Locus kn_0_3626969_0:8-86 [******* ] 28% > Processing Locus kn_0_3819922_1:1787-1865 [******* ] 29% > Processing Locus ler_0_3998132_0:56-141 [******* ] 30% > Processing Locus ler_0_3998410_0:5-163 [******* ] 31% > Processing Locus ler_0_4004770_0:35-164 [******** ] 32% > Processing Locus ler_0_4018856_0:3-175 [******** ] 33% > Processing Locus ler_0_4224097_0:729-928 [******** ] 33% > Processing Locus ler_0_4224097_0:1029-1674 [******** ] 34% > Processing Locus mt_0_4217716_0:0-186 [******** ] 35% > Processing Locus mt_0_4229662_0:8-111 [********* ] 36% > Processing Locus mt_0_4230874_0:40-188 [********* ] 37% > Processing Locus mt_0_4231054_0:0-198 [********* ] 38% > Processing Locus mt_0_4528444_1:1049-1127 [********* ] 39% > Processing Locus no_0_2885444_0:17-110 [********** ] 40% > Processing Locus no_0_2905273_0:0-121 [********** ] 41% > Processing Locus no_0_2934639_0:25-128 [********** ] 41% > Processing Locus no_0_2936769_0:1-149 [********** ] 42% > Processing Locus no_0_2956652_0:9-177 [********** ] 43% > Processing Locus no_0_3113578_1:743-821 [*********** ] 44% > Processing Locus no_0_3116320_0:62-2164 [*********** ] 45% > Processing Locus no_0_3116640_0:168-1875 [*********** ] 46% > Processing Locus no_0_3120392_0:671-749 [*********** ] 47% > Processing Locus no_0_3120392_0:960-1038 [************ ] 48% > Processing Locus no_0_3120392_0:1395-1473 [************ ] 49% > Processing Locus no_0_3120392_0:1773-1894 [************ ] 50% > Processing Locus no_0_3120392_0:2281-2359 [************ ] 50% > Processing Locus no_0_3120392_0:2479-2739 [************ ] 51% > Processing Locus no_0_3128142_0:10-909 [************* ] 52% > Processing Locus no_0_3128142_0:1024-1102 [************* ] 53% > Processing Locus no_0_3128142_0:1255-1388 [************* ] 54% > Processing Locus no_0_3128142_0:1532-2939 [************* ] 55% > Processing Locus oy_0_2965192_0:26-104 [************** ] 56% > Processing Locus oy_0_3001818_0:56-154 [************** ] 57% > Processing Locus oy_0_3121110_0:51-558 [************** ] 58% > Processing Locus oy_0_3148368_0:666-785 [************** ] 58% > Processing Locus oy_0_3148368_0:1084-1162 [************** ] 59% > Processing Locus po_0_3306688_0:18-123 [*************** ] 60% > Processing Locus po_0_3330421_0:1-135 [*************** ] 61% > Processing Locus po_0_3332479_0:0-135 [*************** ] 62% > Processing Locus po_0_3372769_0:0-149 [*************** ] 63% > Processing Locus po_0_3382155_0:2-133 [**************** ] 64% > Processing Locus po_0_3393401_0:32-152 [**************** ] 65% > Processing Locus po_0_3573778_0:336-1283 [**************** ] 66% > Processing Locus rsch_4_4032032_0:4-85 [**************** ] 66% > Processing Locus rsch_4_4055167_0:0-107 [**************** ] 67% > Processing Locus rsch_4_4219071_0:53-430 [***************** ] 68% > Processing Locus rsch_4_4266550_0:9-1148 [***************** ] 69% > Processing Locus rsch_4_4297142_0:30-295 [***************** ] 70% > Processing Locus sf_2_2459023_0:3-110 [***************** ] 71% > Processing Locus sf_2_2486157_0:1-118 [****************** ] 72% > Processing Locus sf_2_2524453_0:1-169 [****************** ] 73% > Processing Locus sf_2_2532172_0:11-171 [****************** ] 74% > Processing Locus sf_2_2682779_0:583-1235 [****************** ] 75% > Processing Locus sf_2_2682779_0:1474-1552 [****************** ] 75% > Processing Locus tsu_0_3222297_0:11-467 [******************* ] 76% > Processing Locus tsu_0_3243273_0:4000-4078 [******************* ] 77% > Processing Locus wil_2_2925323_0:0-104 [******************* ] 78% > Processing Locus wil_2_3050523_0:8-274 [******************* ] 79% > Processing Locus wil_2_3079625_0:308-443 [******************** ] 80% > Processing Locus wil_2_3092619_0:833-952 [******************** ] 81% > Processing Locus wil_2_3092619_0:1251-1329 [******************** ] 82% > Processing Locus ws_0_3182508_0:10-178 [******************** ] 83% > Processing Locus ws_0_3190679_0:24-196 [******************** ] 83% > Processing Locus ws_0_3326342_0:223-409 [********************* ] 84% > Processing Locus ws_0_3349444_1:575-653 [********************* ] 85% > Processing Locus ws_0_3371988_0:1-222 [********************* ] 86% > Processing Locus ws_0_3371988_0:1215-1293 [********************* ] 87% > Processing Locus ws_0_3371988_0:2215-2306 [********************** ] 88% > Processing Locus ws_0_3380934_0:2-211 [********************** ] 89% > Processing Locus ws_0_3381390_0:0-1697 [********************** ] 90% > Processing Locus wu_0_2654219_0:0-149 [********************** ] 91% > Processing Locus wu_0_2678387_0:6-170 [********************** ] 91% > Processing Locus zu_0_3022629_0:0-112 [*********************** ] 92% > Processing Locus zu_0_3082201_0:1-148 [*********************** ] 93% > Processing Locus zu_0_3118546_0:7-165 [*********************** ] 94% > Processing Locus zu_0_3190435_0:31-276 [*********************** ] 95% > Processing Locus zu_0_3242889_0:85-163 [************************ ] 96% > Processing Locus zu_0_3259399_1:53-318 [************************ ] 97% > Processing Locus zu_0_3278243_0:0-120 [************************ ] 98% > Processing Locus zu_0_3289907_1:444-827 [************************ ] 99% > Processed 112 loci. [*************************] 100% [14:10:33] Loading reference annotation and sequence [14:10:33] Learning bias parameters. > Processing Locus bur_0_1804399_0:24-113 [ ] 0% > Processing Locus bur_0_1863298_0:23-141 [ ] 0% > Processing Locus bur_0_1873494_0:38-188 [ ] 1% > Processing Locus bur_0_2025286_0:7-2576 [ ] 2% > Processing Locus can_0_3076940_0:8-137 [ ] 3% > Processing Locus can_0_3189753_0:0-205 [* ] 4% > Processing Locus can_0_3218459_0:23-398 [* ] 5% > Processing Locus can_0_3218459_0:549-899 [* ] 6% > Processing Locus can_0_3231205_0:3-885 [* ] 7% > Processing Locus can_0_3233581_0:48-439 [** ] 8% > Processing Locus can_0_3270131_0:1208-2036 [** ] 8% > Processing Locus ct_1_3082021_0:1-124 [** ] 9% > Processing Locus ct_1_3132277_0:1-168 [** ] 10% > Processing Locus edi_0_2859720_0:126-525 [** ] 11% > Processing Locus edi_0_2871668_0:11-532 [*** ] 12% > Processing Locus hi_0_2778596_0:3-168 [*** ] 13% > Processing Locus hi_0_2795398_0:2-191 [*** ] 14% > Processing Locus kn_0_3605300_0:2-168 [*** ] 15% > Processing Locus kn_0_3613403_0:9-173 [**** ] 16% > Processing Locus ler_0_3998132_0:56-141 [**** ] 16% > Processing Locus ler_0_4018856_0:3-175 [**** ] 17% > Processing Locus ler_0_4224097_0:1029-1674 [**** ] 18% > Processing Locus mt_0_4217716_0:0-186 [**** ] 19% > Processing Locus mt_0_4229662_0:8-111 [***** ] 20% > Processing Locus mt_0_4230874_0:40-188 [***** ] 21% > Processing Locus mt_0_4231054_0:0-198 [***** ] 22% > Processing Locus no_0_2885444_0:17-110 [***** ] 23% > Processing Locus no_0_2905273_0:0-121 [****** ] 24% > Processing Locus no_0_2936769_0:1-149 [****** ] 25% > Processing Locus no_0_2956652_0:9-177 [****** ] 25% > Processing Locus no_0_3116320_0:62-2164 [****** ] 26% > Processing Locus no_0_3116640_0:168-1875 [****** ] 27% > Processing Locus no_0_3128142_0:10-909 [******* ] 28% > Processing Locus no_0_3128142_0:1532-2939 [******* ] 29% > Processing Locus oy_0_3001818_0:56-154 [******* ] 30% > Processing Locus oy_0_3121110_0:51-558 [******* ] 31% > Processing Locus po_0_3306688_0:18-123 [******** ] 32% > Processing Locus po_0_3330421_0:1-135 [******** ] 33% > Processing Locus po_0_3332479_0:0-135 [******** ] 33% > Processing Locus po_0_3372769_0:0-149 [******** ] 34% > Processing Locus po_0_3382155_0:2-133 [******** ] 35% > Processing Locus po_0_3573778_0:336-1283 [********* ] 36% > Processing Locus rsch_4_4055167_0:0-107 [********* ] 37% > Processing Locus rsch_4_4219071_0:53-430 [********* ] 38% > Processing Locus rsch_4_4266550_0:9-1148 [********* ] 39% > Processing Locus rsch_4_4297142_0:30-295 [********** ] 40% > Processing Locus sf_2_2459023_0:3-110 [********** ] 41% > Processing Locus sf_2_2486157_0:1-118 [********** ] 41% > Processing Locus sf_2_2524453_0:1-169 [********** ] 42% > Processing Locus sf_2_2532172_0:11-171 [********** ] 43% > Processing Locus sf_2_2682779_0:583-1235 [*********** ] 44% > Processing Locus tsu_0_3222297_0:11-467 [*********** ] 45% > Processing Locus wil_2_2925323_0:0-104 [*********** ] 46% > Processing Locus wil_2_3050523_0:8-274 [*********** ] 47% > Processing Locus ws_0_3182508_0:10-178 [************ ] 48% > Processing Locus ws_0_3190679_0:24-196 [************ ] 49% > Processing Locus ws_0_3371988_0:1-222 [************ ] 50% > Processing Locus ws_0_3380934_0:2-211 [************ ] 50% > Processing Locus ws_0_3381390_0:0-1697 [************ ] 51% > Processing Locus wu_0_2654219_0:0-149 [************* ] 52% > Processing Locus zu_0_3022629_0:0-112 [************* ] 53% > Processing Locus zu_0_3082201_0:1-148 [************* ] 54% > Processing Locus zu_0_3118546_0:7-165 [************* ] 55% > Processing Locus zu_0_3190435_0:31-276 [************** ] 56% > Processing Locus zu_0_3259399_1:53-318 [************** ] 57% > Processing Locus zu_0_3278243_0:0-120 [************** ] 58% > Processed 66 loci. [*************************] 100% [14:10:33] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:24-113 [ ] 0% > Processing Locus bur_0_1863298_0:23-141 [ ] 0% > Processing Locus bur_0_1873494_0:38-188 [ ] 1% > Processing Locus bur_0_2025286_0:7-2576 [ ] 2% > Processing Locus can_0_3076940_0:8-137 [ ] 3% > Processing Locus can_0_3189753_0:0-205 [* ] 4% > Processing Locus can_0_3218459_0:23-398 [* ] 5% > Processing Locus can_0_3218459_0:549-899 [* ] 6% > Processing Locus can_0_3231205_0:3-885 [* ] 7% > Processing Locus can_0_3233581_0:48-439 [** ] 8% > Processing Locus can_0_3270131_0:1208-2036 [** ] 8% > Processing Locus ct_1_3082021_0:1-124 [** ] 9% > Processing Locus ct_1_3132277_0:1-168 [** ] 10% > Processing Locus edi_0_2859720_0:126-525 [** ] 11% > Processing Locus edi_0_2871668_0:11-532 [*** ] 12% > Processing Locus hi_0_2778596_0:3-168 [*** ] 13% > Processing Locus hi_0_2795398_0:2-191 [*** ] 14% > Processing Locus kn_0_3605300_0:2-168 [*** ] 15% > Processing Locus kn_0_3613403_0:9-173 [**** ] 16% > Processing Locus ler_0_3998132_0:56-141 [**** ] 16% > Processing Locus ler_0_4018856_0:3-175 [**** ] 17% > Processing Locus ler_0_4224097_0:1029-1674 [**** ] 18% > Processing Locus mt_0_4217716_0:0-186 [**** ] 19% > Processing Locus mt_0_4229662_0:8-111 [***** ] 20% > Processing Locus mt_0_4230874_0:40-188 [***** ] 21% > Processing Locus mt_0_4231054_0:0-198 [***** ] 22% > Processing Locus no_0_2885444_0:17-110 [***** ] 23% > Processing Locus no_0_2905273_0:0-121 [****** ] 24% > Processing Locus no_0_2936769_0:1-149 [****** ] 25% > Processing Locus no_0_2956652_0:9-177 [****** ] 25% > Processing Locus no_0_3116320_0:62-2164 [****** ] 26% > Processing Locus no_0_3116640_0:168-1875 [****** ] 27% > Processing Locus no_0_3128142_0:10-909 [******* ] 28% > Processing Locus no_0_3128142_0:1532-2939 [******* ] 29% > Processing Locus oy_0_3001818_0:56-154 [******* ] 30% > Processing Locus oy_0_3121110_0:51-558 [******* ] 31% > Processing Locus po_0_3306688_0:18-123 [******** ] 32% > Processing Locus po_0_3330421_0:1-135 [******** ] 33% > Processing Locus po_0_3332479_0:0-135 [******** ] 33% > Processing Locus po_0_3372769_0:0-149 [******** ] 34% > Processing Locus po_0_3382155_0:2-133 [******** ] 35% > Processing Locus po_0_3573778_0:336-1283 [********* ] 36% > Processing Locus rsch_4_4055167_0:0-107 [********* ] 37% > Processing Locus rsch_4_4219071_0:53-430 [********* ] 38% > Processing Locus rsch_4_4266550_0:9-1148 [********* ] 39% > Processing Locus rsch_4_4297142_0:30-295 [********** ] 40% > Processing Locus sf_2_2459023_0:3-110 [********** ] 41% > Processing Locus sf_2_2486157_0:1-118 [********** ] 41% > Processing Locus sf_2_2524453_0:1-169 [********** ] 42% > Processing Locus sf_2_2532172_0:11-171 [********** ] 43% > Processing Locus sf_2_2682779_0:583-1235 [*********** ] 44% > Processing Locus tsu_0_3222297_0:11-467 [*********** ] 45% > Processing Locus wil_2_2925323_0:0-104 [*********** ] 46% > Processing Locus wil_2_3050523_0:8-274 [*********** ] 47% > Processing Locus ws_0_3182508_0:10-178 [************ ] 48% > Processing Locus ws_0_3190679_0:24-196 [************ ] 49% > Processing Locus ws_0_3371988_0:1-222 [************ ] 50% > Processing Locus ws_0_3380934_0:2-211 [************ ] 50% > Processing Locus ws_0_3381390_0:0-1697 [************ ] 51% > Processing Locus wu_0_2654219_0:0-149 [************* ] 52% > Processing Locus zu_0_3022629_0:0-112 [************* ] 53% > Processing Locus zu_0_3082201_0:1-148 [************* ] 54% > Processing Locus zu_0_3118546_0:7-165 [************* ] 55% > Processing Locus zu_0_3190435_0:31-276 [************** ] 56% > Processing Locus zu_0_3259399_1:53-318 [************** ] 57% > Processing Locus zu_0_3278243_0:0-120 [************** ] 58% > Processed 66 loci. [*************************] 100% [Mon Apr 4 14:10:33 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:10:33 2011] Joining segment hits [Mon Apr 4 14:10:35 2011] Reporting output tracks [Mon Apr 4 14:10:35 2011] Mapping reads against segment_juncs with Bowtie ----------------------------------------------- Run complete [00:01:19 elapsed] [Mon Apr 4 14:10:38 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:10:38 2011] Joining segment hits [Mon Apr 4 14:10:40 2011] Reporting output tracks [Mon Apr 4 14:10:41 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:10:42 2011] Retrieving sequences for splices [Mon Apr 4 14:10:42 2011] Indexing splices [Mon Apr 4 14:10:42 2011] Mapping reads against segment_juncs with Bowtie ----------------------------------------------- Run complete [00:01:24 elapsed] cufflinks -p 4 -o ./Ler_0 -r it2.fa ./Ler_0/accepted_hits.bam [14:10:44] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:1-108 [ ] 0% > Processing Locus bur_0_1863298_0:25-138 [ ] 0% > Processing Locus bur_0_1873494_0:13-183 [ ] 0% > Processing Locus can_0_3076940_0:0-140 [ ] 1% > Processing Locus can_0_3189753_0:9-203 [ ] 1% > Processing Locus can_0_3223655_0:77-655 [ ] 2% > Processing Locus can_0_3233581_0:10-458 [ ] 2% > Processing Locus can_0_3270131_0:53-889 [ ] 2% > Processing Locus can_0_3270131_0:1218-1312 [ ] 2% > Processing Locus can_0_3270131_0:1622-2233 [ ] 2% > Processing Locus ct_1_3082021_0:3-128 [ ] 3% > Processing Locus ct_1_3132277_0:0-174 [ ] 3% > Processing Locus ct_1_3241157_0:5-774 [* ] 4% > Processing Locus ct_1_3247037_0:28-106 [* ] 4% > Processing Locus ct_1_3247037_0:287-510 [* ] 4% > Processing Locus edi_0_2859720_0:146-524 [* ] 5% > Processing Locus edi_0_2918156_0:81-583 [* ] 5% > Processing Locus hi_0_2755116_0:1-83 [* ] 5% > Processing Locus hi_0_2778596_0:4-168 [* ] 6% > Processing Locus hi_0_2916184_0:3-521 [* ] 6% > Processing Locus hi_0_2939638_0:37-631 [* ] 7% > Processing Locus hi_0_2953648_0:4-1321 [* ] 7% > Processing Locus hi_0_2961678_0:97-1501 [* ] 7% > Processing Locus kn_0_3613403_0:16-130 [** ] 8% > Processing Locus kn_0_3751597_0:450-528 [** ] 8% > Processing Locus ler_0_3967940_0:4-134 [** ] 9% > Processing Locus ler_0_3998132_0:53-162 [** ] 9% > Processing Locus ler_0_3998410_0:5-163 [** ] 10% > Processing Locus ler_0_4004770_0:64-158 [** ] 10% > Processing Locus ler_0_4018856_0:3-182 [** ] 10% > Processing Locus ler_0_4165287_0:4-735 [** ] 11% > Processing Locus ler_0_4224097_0:846-1677 [** ] 11% > Processing Locus ler_0_4225073_0:9-690 [*** ] 12% > Processing Locus mt_0_4193196_0:11-166 [*** ] 12% > Processing Locus mt_0_4217716_0:1-180 [*** ] 13% > Processing Locus mt_0_4229662_0:1-197 [*** ] 13% > Processing Locus mt_0_4230874_0:43-197 [*** ] 13% > Processing Locus mt_0_4231054_0:4-82 [*** ] 14% > Processing Locus mt_0_4528444_1:414-1245 [*** ] 14% > Processing Locus no_0_2885444_0:9-109 [*** ] 15% > Processing Locus no_0_2905273_0:7-112 [*** ] 15% > Processing Locus no_0_2934639_0:25-146 [*** ] 15% > Processing Locus no_0_2956652_0:5-177 [**** ] 16% > Processing Locus no_0_3101262_0:39-747 [**** ] 16% > Processing Locus no_0_3128142_0:1768-2936 [**** ] 17% > Processing Locus oy_0_2936927_0:2-118 [**** ] 17% > Processing Locus oy_0_2965192_0:52-135 [**** ] 18% > Processing Locus oy_0_3001818_0:50-154 [**** ] 18% > Processing Locus oy_0_3162092_0:615-693 [**** ] 18% > Processing Locus oy_0_3162092_0:1588-1666 [**** ] 18% > Processing Locus po_0_3299272_0:14-119 [**** ] 19% > Processing Locus po_0_3324652_0:0-130 [**** ] 19% > Processing Locus rsch_4_4032032_0:0-89 [***** ] 20% > Processing Locus rsch_4_4055167_0:0-109 [***** ] 20% > Processing Locus rsch_4_4214541_0:1-234 [***** ] 21% > Processing Locus rsch_4_4219071_0:12-409 [***** ] 21% > Processing Locus rsch_4_4255532_0:5-285 [***** ] 21% > Processing Locus rsch_4_4275442_0:33-621 [***** ] 22% > Processing Locus rsch_4_4292194_1:20-1106 [***** ] 22% > Processing Locus rsch_4_4297142_0:37-304 [***** ] 23% > Processing Locus sf_2_2486157_0:1-128 [***** ] 23% > Processing Locus sf_2_2524453_0:0-168 [***** ] 23% > Processing Locus sf_2_2532172_0:1-181 [****** ] 24% > Processing Locus sf_2_2687774_0:588-1428 [****** ] 24% > Processing Locus sf_2_2687786_0:2-2192 [****** ] 25% > Processing Locus sf_2_2700286_0:0-2492 [****** ] 25% > Processing Locus tsu_0_3036945_0:9-147 [****** ] 26% > Processing Locus tsu_0_3175121_0:563-701 [****** ] 26% > Processing Locus tsu_0_3211741_0:38-788 [****** ] 26% > Processing Locus wil_2_2834553_0:0-104 [****** ] 27% > Processing Locus wil_2_2925323_0:0-192 [****** ] 27% > Processing Locus wil_2_3052273_0:37-985 [******* ] 28% > Processing Locus wil_2_3052273_0:1099-1177 [******* ] 28% > Processing Locus wil_2_3054893_0:37-574 [******* ] 28% > Processing Locus wil_2_3066229_0:217-666 [******* ] 28% > Processing Locus wil_2_3068737_0:390-1187 [******* ] 29% > Processing Locus wil_2_3068737_0:1556-1760 [******* ] 29% > Processing Locus wil_2_3090237_0:267-495 [******* ] 29% > Processing Locus ws_0_3182508_0:5-180 [******* ] 30% > Processing Locus ws_0_3190679_0:45-178 [******* ] 30% > Processing Locus ws_0_3326342_0:12-422 [******* ] 31% > Processing Locus ws_0_3340488_0:199-1139 [******* ] 31% > Processing Locus ws_0_3344070_0:32-913 [******* ] 31% > Processing Locus ws_0_3347582_0:109-760 [******** ] 32% > Processing Locus ws_0_3347582_0:876-977 [******** ] 32% > Processing Locus ws_0_3347582_0:1170-1352 [******** ] 32% > Processing Locus ws_0_3371988_0:1-212 [******** ] 32% > Processing Locus ws_0_3380934_0:2-211 [******** ] 33% > Processing Locus wu_0_2654219_0:40-149 [******** ] 33% > Processing Locus wu_0_2678387_0:8-178 [******** ] 34% > Processing Locus wu_0_2687576_0:15-171 [******** ] 34% > Processing Locus zu_0_3118546_0:4-175 [******** ] 34% > Processing Locus zu_0_3190435_0:19-301 [******** ] 35% > Processing Locus zu_0_3238769_0:27-169 [******** ] 35% > Processing Locus zu_0_3238769_0:354-432 [******** ] 35% > Processing Locus zu_0_3242889_0:3-294 [********* ] 36% > Processing Locus zu_0_3255503_0:1071-1366 [********* ] 36% > Processing Locus zu_0_3260131_0:173-401 [********* ] 36% > Processing Locus zu_0_3277661_0:334-901 [********* ] 37% > Processing Locus zu_0_3278243_0:7-211 [********* ] 37% > Processing Locus zu_0_3278243_0:496-574 [********* ] 37% > Processed 101 loci. [*************************] 100% > Map Properties: > Total Map Mass: 7710.59 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:10:44] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:1-108 [ ] 0% > Processing Locus bur_0_1863298_0:25-138 [ ] 0% > Processing Locus bur_0_1873494_0:13-183 [ ] 1% > Processing Locus can_0_3076940_0:0-140 [ ] 2% > Processing Locus can_0_3189753_0:9-203 [ ] 3% > Processing Locus can_0_3223655_0:77-655 [* ] 4% > Processing Locus can_0_3233581_0:10-458 [* ] 5% > Processing Locus can_0_3270131_0:53-889 [* ] 6% > Processing Locus can_0_3270131_0:1218-1312 [* ] 7% > Processing Locus can_0_3270131_0:1622-2233 [** ] 8% > Processing Locus ct_1_3082021_0:3-128 [** ] 9% > Processing Locus ct_1_3132277_0:0-174 [** ] 10% > Processing Locus ct_1_3241157_0:5-774 [** ] 11% > Processing Locus ct_1_3247037_0:28-106 [*** ] 12% > Processing Locus ct_1_3247037_0:287-510 [*** ] 13% > Processing Locus edi_0_2859720_0:146-524 [*** ] 14% > Processing Locus edi_0_2918156_0:81-583 [*** ] 15% > Processing Locus hi_0_2755116_0:1-83 [**** ] 16% > Processing Locus hi_0_2778596_0:4-168 [**** ] 17% > Processing Locus hi_0_2916184_0:3-521 [**** ] 18% > Processing Locus hi_0_2939638_0:37-631 [**** ] 19% > Processing Locus hi_0_2953648_0:4-1321 [***** ] 20% > Processing Locus hi_0_2961678_0:97-1501 [***** ] 21% > Processing Locus kn_0_3613403_0:16-130 [***** ] 22% > Processing Locus kn_0_3751597_0:450-528 [***** ] 23% > Processing Locus ler_0_3967940_0:4-134 [****** ] 24% > Processing Locus ler_0_3998132_0:53-162 [****** ] 25% > Processing Locus ler_0_3998410_0:5-163 [****** ] 26% > Processing Locus ler_0_4004770_0:64-158 [****** ] 27% > Processing Locus ler_0_4018856_0:3-182 [******* ] 28% > Processing Locus ler_0_4165287_0:4-735 [******* ] 29% > Processing Locus ler_0_4224097_0:846-1677 [******* ] 30% > Processing Locus ler_0_4225073_0:9-690 [******* ] 31% > Processing Locus mt_0_4193196_0:11-166 [******** ] 32% > Processing Locus mt_0_4217716_0:1-180 [******** ] 33% > Processing Locus mt_0_4229662_0:1-197 [******** ] 34% > Processing Locus mt_0_4230874_0:43-197 [******** ] 35% > Processing Locus mt_0_4231054_0:4-82 [********* ] 36% > Processing Locus mt_0_4528444_1:414-1245 [********* ] 37% > Processing Locus no_0_2885444_0:9-109 [********* ] 38% > Processing Locus no_0_2905273_0:7-112 [********* ] 39% > Processing Locus no_0_2934639_0:25-146 [********** ] 40% > Processing Locus no_0_2956652_0:5-177 [********** ] 41% > Processing Locus no_0_3101262_0:39-747 [********** ] 42% > Processing Locus no_0_3128142_0:1768-2936 [********** ] 43% > Processing Locus oy_0_2936927_0:2-118 [*********** ] 44% > Processing Locus oy_0_2965192_0:52-135 [*********** ] 45% > Processing Locus oy_0_3001818_0:50-154 [*********** ] 46% > Processing Locus oy_0_3162092_0:615-693 [*********** ] 47% > Processing Locus oy_0_3162092_0:1588-1666 [************ ] 48% > Processing Locus po_0_3299272_0:14-119 [************ ] 49% > Processing Locus po_0_3324652_0:0-130 [************ ] 50% > Processing Locus rsch_4_4032032_0:0-89 [************ ] 51% > Processing Locus rsch_4_4055167_0:0-109 [************* ] 52% > Processing Locus rsch_4_4214541_0:1-234 [************* ] 53% > Processing Locus rsch_4_4219071_0:12-409 [************* ] 54% > Processing Locus rsch_4_4255532_0:5-285 [************* ] 55% > Processing Locus rsch_4_4275442_0:33-621 [************** ] 56% > Processing Locus rsch_4_4292194_1:20-1106 [************** ] 57% > Processing Locus rsch_4_4297142_0:37-304 [************** ] 58% > Processing Locus sf_2_2486157_0:1-128 [************** ] 59% > Processing Locus sf_2_2524453_0:0-168 [*************** ] 60% > Processing Locus sf_2_2532172_0:1-181 [*************** ] 61% > Processing Locus sf_2_2687774_0:588-1428 [*************** ] 62% > Processing Locus sf_2_2687786_0:2-2192 [*************** ] 63% > Processing Locus sf_2_2700286_0:0-2492 [**************** ] 64% > Processing Locus tsu_0_3036945_0:9-147 [**************** ] 65% > Processing Locus tsu_0_3175121_0:563-701 [**************** ] 66% > Processing Locus tsu_0_3211741_0:38-788 [**************** ] 67% > Processing Locus wil_2_2834553_0:0-104 [***************** ] 68% > Processing Locus wil_2_2925323_0:0-192 [***************** ] 69% > Processing Locus wil_2_3052273_0:37-985 [***************** ] 70% > Processing Locus wil_2_3052273_0:1099-1177 [***************** ] 71% > Processing Locus wil_2_3054893_0:37-574 [****************** ] 72% > Processing Locus wil_2_3066229_0:217-666 [****************** ] 73% > Processing Locus wil_2_3068737_0:390-1187 [****************** ] 74% > Processing Locus wil_2_3068737_0:1556-1760 [****************** ] 75% > Processing Locus wil_2_3090237_0:267-495 [******************* ] 76% > Processing Locus ws_0_3182508_0:5-180 [******************* ] 77% > Processing Locus ws_0_3190679_0:45-178 [******************* ] 78% > Processing Locus ws_0_3326342_0:12-422 [******************* ] 79% > Processing Locus ws_0_3340488_0:199-1139 [******************** ] 80% > Processing Locus ws_0_3344070_0:32-913 [******************** ] 81% > Processing Locus ws_0_3347582_0:109-760 [******************** ] 82% > Processing Locus ws_0_3347582_0:876-977 [******************** ] 83% > Processing Locus ws_0_3347582_0:1170-1352 [********************* ] 84% > Processing Locus ws_0_3371988_0:1-212 [********************* ] 85% > Processing Locus ws_0_3380934_0:2-211 [********************* ] 86% > Processing Locus wu_0_2654219_0:40-149 [********************* ] 87% > Processing Locus wu_0_2678387_0:8-178 [********************** ] 88% > Processing Locus wu_0_2687576_0:15-171 [********************** ] 89% > Processing Locus zu_0_3118546_0:4-175 [********************** ] 90% > Processing Locus zu_0_3190435_0:19-301 [********************** ] 91% > Processing Locus zu_0_3238769_0:27-169 [*********************** ] 92% > Processing Locus zu_0_3238769_0:354-432 [*********************** ] 93% > Processing Locus zu_0_3242889_0:3-294 [*********************** ] 94% > Processing Locus zu_0_3255503_0:1071-1366 [*********************** ] 95% > Processing Locus zu_0_3260131_0:173-401 [************************ ] 96% > Processing Locus zu_0_3277661_0:334-901 [************************ ] 97% > Processing Locus zu_0_3278243_0:7-211 [************************ ] 98% > Processing Locus zu_0_3278243_0:496-574 [************************ ] 99% > Processed 101 loci. [*************************] 100% [14:10:44] Loading reference annotation and sequence [14:10:44] Learning bias parameters. > Processing Locus bur_0_1804399_0:1-108 [ ] 0% > Processing Locus bur_0_1863298_0:25-138 [ ] 0% > Processing Locus bur_0_1873494_0:13-183 [ ] 1% > Processing Locus can_0_3076940_0:0-140 [ ] 2% > Processing Locus can_0_3189753_0:9-203 [ ] 3% > Processing Locus can_0_3223655_0:77-655 [* ] 4% > Processing Locus can_0_3233581_0:10-458 [* ] 5% > Processing Locus can_0_3270131_0:1622-2233 [* ] 6% > Processing Locus ct_1_3082021_0:3-128 [* ] 7% > Processing Locus ct_1_3132277_0:0-174 [** ] 8% > Processing Locus ct_1_3241157_0:5-774 [** ] 9% > Processing Locus edi_0_2859720_0:146-524 [** ] 10% > Processing Locus edi_0_2918156_0:81-583 [** ] 11% > Processing Locus hi_0_2778596_0:4-168 [*** ] 12% > Processing Locus hi_0_2916184_0:3-521 [*** ] 13% > Processing Locus hi_0_2939638_0:37-631 [*** ] 14% > Processing Locus hi_0_2953648_0:4-1321 [*** ] 15% > Processing Locus hi_0_2961678_0:97-1501 [**** ] 16% > Processing Locus kn_0_3613403_0:16-130 [**** ] 17% > Processing Locus ler_0_3967940_0:4-134 [**** ] 18% > Processing Locus ler_0_3998132_0:53-162 [**** ] 19% > Processing Locus ler_0_3998410_0:5-163 [***** ] 20% > Processing Locus ler_0_4018856_0:3-182 [***** ] 21% > Processing Locus ler_0_4165287_0:4-735 [***** ] 22% > Processing Locus ler_0_4224097_0:846-1677 [***** ] 23% > Processing Locus ler_0_4225073_0:29-690 [****** ] 24% > Processing Locus mt_0_4193196_0:11-166 [****** ] 25% > Processing Locus mt_0_4217716_0:1-180 [****** ] 26% > Processing Locus mt_0_4229662_0:1-197 [****** ] 27% > Processing Locus mt_0_4230874_0:43-197 [******* ] 28% > Processing Locus mt_0_4528444_1:414-1245 [******* ] 29% > Processing Locus no_0_2885444_0:9-109 [******* ] 30% > Processing Locus no_0_2905273_0:7-112 [******* ] 31% > Processing Locus no_0_2934639_0:25-146 [******** ] 32% > Processing Locus no_0_2956652_0:5-177 [******** ] 33% > Processing Locus no_0_3101262_0:39-747 [******** ] 34% > Processing Locus no_0_3128142_0:1768-2936 [******** ] 35% > Processing Locus oy_0_2936927_0:2-118 [********* ] 36% > Processing Locus oy_0_3001818_0:50-154 [********* ] 37% > Processing Locus po_0_3299272_0:14-119 [********* ] 38% > Processing Locus po_0_3324652_0:0-130 [********* ] 39% > Processing Locus rsch_4_4032032_0:0-89 [********** ] 40% > Processing Locus rsch_4_4055167_0:0-109 [********** ] 41% > Processing Locus rsch_4_4214541_0:1-234 [********** ] 42% > Processing Locus rsch_4_4255532_0:5-285 [********** ] 43% > Processing Locus rsch_4_4275442_0:33-621 [*********** ] 44% > Processing Locus rsch_4_4292194_1:20-1106 [*********** ] 45% > Processing Locus rsch_4_4297142_0:37-304 [*********** ] 46% > Processing Locus sf_2_2486157_0:1-128 [*********** ] 47% > Processing Locus sf_2_2524453_0:0-168 [************ ] 48% > Processing Locus sf_2_2532172_0:1-181 [************ ] 49% > Processing Locus sf_2_2687774_0:588-1428 [************ ] 50% > Processing Locus sf_2_2687786_0:2-2192 [************ ] 51% > Processing Locus sf_2_2700286_0:0-2492 [************* ] 52% > Processing Locus tsu_0_3175121_0:563-701 [************* ] 53% > Processing Locus tsu_0_3211741_0:38-788 [************* ] 54% > Processing Locus wil_2_2834553_0:0-104 [************* ] 55% > Processing Locus wil_2_2925323_0:0-192 [************** ] 56% > Processing Locus wil_2_3052273_0:37-985 [************** ] 57% > Processing Locus wil_2_3054893_0:37-574 [************** ] 58% > Processing Locus wil_2_3066229_0:217-666 [************** ] 59% > Processing Locus wil_2_3068737_0:390-1187 [*************** ] 60% > Processing Locus wil_2_3068737_0:1556-1760 [*************** ] 61% > Processing Locus ws_0_3182508_0:5-180 [*************** ] 62% > Processing Locus ws_0_3340488_0:199-1139 [*************** ] 63% > Processing Locus ws_0_3344070_0:32-913 [**************** ] 64% > Processing Locus ws_0_3347582_0:109-760 [**************** ] 65% > Processing Locus ws_0_3371988_0:1-212 [**************** ] 66% > Processing Locus ws_0_3380934_0:2-211 [**************** ] 67% > Processing Locus wu_0_2654219_0:40-149 [***************** ] 68% > Processing Locus wu_0_2678387_0:8-178 [***************** ] 69% > Processing Locus wu_0_2687576_0:15-171 [***************** ] 70% > Processing Locus zu_0_3118546_0:4-175 [***************** ] 71% > Processing Locus zu_0_3190435_0:19-301 [****************** ] 72% > Processing Locus zu_0_3242889_0:3-294 [****************** ] 73% > Processing Locus zu_0_3255503_0:1071-1366 [****************** ] 74% > Processing Locus zu_0_3277661_0:334-901 [****************** ] 75% > Processing Locus zu_0_3278243_0:7-211 [******************* ] 76% > Processed 78 loci. [*************************] 100% [14:10:44] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:1-108 [ ] 0% > Processing Locus bur_0_1863298_0:25-138 [ ] 0% > Processing Locus bur_0_1873494_0:13-183 [ ] 1% > Processing Locus can_0_3076940_0:0-140 [ ] 2% > Processing Locus can_0_3189753_0:9-203 [ ] 3% > Processing Locus can_0_3223655_0:77-655 [* ] 4% > Processing Locus can_0_3233581_0:10-458 [* ] 5% > Processing Locus can_0_3270131_0:1622-2233 [* ] 6% > Processing Locus ct_1_3082021_0:3-128 [* ] 7% > Processing Locus ct_1_3132277_0:0-174 [** ] 8% > Processing Locus ct_1_3241157_0:5-774 [** ] 9% > Processing Locus edi_0_2859720_0:146-524 [** ] 10% > Processing Locus edi_0_2918156_0:81-583 [** ] 11% > Processing Locus hi_0_2778596_0:4-168 [*** ] 12% > Processing Locus hi_0_2916184_0:3-521 [*** ] 13% > Processing Locus hi_0_2939638_0:37-631 [*** ] 14% > Processing Locus hi_0_2953648_0:4-1321 [*** ] 15% > Processing Locus hi_0_2961678_0:97-1501 [**** ] 16% > Processing Locus kn_0_3613403_0:16-130 [**** ] 17% > Processing Locus ler_0_3967940_0:4-134 [**** ] 18% > Processing Locus ler_0_3998132_0:53-162 [**** ] 19% > Processing Locus ler_0_3998410_0:5-163 [***** ] 20% > Processing Locus ler_0_4018856_0:3-182 [***** ] 21% > Processing Locus ler_0_4165287_0:4-735 [***** ] 22% > Processing Locus ler_0_4224097_0:846-1677 [***** ] 23% > Processing Locus ler_0_4225073_0:29-690 [****** ] 24% > Processing Locus mt_0_4193196_0:11-166 [****** ] 25% > Processing Locus mt_0_4217716_0:1-180 [****** ] 26% > Processing Locus mt_0_4229662_0:1-197 [****** ] 27% > Processing Locus mt_0_4230874_0:43-197 [******* ] 28% > Processing Locus mt_0_4528444_1:414-1245 [******* ] 29% > Processing Locus no_0_2885444_0:9-109 [******* ] 30% > Processing Locus no_0_2905273_0:7-112 [******* ] 31% > Processing Locus no_0_2934639_0:25-146 [******** ] 32% > Processing Locus no_0_2956652_0:5-177 [******** ] 33% > Processing Locus no_0_3101262_0:39-747 [******** ] 34% > Processing Locus no_0_3128142_0:1768-2936 [******** ] 35% > Processing Locus oy_0_2936927_0:2-118 [********* ] 36% > Processing Locus oy_0_3001818_0:50-154 [********* ] 37% > Processing Locus po_0_3299272_0:14-119 [********* ] 38% > Processing Locus po_0_3324652_0:0-130 [********* ] 39% > Processing Locus rsch_4_4032032_0:0-89 [********** ] 40% > Processing Locus rsch_4_4055167_0:0-109 [********** ] 41% > Processing Locus rsch_4_4214541_0:1-234 [********** ] 42% > Processing Locus rsch_4_4255532_0:5-285 [********** ] 43% > Processing Locus rsch_4_4275442_0:33-621 [*********** ] 44% > Processing Locus rsch_4_4292194_1:20-1106 [*********** ] 45% > Processing Locus rsch_4_4297142_0:37-304 [*********** ] 46% > Processing Locus sf_2_2486157_0:1-128 [*********** ] 47% > Processing Locus sf_2_2524453_0:0-168 [************ ] 48% > Processing Locus sf_2_2532172_0:1-181 [************ ] 49% > Processing Locus sf_2_2687774_0:588-1428 [************ ] 50% > Processing Locus sf_2_2687786_0:2-2192 [************ ] 51% > Processing Locus sf_2_2700286_0:0-2492 [************* ] 52% > Processing Locus tsu_0_3175121_0:563-701 [************* ] 53% > Processing Locus tsu_0_3211741_0:38-788 [************* ] 54% > Processing Locus wil_2_2834553_0:0-104 [************* ] 55% > Processing Locus wil_2_2925323_0:0-192 [************** ] 56% > Processing Locus wil_2_3052273_0:37-985 [************** ] 57% > Processing Locus wil_2_3054893_0:37-574 [************** ] 58% > Processing Locus wil_2_3066229_0:217-666 [************** ] 59% > Processing Locus wil_2_3068737_0:390-1187 [*************** ] 60% > Processing Locus wil_2_3068737_0:1556-1760 [*************** ] 61% > Processing Locus ws_0_3182508_0:5-180 [*************** ] 62% > Processing Locus ws_0_3340488_0:199-1139 [*************** ] 63% > Processing Locus ws_0_3344070_0:32-913 [**************** ] 64% > Processing Locus ws_0_3347582_0:109-760 [**************** ] 65% > Processing Locus ws_0_3371988_0:1-212 [**************** ] 66% > Processing Locus ws_0_3380934_0:2-211 [**************** ] 67% > Processing Locus wu_0_2654219_0:40-149 [***************** ] 68% > Processing Locus wu_0_2678387_0:8-178 [***************** ] 69% > Processing Locus wu_0_2687576_0:15-171 [***************** ] 70% > Processing Locus zu_0_3118546_0:4-175 [***************** ] 71% > Processing Locus zu_0_3190435_0:19-301 [****************** ] 72% > Processing Locus zu_0_3242889_0:3-294 [****************** ] 73% > Processing Locus zu_0_3255503_0:1071-1366 [****************** ] 74% > Processing Locus zu_0_3277661_0:334-901 [****************** ] 75% > Processing Locus zu_0_3278243_0:7-211 [******************* ] 76% > Processed 78 loci. [*************************] 100% [Mon Apr 4 14:10:44 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:10:45 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:10:48 2011] Searching for junctions via segment mapping [Mon Apr 4 14:10:48 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:10:50 2011] Joining segment hits cufflinks -p 4 -o ./Kn_0 -r it2.fa ./Kn_0/accepted_hits.bam [14:10:50] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1863298_0:29-141 [ ] 0% > Processing Locus can_0_3076940_0:0-137 [ ] 0% > Processing Locus can_0_3093852_0:0-129 [ ] 0% > Processing Locus can_0_3189753_0:15-197 [ ] 1% > Processing Locus can_0_3223655_0:139-217 [ ] 1% > Processing Locus can_0_3233581_0:10-444 [ ] 2% > Processing Locus can_0_3270131_0:0-102 [ ] 2% > Processing Locus can_0_3270131_0:218-580 [ ] 2% > Processing Locus can_0_3270131_0:817-2257 [ ] 2% > Processing Locus ct_1_3082021_0:3-126 [ ] 2% > Processing Locus ct_1_3132277_0:0-175 [ ] 3% > Processing Locus ct_1_3247037_0:44-552 [ ] 3% > Processing Locus ct_1_3302721_0:1261-1339 [* ] 4% > Processing Locus edi_0_2723255_0:9-140 [* ] 4% > Processing Locus edi_0_2759827_0:7-176 [* ] 5% > Processing Locus edi_0_2859720_0:122-525 [* ] 5% > Processing Locus edi_0_2871668_0:160-529 [* ] 5% > Processing Locus edi_0_2932438_0:30-288 [* ] 6% > Processing Locus edi_0_2934714_0:153-282 [* ] 6% > Processing Locus edi_0_2934714_0:415-581 [* ] 6% > Processing Locus edi_0_2934714_0:1101-1275 [* ] 6% > Processing Locus edi_0_2934714_0:1866-1958 [* ] 6% > Processing Locus edi_0_2934714_0:2444-3068 [* ] 6% > Processing Locus edi_0_2934714_0:3196-3324 [* ] 6% > Processing Locus edi_0_2934714_0:3476-3554 [* ] 6% > Processing Locus edi_0_2934714_0:3729-3894 [* ] 6% > Processing Locus edi_0_2934714_0:4132-4210 [* ] 6% > Processing Locus edi_0_2934714_0:5019-5097 [* ] 6% > Processing Locus edi_0_2934714_0:5242-5320 [* ] 6% > Processing Locus hi_0_2755116_0:4-82 [* ] 7% > Processing Locus hi_0_2795398_0:0-187 [* ] 7% > Processing Locus hi_0_2939638_0:139-642 [* ] 7% > Processing Locus hi_0_2964064_0:16-1189 [** ] 8% > Processing Locus kn_0_3594465_0:12-155 [** ] 8% > Processing Locus kn_0_3605300_0:1-168 [** ] 9% > Processing Locus kn_0_3613403_0:0-164 [** ] 9% > Processing Locus kn_0_3617271_0:1-178 [** ] 10% > Processing Locus kn_0_3626969_0:0-184 [** ] 10% > Processing Locus kn_0_3799876_0:16-717 [** ] 10% > Processing Locus kn_0_3799876_0:877-1228 [** ] 10% > Processing Locus kn_0_3799876_0:1340-1418 [** ] 10% > Processing Locus kn_0_3802200_0:166-911 [** ] 11% > Processing Locus kn_0_3819922_1:11-314 [** ] 11% > Processing Locus kn_0_3819922_1:493-571 [** ] 11% > Processing Locus kn_0_3819922_1:715-2016 [** ] 11% > Processing Locus ler_0_3998410_0:5-163 [*** ] 12% > Processing Locus ler_0_4004770_0:42-169 [*** ] 12% > Processing Locus ler_0_4018856_0:1-175 [*** ] 13% > Processing Locus ler_0_4165287_0:0-739 [*** ] 13% > Processing Locus ler_0_4224097_0:875-1734 [*** ] 13% > Processing Locus mt_0_4193196_0:12-166 [*** ] 14% > Processing Locus mt_0_4217716_0:4-180 [*** ] 14% > Processing Locus mt_0_4229662_0:1-197 [*** ] 15% > Processing Locus mt_0_4230874_0:41-189 [*** ] 15% > Processing Locus mt_0_4231054_0:1-83 [*** ] 15% > Processing Locus mt_0_4528444_1:560-1139 [**** ] 16% > Processing Locus no_0_2885444_0:6-112 [**** ] 16% > Processing Locus no_0_2905273_0:13-118 [**** ] 17% > Processing Locus no_0_2934639_0:25-135 [**** ] 17% > Processing Locus no_0_2936769_0:2-138 [**** ] 18% > Processing Locus no_0_2951521_0:0-154 [**** ] 18% > Processing Locus no_0_2956652_0:1-177 [**** ] 18% > Processing Locus no_0_2959683_0:0-181 [**** ] 19% > Processing Locus no_0_3113578_1:513-816 [**** ] 19% > Processing Locus oy_0_3001818_0:49-155 [***** ] 20% > Processing Locus oy_0_3121110_0:48-554 [***** ] 20% > Processing Locus oy_0_3148368_0:796-1001 [***** ] 21% > Processing Locus oy_0_3162092_0:186-2058 [***** ] 21% > Processing Locus po_0_3299272_0:0-119 [***** ] 21% > Processing Locus po_0_3306688_0:14-121 [***** ] 22% > Processing Locus po_0_3332479_0:0-135 [***** ] 22% > Processing Locus po_0_3372769_0:35-157 [***** ] 23% > Processing Locus po_0_3382155_0:2-150 [***** ] 23% > Processing Locus po_0_3393401_0:33-145 [***** ] 23% > Processing Locus po_0_3573778_0:336-1289 [****** ] 24% > Processing Locus rsch_4_4032032_0:0-90 [****** ] 24% > Processing Locus rsch_4_4055167_0:0-109 [****** ] 25% > Processing Locus rsch_4_4091241_0:1-137 [****** ] 25% > Processing Locus rsch_4_4118145_0:66-170 [****** ] 26% > Processing Locus rsch_4_4214541_0:2-234 [****** ] 26% > Processing Locus rsch_4_4219071_0:12-412 [****** ] 26% > Processing Locus rsch_4_4255532_0:1-287 [****** ] 27% > Processing Locus rsch_4_4266550_0:5-1148 [****** ] 27% > Processing Locus rsch_4_4292194_1:3-1133 [******* ] 28% > Processing Locus rsch_4_4297142_0:33-301 [******* ] 28% > Processing Locus sf_2_2524453_0:3-167 [******* ] 28% > Processing Locus tsu_0_3215821_0:821-1021 [******* ] 29% > Processing Locus wil_2_2834553_0:0-78 [******* ] 29% > Processing Locus wil_2_2945095_0:15-184 [******* ] 30% > Processing Locus wil_2_3054893_0:20-544 [******* ] 30% > Processing Locus wil_2_3066229_0:0-742 [******* ] 31% > Processing Locus wil_2_3068737_0:351-1796 [******* ] 31% > Processing Locus wil_2_3088151_0:82-336 [******* ] 31% > Processing Locus wil_2_3088151_0:790-884 [******* ] 31% > Processing Locus wil_2_3088151_0:1208-1589 [******* ] 31% > Processing Locus wil_2_3092619_0:963-1041 [******** ] 32% > Processing Locus ws_0_3182508_0:7-165 [******** ] 32% > Processing Locus ws_0_3190679_0:54-194 [******** ] 33% > Processing Locus ws_0_3298283_0:18-502 [******** ] 33% > Processing Locus ws_0_3326342_0:12-442 [******** ] 34% > Processing Locus ws_0_3340488_0:164-1180 [******** ] 34% > Processing Locus ws_0_3371988_0:0-258 [******** ] 34% > Processing Locus ws_0_3380934_0:1-208 [******** ] 35% > Processing Locus ws_0_3381390_0:1-1705 [******** ] 35% > Processing Locus wu_0_2678387_0:7-182 [********* ] 36% > Processing Locus zu_0_3118546_0:4-164 [********* ] 36% > Processing Locus zu_0_3238769_0:80-416 [********* ] 36% > Processing Locus zu_0_3242889_0:12-199 [********* ] 37% > Processing Locus zu_0_3255503_0:1139-1379 [********* ] 37% > Processing Locus zu_0_3259399_1:88-318 [********* ] 38% > Processing Locus zu_0_3277661_0:261-912 [********* ] 38% > Processing Locus zu_0_3278243_0:0-107 [********* ] 39% > Processing Locus zu_0_3278243_0:501-579 [********* ] 39% > Processed 113 loci. [*************************] 100% > Map Properties: > Total Map Mass: 7186.62 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:10:50] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1863298_0:29-141 [ ] 0% > Processing Locus can_0_3076940_0:0-137 [ ] 0% > Processing Locus can_0_3093852_0:0-129 [ ] 1% > Processing Locus can_0_3189753_0:15-197 [ ] 2% > Processing Locus can_0_3223655_0:139-217 [ ] 3% > Processing Locus can_0_3233581_0:10-444 [* ] 4% > Processing Locus can_0_3270131_0:0-102 [* ] 5% > Processing Locus can_0_3270131_0:218-580 [* ] 6% > Processing Locus can_0_3270131_0:817-2257 [* ] 7% > Processing Locus ct_1_3082021_0:3-126 [* ] 7% > Processing Locus ct_1_3132277_0:0-175 [** ] 8% > Processing Locus ct_1_3247037_0:44-552 [** ] 9% > Processing Locus ct_1_3302721_0:1261-1339 [** ] 10% > Processing Locus edi_0_2723255_0:9-140 [** ] 11% > Processing Locus edi_0_2759827_0:7-176 [*** ] 12% > Processing Locus edi_0_2859720_0:122-525 [*** ] 13% > Processing Locus edi_0_2871668_0:160-529 [*** ] 14% > Processing Locus edi_0_2932438_0:30-288 [*** ] 15% > Processing Locus edi_0_2934714_0:153-282 [*** ] 15% > Processing Locus edi_0_2934714_0:415-581 [**** ] 16% > Processing Locus edi_0_2934714_0:1101-1275 [**** ] 17% > Processing Locus edi_0_2934714_0:1866-1958 [**** ] 18% > Processing Locus edi_0_2934714_0:2444-3068 [**** ] 19% > Processing Locus edi_0_2934714_0:3196-3324 [***** ] 20% > Processing Locus edi_0_2934714_0:3476-3554 [***** ] 21% > Processing Locus edi_0_2934714_0:3729-3894 [***** ] 22% > Processing Locus edi_0_2934714_0:4132-4210 [***** ] 23% > Processing Locus edi_0_2934714_0:5019-5097 [***** ] 23% > Processing Locus edi_0_2934714_0:5242-5320 [****** ] 24% > Processing Locus hi_0_2755116_0:4-82 [****** ] 25% > Processing Locus hi_0_2795398_0:0-187 [****** ] 26% > Processing Locus hi_0_2939638_0:139-642 [****** ] 27% > Processing Locus hi_0_2964064_0:16-1189 [******* ] 28% > Processing Locus kn_0_3594465_0:12-155 [******* ] 29% > Processing Locus kn_0_3605300_0:1-168 [******* ] 30% > Processing Locus kn_0_3613403_0:0-164 [******* ] 30% > Processing Locus kn_0_3617271_0:1-178 [******* ] 31% > Processing Locus kn_0_3626969_0:0-184 [******** ] 32% > Processing Locus kn_0_3799876_0:16-717 [******** ] 33% > Processing Locus kn_0_3799876_0:877-1228 [******** ] 34% > Processing Locus kn_0_3799876_0:1340-1418 [******** ] 35% > Processing Locus kn_0_3802200_0:166-911 [********* ] 36% > Processing Locus kn_0_3819922_1:11-314 [********* ] 37% > Processing Locus kn_0_3819922_1:493-571 [********* ] 38% > Processing Locus kn_0_3819922_1:715-2016 [********* ] 38% > Processing Locus ler_0_3998410_0:5-163 [********* ] 39% > Processing Locus ler_0_4004770_0:42-169 [********** ] 40% > Processing Locus ler_0_4018856_0:1-175 [********** ] 41% > Processing Locus ler_0_4165287_0:0-739 [********** ] 42% > Processing Locus ler_0_4224097_0:875-1734 [********** ] 43% > Processing Locus mt_0_4193196_0:12-166 [*********** ] 44% > Processing Locus mt_0_4217716_0:4-180 [*********** ] 45% > Processing Locus mt_0_4229662_0:1-197 [*********** ] 46% > Processing Locus mt_0_4230874_0:41-189 [*********** ] 46% > Processing Locus mt_0_4231054_0:1-83 [*********** ] 47% > Processing Locus mt_0_4528444_1:560-1139 [************ ] 48% > Processing Locus no_0_2885444_0:6-112 [************ ] 49% > Processing Locus no_0_2905273_0:13-118 [************ ] 50% > Processing Locus no_0_2934639_0:25-135 [************ ] 51% > Processing Locus no_0_2936769_0:2-138 [************* ] 52% > Processing Locus no_0_2951521_0:0-154 [************* ] 53% > Processing Locus no_0_2956652_0:1-177 [************* ] 53% > Processing Locus no_0_2959683_0:0-181 [************* ] 54% > Processing Locus no_0_3113578_1:513-816 [************* ] 55% > Processing Locus oy_0_3001818_0:49-155 [************** ] 56% > Processing Locus oy_0_3121110_0:48-554 [************** ] 57% > Processing Locus oy_0_3148368_0:796-1001 [************** ] 58% > Processing Locus oy_0_3162092_0:186-2058 [************** ] 59% > Processing Locus po_0_3299272_0:0-119 [*************** ] 60% > Processing Locus po_0_3306688_0:14-121 [*************** ] 61% > Processing Locus po_0_3332479_0:0-135 [*************** ] 61% > Processing Locus po_0_3372769_0:35-157 [*************** ] 62% > Processing Locus po_0_3382155_0:2-150 [*************** ] 63% > Processing Locus po_0_3393401_0:33-145 [**************** ] 64% > Processing Locus po_0_3573778_0:336-1289 [**************** ] 65% > Processing Locus rsch_4_4032032_0:0-90 [**************** ] 66% > Processing Locus rsch_4_4055167_0:0-109 [**************** ] 67% > Processing Locus rsch_4_4091241_0:1-137 [***************** ] 68% > Processing Locus rsch_4_4118145_0:66-170 [***************** ] 69% > Processing Locus rsch_4_4214541_0:2-234 [***************** ] 69% > Processing Locus rsch_4_4219071_0:12-412 [***************** ] 70% > Processing Locus rsch_4_4255532_0:1-287 [***************** ] 71% > Processing Locus rsch_4_4266550_0:5-1148 [****************** ] 72% > Processing Locus rsch_4_4292194_1:3-1133 [****************** ] 73% > Processing Locus rsch_4_4297142_0:33-301 [****************** ] 74% > Processing Locus sf_2_2524453_0:3-167 [****************** ] 75% > Processing Locus tsu_0_3215821_0:821-1021 [******************* ] 76% > Processing Locus wil_2_2834553_0:0-78 [******************* ] 76% > Processing Locus wil_2_2945095_0:15-184 [******************* ] 77% > Processing Locus wil_2_3054893_0:20-544 [******************* ] 78% > Processing Locus wil_2_3066229_0:0-742 [******************* ] 79% > Processing Locus wil_2_3068737_0:351-1796 [******************** ] 80% > Processing Locus wil_2_3088151_0:82-336 [******************** ] 81% > Processing Locus wil_2_3088151_0:790-884 [******************** ] 82% > Processing Locus wil_2_3088151_0:1208-1589 [******************** ] 83% > Processing Locus wil_2_3092619_0:963-1041 [********************* ] 84% > Processing Locus ws_0_3182508_0:7-165 [********************* ] 84% > Processing Locus ws_0_3190679_0:54-194 [********************* ] 85% > Processing Locus ws_0_3298283_0:18-502 [********************* ] 86% > Processing Locus ws_0_3326342_0:12-442 [********************* ] 87% > Processing Locus ws_0_3340488_0:164-1180 [********************** ] 88% > Processing Locus ws_0_3371988_0:0-258 [********************** ] 89% > Processing Locus ws_0_3380934_0:1-208 [********************** ] 90% > Processing Locus ws_0_3381390_0:1-1705 [********************** ] 91% > Processing Locus wu_0_2678387_0:7-182 [*********************** ] 92% > Processing Locus zu_0_3118546_0:4-164 [*********************** ] 92% > Processing Locus zu_0_3238769_0:80-416 [*********************** ] 93% > Processing Locus zu_0_3242889_0:12-199 [*********************** ] 94% > Processing Locus zu_0_3255503_0:1139-1379 [*********************** ] 95% > Processing Locus zu_0_3259399_1:88-318 [************************ ] 96% > Processing Locus zu_0_3277661_0:261-912 [************************ ] 97% > Processing Locus zu_0_3278243_0:0-107 [************************ ] 98% > Processing Locus zu_0_3278243_0:501-579 [************************ ] 99% > Processed 113 loci. [*************************] 100% [14:10:50] Loading reference annotation and sequence [14:10:50] Learning bias parameters. > Processing Locus bur_0_1863298_0:29-141 [ ] 0% > Processing Locus can_0_3076940_0:0-137 [ ] 0% > Processing Locus can_0_3189753_0:15-197 [ ] 1% > Processing Locus can_0_3233581_0:10-444 [ ] 2% > Processing Locus can_0_3270131_0:817-2257 [ ] 3% > Processing Locus ct_1_3082021_0:3-126 [* ] 4% > Processing Locus ct_1_3132277_0:0-175 [* ] 5% > Processing Locus ct_1_3247037_0:44-552 [* ] 6% > Processing Locus edi_0_2723255_0:9-140 [* ] 7% > Processing Locus edi_0_2759827_0:7-176 [* ] 7% > Processing Locus edi_0_2859720_0:122-525 [** ] 8% > Processing Locus edi_0_2871668_0:160-529 [** ] 9% > Processing Locus edi_0_2932438_0:30-288 [** ] 10% > Processing Locus hi_0_2795398_0:0-187 [** ] 11% > Processing Locus hi_0_2939638_0:139-642 [*** ] 12% > Processing Locus hi_0_2964064_0:16-1189 [*** ] 13% > Processing Locus kn_0_3594465_0:12-155 [*** ] 14% > Processing Locus kn_0_3605300_0:1-168 [*** ] 15% > Processing Locus kn_0_3613403_0:0-164 [*** ] 15% > Processing Locus kn_0_3617271_0:1-178 [**** ] 16% > Processing Locus kn_0_3626969_0:0-184 [**** ] 17% > Processing Locus kn_0_3799876_0:16-717 [**** ] 18% > Processing Locus kn_0_3799876_0:877-1228 [**** ] 19% > Processing Locus kn_0_3802200_0:166-911 [***** ] 20% > Processing Locus kn_0_3819922_1:715-2016 [***** ] 21% > Processing Locus ler_0_3998410_0:5-163 [***** ] 22% > Processing Locus ler_0_4018856_0:1-175 [***** ] 23% > Processing Locus ler_0_4165287_0:0-739 [***** ] 23% > Processing Locus ler_0_4224097_0:875-1734 [****** ] 24% > Processing Locus mt_0_4193196_0:12-166 [****** ] 25% > Processing Locus mt_0_4217716_0:4-180 [****** ] 26% > Processing Locus mt_0_4229662_0:1-197 [****** ] 27% > Processing Locus mt_0_4230874_0:41-189 [******* ] 28% > Processing Locus mt_0_4231054_0:1-83 [******* ] 29% > Processing Locus mt_0_4528444_1:569-1139 [******* ] 30% > Processing Locus no_0_2885444_0:6-112 [******* ] 30% > Processing Locus no_0_2905273_0:13-118 [******* ] 31% > Processing Locus no_0_2934639_0:25-135 [******** ] 32% > Processing Locus no_0_2936769_0:2-138 [******** ] 33% > Processing Locus no_0_2951521_0:0-154 [******** ] 34% > Processing Locus no_0_2956652_0:1-177 [******** ] 35% > Processing Locus no_0_2959683_0:0-181 [********* ] 36% > Processing Locus oy_0_3001818_0:49-155 [********* ] 37% > Processing Locus oy_0_3121110_0:48-554 [********* ] 38% > Processing Locus oy_0_3162092_0:186-2058 [********* ] 38% > Processing Locus po_0_3299272_0:0-119 [********* ] 39% > Processing Locus po_0_3306688_0:14-121 [********** ] 40% > Processing Locus po_0_3332479_0:0-135 [********** ] 41% > Processing Locus po_0_3372769_0:35-157 [********** ] 42% > Processing Locus po_0_3382155_0:2-150 [********** ] 43% > Processing Locus po_0_3573778_0:336-1289 [*********** ] 44% > Processing Locus rsch_4_4032032_0:0-90 [*********** ] 45% > Processing Locus rsch_4_4055167_0:0-109 [*********** ] 46% > Processing Locus rsch_4_4091241_0:1-137 [*********** ] 46% > Processing Locus rsch_4_4118145_0:66-170 [*********** ] 47% > Processing Locus rsch_4_4214541_0:2-234 [************ ] 48% > Processing Locus rsch_4_4255532_0:1-287 [************ ] 49% > Processing Locus rsch_4_4266550_0:5-1148 [************ ] 50% > Processing Locus rsch_4_4292194_1:3-1133 [************ ] 51% > Processing Locus rsch_4_4297142_0:33-301 [************* ] 52% > Processing Locus sf_2_2524453_0:3-167 [************* ] 53% > Processing Locus wil_2_2945095_0:15-184 [************* ] 53% > Processing Locus wil_2_3054893_0:20-544 [************* ] 54% > Processing Locus wil_2_3066229_0:0-742 [************* ] 55% > Processing Locus wil_2_3068737_0:351-1796 [************** ] 56% > Processing Locus ws_0_3298283_0:18-502 [************** ] 57% > Processing Locus ws_0_3340488_0:164-1142 [************** ] 58% > Processing Locus ws_0_3371988_0:0-258 [************** ] 59% > Processing Locus ws_0_3380934_0:1-208 [*************** ] 60% > Processing Locus ws_0_3381390_0:1-1705 [*************** ] 61% > Processing Locus wu_0_2678387_0:7-182 [*************** ] 61% > Processing Locus zu_0_3118546_0:4-164 [*************** ] 62% > Processing Locus zu_0_3242889_0:12-199 [*************** ] 63% > Processing Locus zu_0_3255503_0:1139-1379 [**************** ] 64% > Processing Locus zu_0_3259399_1:88-318 [**************** ] 65% > Processing Locus zu_0_3277661_0:261-912 [**************** ] 66% > Processing Locus zu_0_3278243_0:0-107 [**************** ] 67% > Processed 77 loci. [*************************] 100% [14:10:50] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1863298_0:29-141 [ ] 0% > Processing Locus can_0_3076940_0:0-137 [ ] 0% > Processing Locus can_0_3189753_0:15-197 [ ] 1% > Processing Locus can_0_3233581_0:10-444 [ ] 2% > Processing Locus can_0_3270131_0:817-2257 [ ] 3% > Processing Locus ct_1_3082021_0:3-126 [* ] 4% > Processing Locus ct_1_3132277_0:0-175 [* ] 5% > Processing Locus ct_1_3247037_0:44-552 [* ] 6% > Processing Locus edi_0_2723255_0:9-140 [* ] 7% > Processing Locus edi_0_2759827_0:7-176 [* ] 7% > Processing Locus edi_0_2859720_0:122-525 [** ] 8% > Processing Locus edi_0_2871668_0:160-529 [** ] 9% > Processing Locus edi_0_2932438_0:30-288 [** ] 10% > Processing Locus hi_0_2795398_0:0-187 [** ] 11% > Processing Locus hi_0_2939638_0:139-642 [*** ] 12% > Processing Locus hi_0_2964064_0:16-1189 [*** ] 13% > Processing Locus kn_0_3594465_0:12-155 [*** ] 14% > Processing Locus kn_0_3605300_0:1-168 [*** ] 15% > Processing Locus kn_0_3613403_0:0-164 [*** ] 15% > Processing Locus kn_0_3617271_0:1-178 [**** ] 16% > Processing Locus kn_0_3626969_0:0-184 [**** ] 17% > Processing Locus kn_0_3799876_0:16-717 [**** ] 18% > Processing Locus kn_0_3799876_0:877-1228 [**** ] 19% > Processing Locus kn_0_3802200_0:166-911 [***** ] 20% > Processing Locus kn_0_3819922_1:715-2016 [***** ] 21% > Processing Locus ler_0_3998410_0:5-163 [***** ] 22% > Processing Locus ler_0_4018856_0:1-175 [***** ] 23% > Processing Locus ler_0_4165287_0:0-739 [***** ] 23% > Processing Locus ler_0_4224097_0:875-1734 [****** ] 24% > Processing Locus mt_0_4193196_0:12-166 [****** ] 25% > Processing Locus mt_0_4217716_0:4-180 [****** ] 26% > Processing Locus mt_0_4229662_0:1-197 [****** ] 27% > Processing Locus mt_0_4230874_0:41-189 [******* ] 28% > Processing Locus mt_0_4231054_0:1-83 [******* ] 29% > Processing Locus mt_0_4528444_1:569-1139 [******* ] 30% > Processing Locus no_0_2885444_0:6-112 [******* ] 30% > Processing Locus no_0_2905273_0:13-118 [******* ] 31% > Processing Locus no_0_2934639_0:25-135 [******** ] 32% > Processing Locus no_0_2936769_0:2-138 [******** ] 33% > Processing Locus no_0_2951521_0:0-154 [******** ] 34% > Processing Locus no_0_2956652_0:1-177 [******** ] 35% > Processing Locus no_0_2959683_0:0-181 [********* ] 36% > Processing Locus oy_0_3001818_0:49-155 [********* ] 37% > Processing Locus oy_0_3121110_0:48-554 [********* ] 38% > Processing Locus oy_0_3162092_0:186-2058 [********* ] 38% > Processing Locus po_0_3299272_0:0-119 [********* ] 39% > Processing Locus po_0_3306688_0:14-121 [********** ] 40% > Processing Locus po_0_3332479_0:0-135 [********** ] 41% > Processing Locus po_0_3372769_0:35-157 [********** ] 42% > Processing Locus po_0_3382155_0:2-150 [********** ] 43% > Processing Locus po_0_3573778_0:336-1289 [*********** ] 44% > Processing Locus rsch_4_4032032_0:0-90 [*********** ] 45% > Processing Locus rsch_4_4055167_0:0-109 [*********** ] 46% > Processing Locus rsch_4_4091241_0:1-137 [*********** ] 46% > Processing Locus rsch_4_4118145_0:66-170 [*********** ] 47% > Processing Locus rsch_4_4214541_0:2-234 [************ ] 48% > Processing Locus rsch_4_4255532_0:1-287 [************ ] 49% > Processing Locus rsch_4_4266550_0:5-1148 [************ ] 50% > Processing Locus rsch_4_4292194_1:3-1133 [************ ] 51% > Processing Locus rsch_4_4297142_0:33-301 [************* ] 52% > Processing Locus sf_2_2524453_0:3-167 [************* ] 53% > Processing Locus wil_2_2945095_0:15-184 [************* ] 53% > Processing Locus wil_2_3054893_0:20-544 [************* ] 54% > Processing Locus wil_2_3066229_0:0-742 [************* ] 55% > Processing Locus wil_2_3068737_0:351-1796 [************** ] 56% > Processing Locus ws_0_3298283_0:18-502 [************** ] 57% > Processing Locus ws_0_3340488_0:164-1142 [************** ] 58% > Processing Locus ws_0_3371988_0:0-258 [************** ] 59% > Processing Locus ws_0_3380934_0:1-208 [*************** ] 60% > Processing Locus ws_0_3381390_0:1-1705 [*************** ] 61% > Processing Locus wu_0_2678387_0:7-182 [*************** ] 61% > Processing Locus zu_0_3118546_0:4-164 [*************** ] 62% > Processing Locus zu_0_3242889_0:12-199 [*************** ] 63% > Processing Locus zu_0_3255503_0:1139-1379 [**************** ] 64% > Processing Locus zu_0_3259399_1:88-318 [**************** ] 65% > Processing Locus zu_0_3277661_0:261-912 [**************** ] 66% > Processing Locus zu_0_3278243_0:0-107 [**************** ] 67% > Processed 77 loci. [*************************] 100% [Mon Apr 4 14:10:52 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:25 elapsed] cufflinks -p 4 -o ./Mt_0 -r it2.fa ./Mt_0/accepted_hits.bam [14:10:58] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:9-90 [ ] 0% > Processing Locus bur_0_1863298_0:23-152 [ ] 0% > Processing Locus bur_0_2020452_0:1-1367 [ ] 0% > Processing Locus bur_0_2020452_0:1727-2190 [ ] 0% > Processing Locus can_0_3076940_0:0-142 [ ] 1% > Processing Locus can_0_3233581_0:19-462 [ ] 1% > Processing Locus can_0_3258779_0:132-658 [ ] 2% > Processing Locus can_0_3270131_0:112-951 [ ] 2% > Processing Locus can_0_3270131_0:1140-1218 [ ] 2% > Processing Locus can_0_3270131_0:1508-2264 [ ] 2% > Processing Locus ct_1_3082021_0:13-124 [ ] 2% > Processing Locus ct_1_3133451_0:21-193 [ ] 3% > Processing Locus ct_1_3133995_0:79-195 [ ] 3% > Processing Locus ct_1_3247037_0:133-211 [* ] 4% > Processing Locus ct_1_3247037_0:320-505 [* ] 4% > Processing Locus edi_0_2759827_0:7-176 [* ] 4% > Processing Locus edi_0_2859720_0:144-525 [* ] 5% > Processing Locus edi_0_2889434_0:4-919 [* ] 5% > Processing Locus edi_0_2932438_0:28-288 [* ] 5% > Processing Locus edi_0_2934714_0:861-939 [* ] 6% > Processing Locus edi_0_2934714_0:1427-1505 [* ] 6% > Processing Locus edi_0_2934714_0:2077-2155 [* ] 6% > Processing Locus edi_0_2934714_0:3150-3228 [* ] 6% > Processing Locus edi_0_2934714_0:3500-3578 [* ] 6% > Processing Locus edi_0_2934714_0:4714-4792 [* ] 6% > Processing Locus hi_0_2778596_0:11-168 [* ] 6% > Processing Locus hi_0_2795398_0:1-187 [* ] 7% > Processing Locus hi_0_2939638_0:39-639 [* ] 7% > Processing Locus kn_0_3594465_0:74-152 [* ] 7% > Processing Locus kn_0_3605300_0:1-168 [** ] 8% > Processing Locus kn_0_3613403_0:0-139 [** ] 8% > Processing Locus kn_0_3819922_1:133-230 [** ] 9% > Processing Locus kn_0_3819922_1:365-758 [** ] 9% > Processing Locus kn_0_3819922_1:940-2053 [** ] 9% > Processing Locus ler_0_3998410_0:4-163 [** ] 9% > Processing Locus ler_0_4018856_0:1-186 [** ] 10% > Processing Locus mt_0_4193196_0:0-166 [** ] 10% > Processing Locus mt_0_4213448_0:2-182 [** ] 10% > Processing Locus mt_0_4217716_0:0-181 [** ] 11% > Processing Locus mt_0_4229662_0:1-196 [** ] 11% > Processing Locus mt_0_4230874_0:31-188 [*** ] 12% > Processing Locus mt_0_4231054_0:0-83 [*** ] 12% > Processing Locus mt_0_4399784_0:13-223 [*** ] 13% > Processing Locus mt_0_4528444_1:552-1231 [*** ] 13% > Processing Locus no_0_2885444_0:3-110 [*** ] 13% > Processing Locus no_0_2905273_0:15-121 [*** ] 14% > Processing Locus no_0_2934639_0:6-146 [*** ] 14% > Processing Locus no_0_2956652_0:1-178 [*** ] 15% > Processing Locus no_0_3088052_0:654-732 [*** ] 15% > Processing Locus no_0_3101262_0:99-733 [*** ] 15% > Processing Locus no_0_3116640_0:451-1883 [**** ] 16% > Processing Locus no_0_3128142_0:68-1326 [**** ] 16% > Processing Locus no_0_3128142_0:1616-2877 [**** ] 16% > Processing Locus oy_0_2965192_0:0-111 [**** ] 17% > Processing Locus oy_0_3001818_0:56-154 [**** ] 17% > Processing Locus oy_0_3148368_0:155-233 [**** ] 18% > Processing Locus po_0_3299272_0:0-119 [**** ] 18% > Processing Locus po_0_3332479_0:0-136 [**** ] 18% > Processing Locus po_0_3340213_0:12-90 [**** ] 19% > Processing Locus po_0_3606391_0:866-2776 [**** ] 19% > Processing Locus po_0_3606391_1:149-990 [***** ] 20% > Processing Locus rsch_4_4032032_0:0-89 [***** ] 20% > Processing Locus rsch_4_4055167_0:0-107 [***** ] 21% > Processing Locus rsch_4_4110791_0:3-158 [***** ] 21% > Processing Locus rsch_4_4214541_0:0-234 [***** ] 21% > Processing Locus rsch_4_4255532_0:0-287 [***** ] 22% > Processing Locus rsch_4_4275442_0:165-595 [***** ] 22% > Processing Locus rsch_4_4292194_1:8-1134 [***** ] 23% > Processing Locus sf_2_2486157_0:1-118 [***** ] 23% > Processing Locus sf_2_2488391_0:4-124 [***** ] 23% > Processing Locus sf_2_2524453_0:0-165 [****** ] 24% > Processing Locus sf_2_2680171_0:7-283 [****** ] 24% > Processing Locus tsu_0_3036945_0:27-149 [****** ] 25% > Processing Locus tsu_0_3215821_0:594-913 [****** ] 25% > Processing Locus wil_2_2834553_0:0-78 [****** ] 26% > Processing Locus wil_2_2915899_0:46-154 [****** ] 26% > Processing Locus wil_2_3088151_0:17-1644 [****** ] 26% > Processing Locus wil_2_3090237_0:265-494 [****** ] 27% > Processing Locus wil_2_3092619_0:324-402 [****** ] 27% > Processing Locus ws_0_3182508_0:4-177 [******* ] 28% > Processing Locus ws_0_3340488_0:199-1139 [******* ] 28% > Processing Locus ws_0_3347582_0:71-859 [******* ] 28% > Processing Locus ws_0_3347582_0:1091-1368 [******* ] 28% > Processing Locus ws_0_3349444_1:573-748 [******* ] 29% > Processing Locus ws_0_3371988_0:15-101 [******* ] 29% > Processing Locus ws_0_3371988_0:204-323 [******* ] 29% > Processing Locus ws_0_3380934_0:7-188 [******* ] 30% > Processing Locus ws_0_3381390_0:108-1615 [******* ] 30% > Processing Locus wu_0_2654219_0:4-125 [******* ] 31% > Processing Locus wu_0_2678387_0:0-169 [******* ] 31% > Processing Locus wu_0_2824308_0:316-710 [******* ] 31% > Processing Locus zu_0_3092045_0:7-157 [******** ] 32% > Processing Locus zu_0_3238769_0:182-290 [******** ] 32% > Processing Locus zu_0_3242889_0:12-186 [******** ] 33% > Processing Locus zu_0_3255503_0:1066-1389 [******** ] 33% > Processing Locus zu_0_3260131_0:171-400 [******** ] 34% > Processing Locus zu_0_3277661_0:334-912 [******** ] 34% > Processing Locus zu_0_3280213_0:493-645 [******** ] 34% > Processing Locus zu_0_3280213_0:772-1726 [******** ] 34% > Processing Locus zu_0_3280213_0:1982-2061 [******** ] 34% > Processed 100 loci. [*************************] 100% > Map Properties: > Total Map Mass: 6339.51 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:10:58] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:9-90 [ ] 0% > Processing Locus bur_0_1863298_0:23-152 [ ] 1% > Processing Locus bur_0_2020452_0:1-1367 [ ] 2% > Processing Locus bur_0_2020452_0:1727-2190 [ ] 3% > Processing Locus can_0_3076940_0:0-142 [* ] 4% > Processing Locus can_0_3233581_0:19-459 [* ] 5% > Processing Locus can_0_3258779_0:132-658 [* ] 6% > Processing Locus can_0_3270131_0:112-951 [* ] 7% > Processing Locus can_0_3270131_0:1140-1218 [** ] 8% > Processing Locus can_0_3270131_0:1508-2264 [** ] 9% > Processing Locus ct_1_3082021_0:13-124 [** ] 10% > Processing Locus ct_1_3133451_0:21-193 [** ] 11% > Processing Locus ct_1_3133995_0:79-195 [*** ] 12% > Processing Locus ct_1_3247037_0:133-211 [*** ] 13% > Processing Locus ct_1_3247037_0:320-505 [*** ] 14% > Processing Locus edi_0_2759827_0:7-176 [*** ] 15% > Processing Locus edi_0_2859720_0:144-522 [**** ] 16% > Processing Locus edi_0_2889434_0:4-919 [**** ] 17% > Processing Locus edi_0_2932438_0:28-288 [**** ] 18% > Processing Locus edi_0_2934714_0:861-939 [**** ] 19% > Processing Locus edi_0_2934714_0:1427-1505 [***** ] 20% > Processing Locus edi_0_2934714_0:2077-2155 [***** ] 21% > Processing Locus edi_0_2934714_0:3150-3228 [***** ] 22% > Processing Locus edi_0_2934714_0:3500-3578 [***** ] 23% > Processing Locus edi_0_2934714_0:4714-4792 [****** ] 24% > Processing Locus hi_0_2778596_0:11-168 [****** ] 25% > Processing Locus hi_0_2795398_0:1-187 [****** ] 26% > Processing Locus hi_0_2939638_0:39-639 [****** ] 27% > Processing Locus kn_0_3594465_0:74-152 [******* ] 28% > Processing Locus kn_0_3605300_0:1-168 [******* ] 29% > Processing Locus kn_0_3613403_0:0-139 [******* ] 30% > Processing Locus kn_0_3819922_1:133-230 [******* ] 31% > Processing Locus kn_0_3819922_1:365-758 [******** ] 32% > Processing Locus kn_0_3819922_1:940-2053 [******** ] 33% > Processing Locus ler_0_3998410_0:4-163 [******** ] 34% > Processing Locus ler_0_4018856_0:1-186 [******** ] 35% > Processing Locus mt_0_4193196_0:0-166 [********* ] 36% > Processing Locus mt_0_4213448_0:2-182 [********* ] 37% > Processing Locus mt_0_4217716_0:0-181 [********* ] 38% > Processing Locus mt_0_4229662_0:1-196 [********* ] 39% > Processing Locus mt_0_4230874_0:31-188 [********** ] 40% > Processing Locus mt_0_4231054_0:0-83 [********** ] 41% > Processing Locus mt_0_4399784_0:13-223 [********** ] 42% > Processing Locus mt_0_4528444_1:552-1231 [********** ] 43% > Processing Locus no_0_2885444_0:3-110 [*********** ] 44% > Processing Locus no_0_2905273_0:15-121 [*********** ] 45% > Processing Locus no_0_2934639_0:6-146 [*********** ] 46% > Processing Locus no_0_2956652_0:1-178 [*********** ] 47% > Processing Locus no_0_3088052_0:654-732 [************ ] 48% > Processing Locus no_0_3101262_0:99-733 [************ ] 49% > Processing Locus no_0_3116640_0:451-1883 [************ ] 50% > Processing Locus no_0_3128142_0:68-1326 [************ ] 51% > Processing Locus no_0_3128142_0:1616-2877 [************* ] 52% > Processing Locus oy_0_2965192_0:0-111 [************* ] 53% > Processing Locus oy_0_3001818_0:56-154 [************* ] 54% > Processing Locus oy_0_3148368_0:155-233 [************* ] 55% > Processing Locus po_0_3299272_0:0-119 [************** ] 56% > Processing Locus po_0_3332479_0:0-136 [************** ] 57% > Processing Locus po_0_3340213_0:12-90 [************** ] 58% > Processing Locus po_0_3606391_0:866-2776 [************** ] 59% > Processing Locus po_0_3606391_1:149-990 [*************** ] 60% > Processing Locus rsch_4_4032032_0:0-89 [*************** ] 61% > Processing Locus rsch_4_4055167_0:0-107 [*************** ] 62% > Processing Locus rsch_4_4110791_0:3-158 [*************** ] 63% > Processing Locus rsch_4_4214541_0:0-234 [**************** ] 64% > Processing Locus rsch_4_4255532_0:0-287 [**************** ] 65% > Processing Locus rsch_4_4275442_0:165-595 [**************** ] 66% > Processing Locus rsch_4_4292194_1:8-1134 [**************** ] 67% > Processing Locus sf_2_2486157_0:1-118 [***************** ] 68% > Processing Locus sf_2_2488391_0:4-124 [***************** ] 69% > Processing Locus sf_2_2524453_0:0-165 [***************** ] 70% > Processing Locus sf_2_2680171_0:7-283 [***************** ] 71% > Processing Locus tsu_0_3036945_0:27-149 [****************** ] 72% > Processing Locus tsu_0_3215821_0:594-913 [****************** ] 73% > Processing Locus wil_2_2834553_0:0-78 [****************** ] 74% > Processing Locus wil_2_2915899_0:46-154 [****************** ] 75% > Processing Locus wil_2_3088151_0:17-1644 [******************* ] 76% > Processing Locus wil_2_3090237_0:265-494 [******************* ] 77% > Processing Locus wil_2_3092619_0:324-402 [******************* ] 78% > Processing Locus ws_0_3182508_0:4-177 [******************* ] 79% > Processing Locus ws_0_3340488_0:199-1139 [******************** ] 80% > Processing Locus ws_0_3347582_0:71-859 [******************** ] 81% > Processing Locus ws_0_3347582_0:1091-1368 [******************** ] 82% > Processing Locus ws_0_3349444_1:573-748 [******************** ] 83% > Processing Locus ws_0_3371988_0:15-101 [********************* ] 84% > Processing Locus ws_0_3371988_0:204-323 [********************* ] 85% > Processing Locus ws_0_3380934_0:7-188 [********************* ] 86% > Processing Locus ws_0_3381390_0:108-1615 [********************* ] 87% > Processing Locus wu_0_2654219_0:4-125 [********************** ] 88% > Processing Locus wu_0_2678387_0:0-169 [********************** ] 89% > Processing Locus wu_0_2824308_0:316-710 [********************** ] 90% > Processing Locus zu_0_3092045_0:7-157 [********************** ] 91% > Processing Locus zu_0_3238769_0:182-290 [*********************** ] 92% > Processing Locus zu_0_3242889_0:12-186 [*********************** ] 93% > Processing Locus zu_0_3255503_0:1066-1389 [*********************** ] 94% > Processing Locus zu_0_3260131_0:171-400 [*********************** ] 95% > Processing Locus zu_0_3277661_0:334-912 [************************ ] 96% > Processing Locus zu_0_3280213_0:493-645 [************************ ] 97% > Processing Locus zu_0_3280213_0:772-1726 [************************ ] 98% > Processing Locus zu_0_3280213_0:1982-2061 [************************ ] 99% > Processed 100 loci. [*************************] 100% [14:10:58] Loading reference annotation and sequence [14:10:58] Learning bias parameters. > Processing Locus bur_0_1863298_0:23-152 [ ] 0% > Processing Locus bur_0_2020452_0:1-1367 [ ] 1% > Processing Locus can_0_3076940_0:0-142 [ ] 2% > Processing Locus can_0_3233581_0:19-459 [ ] 3% > Processing Locus can_0_3258779_0:132-658 [* ] 4% > Processing Locus can_0_3270131_0:112-951 [* ] 5% > Processing Locus can_0_3270131_0:1508-2264 [* ] 6% > Processing Locus ct_1_3082021_0:13-124 [* ] 7% > Processing Locus ct_1_3133451_0:21-193 [** ] 8% > Processing Locus ct_1_3133995_0:79-195 [** ] 9% > Processing Locus edi_0_2759827_0:7-176 [** ] 10% > Processing Locus edi_0_2859720_0:144-522 [** ] 11% > Processing Locus edi_0_2889434_0:4-919 [*** ] 12% > Processing Locus edi_0_2932438_0:28-288 [*** ] 13% > Processing Locus hi_0_2778596_0:11-168 [*** ] 14% > Processing Locus hi_0_2795398_0:1-187 [*** ] 15% > Processing Locus hi_0_2939638_0:39-639 [**** ] 16% > Processing Locus kn_0_3605300_0:1-168 [**** ] 17% > Processing Locus kn_0_3613403_0:0-139 [**** ] 18% > Processing Locus kn_0_3819922_1:365-758 [**** ] 19% > Processing Locus kn_0_3819922_1:940-2053 [***** ] 20% > Processing Locus ler_0_3998410_0:4-163 [***** ] 21% > Processing Locus ler_0_4018856_0:1-186 [***** ] 22% > Processing Locus mt_0_4193196_0:0-166 [***** ] 23% > Processing Locus mt_0_4213448_0:2-182 [****** ] 24% > Processing Locus mt_0_4217716_0:0-181 [****** ] 25% > Processing Locus mt_0_4229662_0:1-196 [****** ] 26% > Processing Locus mt_0_4230874_0:31-188 [****** ] 27% > Processing Locus mt_0_4399784_0:13-223 [******* ] 28% > Processing Locus mt_0_4528444_1:552-1231 [******* ] 29% > Processing Locus no_0_2885444_0:3-110 [******* ] 30% > Processing Locus no_0_2905273_0:15-121 [******* ] 31% > Processing Locus no_0_2934639_0:6-146 [******** ] 32% > Processing Locus no_0_2956652_0:1-178 [******** ] 33% > Processing Locus no_0_3101262_0:99-733 [******** ] 34% > Processing Locus no_0_3116640_0:451-1883 [******** ] 35% > Processing Locus no_0_3128142_0:68-1326 [********* ] 36% > Processing Locus no_0_3128142_0:1616-2877 [********* ] 37% > Processing Locus oy_0_2965192_0:0-111 [********* ] 38% > Processing Locus oy_0_3001818_0:56-154 [********* ] 39% > Processing Locus po_0_3299272_0:0-119 [********** ] 40% > Processing Locus po_0_3332479_0:0-136 [********** ] 41% > Processing Locus po_0_3606391_0:866-2776 [********** ] 42% > Processing Locus po_0_3606391_1:149-990 [********** ] 43% > Processing Locus rsch_4_4032032_0:0-89 [*********** ] 44% > Processing Locus rsch_4_4055167_0:0-107 [*********** ] 45% > Processing Locus rsch_4_4214541_0:0-234 [*********** ] 46% > Processing Locus rsch_4_4255532_0:0-287 [*********** ] 47% > Processing Locus rsch_4_4275442_0:165-595 [************ ] 48% > Processing Locus rsch_4_4292194_1:8-1134 [************ ] 49% > Processing Locus sf_2_2486157_0:1-118 [************ ] 50% > Processing Locus sf_2_2488391_0:4-124 [************ ] 51% > Processing Locus sf_2_2524453_0:0-165 [************* ] 52% > Processing Locus wil_2_3088151_0:17-1644 [************* ] 53% > Processing Locus ws_0_3182508_0:4-177 [************* ] 54% > Processing Locus ws_0_3340488_0:199-1139 [************* ] 55% > Processing Locus ws_0_3347582_0:71-859 [************** ] 56% > Processing Locus ws_0_3349444_1:573-748 [************** ] 57% > Processing Locus ws_0_3381390_0:108-1118 [************** ] 58% > Processing Locus ws_0_3381390_0:1182-1615 [************** ] 59% > Processing Locus wu_0_2654219_0:4-125 [*************** ] 60% > Processing Locus wu_0_2678387_0:0-169 [*************** ] 61% > Processing Locus wu_0_2824308_0:316-710 [*************** ] 62% > Processing Locus zu_0_3092045_0:7-157 [*************** ] 63% > Processing Locus zu_0_3242889_0:12-186 [**************** ] 64% > Processing Locus zu_0_3255503_0:1066-1389 [**************** ] 65% > Processing Locus zu_0_3277661_0:334-912 [**************** ] 66% > Processed 67 loci. [*************************] 100% [14:10:58] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1863298_0:23-152 [ ] 0% > Processing Locus bur_0_2020452_0:1-1367 [ ] 1% > Processing Locus can_0_3076940_0:0-142 [ ] 2% > Processing Locus can_0_3233581_0:19-459 [ ] 3% > Processing Locus can_0_3258779_0:132-658 [* ] 4% > Processing Locus can_0_3270131_0:112-951 [* ] 5% > Processing Locus can_0_3270131_0:1508-2264 [* ] 6% > Processing Locus ct_1_3082021_0:13-124 [* ] 7% > Processing Locus ct_1_3133451_0:21-193 [** ] 8% > Processing Locus ct_1_3133995_0:79-195 [** ] 9% > Processing Locus edi_0_2759827_0:7-176 [** ] 10% > Processing Locus edi_0_2859720_0:144-522 [** ] 11% > Processing Locus edi_0_2889434_0:4-919 [*** ] 12% > Processing Locus edi_0_2932438_0:28-288 [*** ] 13% > Processing Locus hi_0_2778596_0:11-168 [*** ] 14% > Processing Locus hi_0_2795398_0:1-187 [*** ] 15% > Processing Locus hi_0_2939638_0:39-639 [**** ] 16% > Processing Locus kn_0_3605300_0:1-168 [**** ] 17% > Processing Locus kn_0_3613403_0:0-139 [**** ] 18% > Processing Locus kn_0_3819922_1:365-758 [**** ] 19% > Processing Locus kn_0_3819922_1:940-2053 [***** ] 20% > Processing Locus ler_0_3998410_0:4-163 [***** ] 21% > Processing Locus ler_0_4018856_0:1-186 [***** ] 22% > Processing Locus mt_0_4193196_0:0-166 [***** ] 23% > Processing Locus mt_0_4213448_0:2-182 [****** ] 24% > Processing Locus mt_0_4217716_0:0-181 [****** ] 25% > Processing Locus mt_0_4229662_0:1-196 [****** ] 26% > Processing Locus mt_0_4230874_0:31-188 [****** ] 27% > Processing Locus mt_0_4399784_0:13-223 [******* ] 28% > Processing Locus mt_0_4528444_1:552-1231 [******* ] 29% > Processing Locus no_0_2885444_0:3-110 [******* ] 30% > Processing Locus no_0_2905273_0:15-121 [******* ] 31% > Processing Locus no_0_2934639_0:6-146 [******** ] 32% > Processing Locus no_0_2956652_0:1-178 [******** ] 33% > Processing Locus no_0_3101262_0:99-733 [******** ] 34% > Processing Locus no_0_3116640_0:451-1883 [******** ] 35% > Processing Locus no_0_3128142_0:68-1326 [********* ] 36% > Processing Locus no_0_3128142_0:1616-2877 [********* ] 37% > Processing Locus oy_0_2965192_0:0-111 [********* ] 38% > Processing Locus oy_0_3001818_0:56-154 [********* ] 39% > Processing Locus po_0_3299272_0:0-119 [********** ] 40% > Processing Locus po_0_3332479_0:0-136 [********** ] 41% > Processing Locus po_0_3606391_0:866-2776 [********** ] 42% > Processing Locus po_0_3606391_1:149-990 [********** ] 43% > Processing Locus rsch_4_4032032_0:0-89 [*********** ] 44% > Processing Locus rsch_4_4055167_0:0-107 [*********** ] 45% > Processing Locus rsch_4_4214541_0:0-234 [*********** ] 46% > Processing Locus rsch_4_4255532_0:0-287 [*********** ] 47% > Processing Locus rsch_4_4275442_0:165-595 [************ ] 48% > Processing Locus rsch_4_4292194_1:8-1134 [************ ] 49% > Processing Locus sf_2_2486157_0:1-118 [************ ] 50% > Processing Locus sf_2_2488391_0:4-124 [************ ] 51% > Processing Locus sf_2_2524453_0:0-165 [************* ] 52% > Processing Locus wil_2_3088151_0:17-1644 [************* ] 53% > Processing Locus ws_0_3182508_0:4-177 [************* ] 54% > Processing Locus ws_0_3340488_0:199-1139 [************* ] 55% > Processing Locus ws_0_3347582_0:71-859 [************** ] 56% > Processing Locus ws_0_3349444_1:573-748 [************** ] 57% > Processing Locus ws_0_3381390_0:108-1118 [************** ] 58% > Processing Locus ws_0_3381390_0:1182-1615 [************** ] 59% > Processing Locus wu_0_2654219_0:4-125 [*************** ] 60% > Processing Locus wu_0_2678387_0:0-169 [*************** ] 61% > Processing Locus wu_0_2824308_0:316-710 [*************** ] 62% > Processing Locus zu_0_3092045_0:7-157 [*************** ] 63% > Processing Locus zu_0_3242889_0:12-186 [**************** ] 64% > Processing Locus zu_0_3255503_0:1066-1389 [**************** ] 65% > Processing Locus zu_0_3277661_0:334-912 [**************** ] 66% > Processed 67 loci. [*************************] 100% [Mon Apr 4 14:11:02 2011] Retrieving sequences for splices [Mon Apr 4 14:11:02 2011] Indexing splices [Mon Apr 4 14:11:02 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:11:04 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:11:06 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:11:07 2011] Joining segment hits [Mon Apr 4 14:11:09 2011] Reporting output tracks 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 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 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 $RNAGI/rnagi.sh -o ./Po_0 -n it2.fa Po_0.Toit2.merge.fq reference: it2.fa ----------------------------------------------- Run complete [00:01:04 elapsed] $RNAGI/rnagi.sh -o ./Rsch_4 -n it2.fa Rsch_4.Toit2.merge.fq reference: it2.fa $RNAGI/rnagi.sh -o ./Sf_2 -n it2.fa Sf_2.Toit2.merge.fq reference: it2.fa $RNAGI/rnagi.sh -o ./Tsu_0 -n it2.fa Tsu_0.Toit2.merge.fq reference: it2.fa cufflinks -p 4 -o ./Oy_0 -r it2.fa ./Oy_0/accepted_hits.bam [14:11:14] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:9-111 [ ] 0% > Processing Locus bur_0_2032354_0:67-1330 [ ] 0% > Processing Locus bur_0_2032354_0:1535-2016 [ ] 0% > Processing Locus can_0_3076940_0:7-132 [ ] 0% > Processing Locus can_0_3189753_0:45-203 [ ] 1% > Processing Locus can_0_3217045_0:33-730 [ ] 1% > Processing Locus can_0_3218459_0:10-897 [ ] 2% > Processing Locus can_0_3270131_0:56-284 [ ] 2% > Processing Locus can_0_3270131_0:803-1067 [ ] 2% > Processing Locus can_0_3270131_0:1697-1970 [ ] 2% > Processing Locus ct_1_3082021_0:2-125 [ ] 2% > Processing Locus ct_1_3132277_0:0-169 [ ] 3% > Processing Locus ct_1_3133451_0:22-184 [ ] 3% > Processing Locus ct_1_3133995_0:79-195 [* ] 4% > Processing Locus ct_1_3241157_0:4-734 [* ] 4% > Processing Locus ct_1_3247037_0:199-411 [* ] 5% > Processing Locus ct_1_3302721_0:1261-1339 [* ] 5% > Processing Locus edi_0_2859720_0:155-523 [* ] 5% > Processing Locus edi_0_2871668_0:191-529 [* ] 6% > Processing Locus edi_0_2889434_0:0-880 [* ] 6% > Processing Locus edi_0_2918156_0:79-583 [* ] 7% > Processing Locus edi_0_2932438_0:31-289 [* ] 7% > Processing Locus hi_0_2773206_0:25-127 [* ] 7% > Processing Locus hi_0_2778596_0:8-167 [** ] 8% > Processing Locus hi_0_2939638_0:45-639 [** ] 8% > Processing Locus kn_0_3613403_0:0-176 [** ] 9% > Processing Locus kn_0_3819922_1:49-1863 [** ] 9% > Processing Locus ler_0_3998410_0:0-164 [** ] 10% > Processing Locus ler_0_4018856_0:1-186 [** ] 10% > Processing Locus mt_0_4217716_0:0-182 [** ] 10% > Processing Locus mt_0_4229662_0:21-99 [** ] 11% > Processing Locus mt_0_4231054_0:3-83 [** ] 11% > Processing Locus mt_0_4528444_1:552-1235 [*** ] 12% > Processing Locus no_0_2885444_0:3-111 [*** ] 12% > Processing Locus no_0_2905273_0:8-121 [*** ] 13% > Processing Locus no_0_2956652_0:1-177 [*** ] 13% > Processing Locus oy_0_2936927_0:34-112 [*** ] 13% > Processing Locus oy_0_2965192_0:1-111 [*** ] 14% > Processing Locus oy_0_2966542_0:0-101 [*** ] 14% > Processing Locus oy_0_3001818_0:25-154 [*** ] 15% > Processing Locus oy_0_3098144_0:3-297 [*** ] 15% > Processing Locus oy_0_3162092_0:187-1324 [*** ] 15% > Processing Locus oy_0_3162092_0:1435-1984 [*** ] 15% > Processing Locus po_0_3293868_0:0-117 [**** ] 16% > Processing Locus po_0_3332479_0:1-136 [**** ] 16% > Processing Locus rsch_4_4032032_0:0-86 [**** ] 17% > Processing Locus rsch_4_4055167_0:0-109 [**** ] 17% > Processing Locus rsch_4_4110791_0:5-160 [**** ] 18% > Processing Locus rsch_4_4214541_0:1-234 [**** ] 18% > Processing Locus rsch_4_4219071_0:7-435 [**** ] 18% > Processing Locus rsch_4_4255532_0:7-287 [**** ] 19% > Processing Locus rsch_4_4292194_1:19-1127 [**** ] 19% > Processing Locus sf_2_2459023_0:3-110 [***** ] 20% > Processing Locus sf_2_2486157_0:0-118 [***** ] 20% > Processing Locus sf_2_2524453_0:1-164 [***** ] 21% > Processing Locus sf_2_2680171_0:8-654 [***** ] 21% > Processing Locus sf_2_2680171_0:766-1170 [***** ] 21% > Processing Locus sf_2_2682779_0:590-991 [***** ] 21% > Processing Locus tsu_0_3211741_0:3-781 [***** ] 22% > Processing Locus wil_2_2834553_0:23-103 [***** ] 22% > Processing Locus wil_2_2925323_0:0-104 [***** ] 23% > Processing Locus ws_0_3182508_0:4-164 [***** ] 23% > Processing Locus ws_0_3326342_0:7-96 [***** ] 23% > Processing Locus ws_0_3326342_0:198-410 [***** ] 23% > Processing Locus ws_0_3340488_0:199-1181 [****** ] 24% > Processing Locus ws_0_3347582_0:122-611 [****** ] 24% > Processing Locus ws_0_3347582_0:821-972 [****** ] 24% > Processing Locus ws_0_3347582_0:1186-1377 [****** ] 24% > Processing Locus wu_0_2654219_0:15-137 [****** ] 25% > Processing Locus wu_0_2678387_0:1-182 [****** ] 25% > Processing Locus wu_0_2687576_0:12-172 [****** ] 26% > Processing Locus wu_0_2824308_0:26-104 [****** ] 26% > Processing Locus wu_0_2824308_0:259-797 [****** ] 26% > Processing Locus zu_0_3238769_0:130-208 [****** ] 26% > Processing Locus zu_0_3238769_0:342-434 [****** ] 26% > Processing Locus zu_0_3242889_0:13-182 [****** ] 27% > Processing Locus zu_0_3255169_0:60-1061 [****** ] 27% > Processing Locus zu_0_3255503_0:1070-1367 [******* ] 28% > Processing Locus zu_0_3277661_0:255-900 [******* ] 28% > Processing Locus zu_0_3289907_1:260-513 [******* ] 28% > Processing Locus zu_0_3289907_1:961-1262 [******* ] 28% > Processing Locus zu_0_3289907_1:1392-2670 [******* ] 28% > Processing Locus zu_0_3289907_1:2796-4522 [******* ] 28% > Processed 83 loci. [*************************] 100% > Map Properties: > Total Map Mass: 4915.66 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:11:14] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:9-111 [ ] 0% > Processing Locus bur_0_2032354_0:67-1330 [ ] 1% > Processing Locus bur_0_2032354_0:1535-2016 [ ] 2% > Processing Locus can_0_3076940_0:7-132 [ ] 3% > Processing Locus can_0_3189753_0:45-203 [* ] 4% > Processing Locus can_0_3217045_0:33-730 [* ] 6% > Processing Locus can_0_3218459_0:10-897 [* ] 7% > Processing Locus can_0_3270131_0:56-284 [** ] 8% > Processing Locus can_0_3270131_0:803-1067 [** ] 9% > Processing Locus can_0_3270131_0:1697-1970 [** ] 10% > Processing Locus ct_1_3082021_0:2-125 [*** ] 12% > Processing Locus ct_1_3132277_0:0-169 [*** ] 13% > Processing Locus ct_1_3133451_0:22-184 [*** ] 14% > Processing Locus ct_1_3133995_0:79-195 [*** ] 15% > Processing Locus ct_1_3241157_0:4-734 [**** ] 16% > Processing Locus ct_1_3247037_0:199-411 [**** ] 18% > Processing Locus ct_1_3302721_0:1261-1339 [**** ] 19% > Processing Locus edi_0_2859720_0:155-523 [***** ] 20% > Processing Locus edi_0_2871668_0:191-529 [***** ] 21% > Processing Locus edi_0_2889434_0:0-880 [***** ] 22% > Processing Locus edi_0_2918156_0:79-583 [****** ] 24% > Processing Locus edi_0_2932438_0:31-289 [****** ] 25% > Processing Locus hi_0_2773206_0:25-127 [****** ] 26% > Processing Locus hi_0_2778596_0:8-167 [****** ] 27% > Processing Locus hi_0_2939638_0:45-639 [******* ] 28% > Processing Locus kn_0_3613403_0:0-176 [******* ] 30% > Processing Locus kn_0_3819922_1:49-1863 [******* ] 31% > Processing Locus ler_0_3998410_0:0-164 [******** ] 32% > Processing Locus ler_0_4018856_0:1-186 [******** ] 33% > Processing Locus mt_0_4217716_0:0-182 [******** ] 34% > Processing Locus mt_0_4229662_0:21-99 [********* ] 36% > Processing Locus mt_0_4231054_0:3-83 [********* ] 37% > Processing Locus mt_0_4528444_1:552-1235 [********* ] 38% > Processing Locus no_0_2885444_0:3-111 [********* ] 39% > Processing Locus no_0_2905273_0:8-121 [********** ] 40% > Processing Locus no_0_2956652_0:1-177 [********** ] 42% > Processing Locus oy_0_2936927_0:34-112 [********** ] 43% > Processing Locus oy_0_2965192_0:1-111 [*********** ] 44% > Processing Locus oy_0_2966542_0:0-101 [*********** ] 45% > Processing Locus oy_0_3001818_0:25-154 [*********** ] 46% > Processing Locus oy_0_3098144_0:3-297 [************ ] 48% > Processing Locus oy_0_3162092_0:187-1324 [************ ] 49% > Processing Locus oy_0_3162092_0:1435-1984 [************ ] 50% > Processing Locus po_0_3293868_0:0-117 [************ ] 51% > Processing Locus po_0_3332479_0:1-136 [************* ] 53% > Processing Locus rsch_4_4032032_0:0-86 [************* ] 54% > Processing Locus rsch_4_4055167_0:0-109 [************* ] 55% > Processing Locus rsch_4_4110791_0:5-160 [************** ] 56% > Processing Locus rsch_4_4214541_0:1-234 [************** ] 57% > Processing Locus rsch_4_4219071_0:7-435 [************** ] 59% > Processing Locus rsch_4_4255532_0:7-287 [*************** ] 60% > Processing Locus rsch_4_4292194_1:19-1127 [*************** ] 61% > Processing Locus sf_2_2459023_0:3-110 [*************** ] 62% > Processing Locus sf_2_2486157_0:0-118 [*************** ] 63% > Processing Locus sf_2_2524453_0:1-164 [**************** ] 65% > Processing Locus sf_2_2680171_0:8-654 [**************** ] 66% > Processing Locus sf_2_2680171_0:766-1170 [**************** ] 67% > Processing Locus sf_2_2682779_0:590-991 [***************** ] 68% > Processing Locus tsu_0_3211741_0:3-781 [***************** ] 69% > Processing Locus wil_2_2834553_0:23-103 [***************** ] 71% > Processing Locus wil_2_2925323_0:0-104 [****************** ] 72% > Processing Locus ws_0_3182508_0:4-164 [****************** ] 73% > Processing Locus ws_0_3326342_0:7-96 [****************** ] 74% > Processing Locus ws_0_3326342_0:198-410 [****************** ] 75% > Processing Locus ws_0_3340488_0:199-1181 [******************* ] 77% > Processing Locus ws_0_3347582_0:122-611 [******************* ] 78% > Processing Locus ws_0_3347582_0:821-972 [******************* ] 79% > Processing Locus ws_0_3347582_0:1186-1377 [******************** ] 80% > Processing Locus wu_0_2654219_0:15-137 [******************** ] 81% > Processing Locus wu_0_2678387_0:1-182 [******************** ] 83% > Processing Locus wu_0_2687576_0:12-172 [********************* ] 84% > Processing Locus wu_0_2824308_0:26-104 [********************* ] 85% > Processing Locus wu_0_2824308_0:259-797 [********************* ] 86% > Processing Locus zu_0_3238769_0:130-208 [********************* ] 87% > Processing Locus zu_0_3238769_0:342-434 [********************** ] 89% > Processing Locus zu_0_3242889_0:13-182 [********************** ] 90% > Processing Locus zu_0_3255169_0:60-1061 [********************** ] 91% > Processing Locus zu_0_3255503_0:1070-1367 [*********************** ] 92% > Processing Locus zu_0_3277661_0:255-900 [*********************** ] 93% > Processing Locus zu_0_3289907_1:260-513 [*********************** ] 95% > Processing Locus zu_0_3289907_1:961-1262 [************************ ] 96% > Processing Locus zu_0_3289907_1:1392-2670 [************************ ] 97% > Processing Locus zu_0_3289907_1:2796-4522 [************************ ] 98% > Processed 83 loci. [*************************] 100% [14:11:14] Loading reference annotation and sequence [14:11:14] Learning bias parameters. > Processing Locus bur_0_1804399_0:9-111 [ ] 0% > Processing Locus bur_0_2032354_0:67-1096 [ ] 1% > Processing Locus bur_0_2032354_0:1535-2016 [ ] 2% > Processing Locus can_0_3076940_0:7-132 [ ] 3% > Processing Locus can_0_3189753_0:45-203 [* ] 4% > Processing Locus can_0_3217045_0:33-730 [* ] 6% > Processing Locus can_0_3218459_0:10-897 [* ] 7% > Processing Locus ct_1_3082021_0:2-125 [** ] 8% > Processing Locus ct_1_3132277_0:0-169 [** ] 9% > Processing Locus ct_1_3133451_0:22-184 [** ] 10% > Processing Locus ct_1_3133995_0:79-195 [*** ] 12% > Processing Locus ct_1_3241157_0:4-734 [*** ] 13% > Processing Locus edi_0_2859720_0:155-523 [*** ] 14% > Processing Locus edi_0_2871668_0:191-529 [*** ] 15% > Processing Locus edi_0_2889434_0:0-880 [**** ] 16% > Processing Locus edi_0_2918156_0:79-583 [**** ] 18% > Processing Locus edi_0_2932438_0:31-289 [**** ] 19% > Processing Locus hi_0_2778596_0:8-167 [***** ] 20% > Processing Locus hi_0_2939638_0:45-639 [***** ] 21% > Processing Locus kn_0_3613403_0:0-176 [***** ] 22% > Processing Locus kn_0_3819922_1:49-1863 [****** ] 24% > Processing Locus ler_0_3998410_0:0-164 [****** ] 25% > Processing Locus ler_0_4018856_0:1-186 [****** ] 26% > Processing Locus mt_0_4217716_0:0-182 [****** ] 27% > Processing Locus mt_0_4231054_0:3-83 [******* ] 28% > Processing Locus mt_0_4528444_1:552-1235 [******* ] 30% > Processing Locus no_0_2885444_0:3-111 [******* ] 31% > Processing Locus no_0_2905273_0:8-121 [******** ] 32% > Processing Locus no_0_2956652_0:1-177 [******** ] 33% > Processing Locus oy_0_2965192_0:1-111 [******** ] 34% > Processing Locus oy_0_2966542_0:0-101 [********* ] 36% > Processing Locus oy_0_3001818_0:25-154 [********* ] 37% > Processing Locus oy_0_3098144_0:3-297 [********* ] 38% > Processing Locus oy_0_3162092_0:187-1324 [********* ] 39% > Processing Locus oy_0_3162092_0:1435-1984 [********** ] 40% > Processing Locus po_0_3293868_0:0-117 [********** ] 42% > Processing Locus po_0_3332479_0:1-136 [********** ] 43% > Processing Locus rsch_4_4032032_0:0-86 [*********** ] 44% > Processing Locus rsch_4_4055167_0:0-109 [*********** ] 45% > Processing Locus rsch_4_4214541_0:1-234 [*********** ] 46% > Processing Locus rsch_4_4219071_0:7-435 [************ ] 48% > Processing Locus rsch_4_4255532_0:7-287 [************ ] 49% > Processing Locus rsch_4_4292194_1:19-1127 [************ ] 50% > Processing Locus sf_2_2459023_0:3-110 [************ ] 51% > Processing Locus sf_2_2486157_0:0-118 [************* ] 53% > Processing Locus sf_2_2524453_0:1-164 [************* ] 54% > Processing Locus sf_2_2680171_0:8-654 [************* ] 55% > Processing Locus sf_2_2680171_0:766-1170 [************** ] 56% > Processing Locus sf_2_2682779_0:590-991 [************** ] 57% > Processing Locus tsu_0_3211741_0:3-781 [************** ] 59% > Processing Locus wil_2_2925323_0:0-104 [*************** ] 60% > Processing Locus ws_0_3340488_0:199-1181 [*************** ] 61% > Processing Locus ws_0_3347582_0:122-611 [*************** ] 62% > Processing Locus wu_0_2654219_0:15-137 [*************** ] 63% > Processing Locus wu_0_2678387_0:1-182 [**************** ] 65% > Processing Locus wu_0_2687576_0:12-172 [**************** ] 66% > Processing Locus wu_0_2824308_0:259-797 [**************** ] 67% > Processing Locus zu_0_3242889_0:13-182 [***************** ] 68% > Processing Locus zu_0_3255169_0:60-1061 [***************** ] 69% > Processing Locus zu_0_3255503_0:1070-1367 [***************** ] 71% > Processing Locus zu_0_3277661_0:255-900 [****************** ] 72% > Processing Locus zu_0_3289907_1:1392-2670 [****************** ] 73% > Processing Locus zu_0_3289907_1:2802-4522 [****************** ] 74% > Processed 63 loci. [*************************] 100% [14:11:14] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:9-111 [ ] 0% > Processing Locus bur_0_2032354_0:67-1096 [ ] 1% > Processing Locus bur_0_2032354_0:1535-2016 [ ] 2% > Processing Locus can_0_3076940_0:7-132 [ ] 3% > Processing Locus can_0_3189753_0:45-203 [* ] 4% > Processing Locus can_0_3217045_0:33-730 [* ] 6% > Processing Locus can_0_3218459_0:10-897 [* ] 7% > Processing Locus ct_1_3082021_0:2-125 [** ] 8% > Processing Locus ct_1_3132277_0:0-169 [** ] 9% > Processing Locus ct_1_3133451_0:22-184 [** ] 10% > Processing Locus ct_1_3133995_0:79-195 [*** ] 12% > Processing Locus ct_1_3241157_0:4-734 [*** ] 13% > Processing Locus edi_0_2859720_0:155-523 [*** ] 14% > Processing Locus edi_0_2871668_0:191-529 [*** ] 15% > Processing Locus edi_0_2889434_0:0-880 [**** ] 16% > Processing Locus edi_0_2918156_0:79-583 [**** ] 18% > Processing Locus edi_0_2932438_0:31-289 [**** ] 19% > Processing Locus hi_0_2778596_0:8-167 [***** ] 20% > Processing Locus hi_0_2939638_0:45-639 [***** ] 21% > Processing Locus kn_0_3613403_0:0-176 [***** ] 22% > Processing Locus kn_0_3819922_1:49-1863 [****** ] 24% > Processing Locus ler_0_3998410_0:0-164 [****** ] 25% > Processing Locus ler_0_4018856_0:1-186 [****** ] 26% > Processing Locus mt_0_4217716_0:0-182 [****** ] 27% > Processing Locus mt_0_4231054_0:3-83 [******* ] 28% > Processing Locus mt_0_4528444_1:552-1235 [******* ] 30% > Processing Locus no_0_2885444_0:3-111 [******* ] 31% > Processing Locus no_0_2905273_0:8-121 [******** ] 32% > Processing Locus no_0_2956652_0:1-177 [******** ] 33% > Processing Locus oy_0_2965192_0:1-111 [******** ] 34% > Processing Locus oy_0_2966542_0:0-101 [********* ] 36% > Processing Locus oy_0_3001818_0:25-154 [********* ] 37% > Processing Locus oy_0_3098144_0:3-297 [********* ] 38% > Processing Locus oy_0_3162092_0:187-1324 [********* ] 39% > Processing Locus oy_0_3162092_0:1435-1984 [********** ] 40% > Processing Locus po_0_3293868_0:0-117 [********** ] 42% > Processing Locus po_0_3332479_0:1-136 [********** ] 43% > Processing Locus rsch_4_4032032_0:0-86 [*********** ] 44% > Processing Locus rsch_4_4055167_0:0-109 [*********** ] 45% > Processing Locus rsch_4_4214541_0:1-234 [*********** ] 46% > Processing Locus rsch_4_4219071_0:7-435 [************ ] 48% > Processing Locus rsch_4_4255532_0:7-287 [************ ] 49% > Processing Locus rsch_4_4292194_1:19-1127 [************ ] 50% > Processing Locus sf_2_2459023_0:3-110 [************ ] 51% > Processing Locus sf_2_2486157_0:0-118 [************* ] 53% > Processing Locus sf_2_2524453_0:1-164 [************* ] 54% > Processing Locus sf_2_2680171_0:8-654 [************* ] 55% > Processing Locus sf_2_2680171_0:766-1170 [************** ] 56% > Processing Locus sf_2_2682779_0:590-991 [************** ] 57% > Processing Locus tsu_0_3211741_0:3-781 [************** ] 59% > Processing Locus wil_2_2925323_0:0-104 [*************** ] 60% > Processing Locus ws_0_3340488_0:199-1181 [*************** ] 61% > Processing Locus ws_0_3347582_0:122-611 [*************** ] 62% > Processing Locus wu_0_2654219_0:15-137 [*************** ] 63% > Processing Locus wu_0_2678387_0:1-182 [**************** ] 65% > Processing Locus wu_0_2687576_0:12-172 [**************** ] 66% > Processing Locus wu_0_2824308_0:259-797 [**************** ] 67% > Processing Locus zu_0_3242889_0:13-182 [***************** ] 68% > Processing Locus zu_0_3255169_0:60-1061 [***************** ] 69% > Processing Locus zu_0_3255503_0:1070-1367 [***************** ] 71% > Processing Locus zu_0_3277661_0:255-900 [****************** ] 72% > Processing Locus zu_0_3289907_1:1392-2670 [****************** ] 73% > Processing Locus zu_0_3289907_1:2802-4522 [****************** ] 74% > Processed 63 loci. [*************************] 100% tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Po_0 it2.fa ./Po_0/Po_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:11:21 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:11:21 2011] Preparing output location ./Po_0// [Mon Apr 4 14:11:21 2011] Checking for Bowtie index files [Mon Apr 4 14:11:21 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:11:21 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:11:21 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:11:21 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:11:21 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Rsch_4 it2.fa ./Rsch_4/Rsch_4.Toit2.merge.flt_1.fq [Mon Apr 4 14:11:23 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:11:23 2011] Preparing output location ./Rsch_4// [Mon Apr 4 14:11:23 2011] Checking for Bowtie index files [Mon Apr 4 14:11:23 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:11:23 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:11:23 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:11:23 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:11:23 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Tsu_0 it2.fa ./Tsu_0/Tsu_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:11:26 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:11:26 2011] Preparing output location ./Tsu_0// [Mon Apr 4 14:11:26 2011] Checking for Bowtie index files [Mon Apr 4 14:11:26 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:11:26 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:11:26 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:11:26 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:11:26 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 it2.fa ./Sf_2/Sf_2.Toit2.merge.flt_1.fq [Mon Apr 4 14:11:32 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:11:32 2011] Preparing output location ./Sf_2// [Mon Apr 4 14:11:32 2011] Checking for Bowtie index files [Mon Apr 4 14:11:32 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:11:32 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:11:32 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:11:32 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:11:32 2011] Checking reads min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 14:11:33 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:11:34 2011] Mapping reads against it2.fa with Bowtie min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 14:11:37 2011] Joining segment hits [Mon Apr 4 14:11:37 2011] Joining segment hits [Mon Apr 4 14:11:38 2011] Mapping reads against it2.fa with Bowtie 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 $RNAGI/rnagi.sh -o ./Wil_2 -n it2.fa Wil_2.Toit2.merge.fq reference: it2.fa [Mon Apr 4 14:11:42 2011] Joining segment hits min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 14:11:45 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:11:47 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:11:48 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:11:49 2011] Joining segment hits [Mon Apr 4 14:11:50 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:11:52 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:11:54 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:11:55 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:11:56 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:11:57 2011] Searching for junctions via segment mapping tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Wil_2 it2.fa ./Wil_2/Wil_2.Toit2.merge.flt_1.fq [Mon Apr 4 14:11:58 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:11:58 2011] Preparing output location ./Wil_2// [Mon Apr 4 14:11:58 2011] Checking for Bowtie index files [Mon Apr 4 14:11:58 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:11:58 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:11:58 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:11:58 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:11:58 2011] Checking reads [Mon Apr 4 14:11:59 2011] Searching for junctions via segment mapping [Mon Apr 4 14:11:59 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:12:03 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:12:03 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:12:06 2011] Searching for junctions via segment mapping [Mon Apr 4 14:12:07 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:12:10 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:12:12 2011] Retrieving sequences for splices [Mon Apr 4 14:12:12 2011] Indexing splices [Mon Apr 4 14:12:13 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 14:12:13 2011] Searching for junctions via segment mapping [Mon Apr 4 14:12:15 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:12:17 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:12:17 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:12:19 2011] Retrieving sequences for splices [Mon Apr 4 14:12:19 2011] Indexing splices [Mon Apr 4 14:12:19 2011] Joining segment hits [Mon Apr 4 14:12:19 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:12:21 2011] Reporting output tracks [Mon Apr 4 14:12:21 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:12:22 2011] Joining segment hits ----------------------------------------------- Run complete [00:01:01 elapsed] [Mon Apr 4 14:12:23 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:12:25 2011] Joining segment hits [Mon Apr 4 14:12:27 2011] Reporting output tracks [Mon Apr 4 14:12:27 2011] Retrieving sequences for splices [Mon Apr 4 14:12:27 2011] Indexing splices [Mon Apr 4 14:12:27 2011] Mapping reads against segment_juncs with Bowtie ----------------------------------------------- Run complete [00:01:05 elapsed] cufflinks -p 4 -o ./Po_0 -r it2.fa ./Po_0/accepted_hits.bam [14:12:29] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:9-113 [ ] 0% > Processing Locus bur_0_2020452_0:1-1386 [ ] 0% > Processing Locus bur_0_2020452_0:2100-2306 [ ] 0% > Processing Locus bur_0_2025286_0:118-888 [ ] 0% > Processing Locus bur_0_2025286_0:1186-1388 [ ] 0% > Processing Locus bur_0_2025286_0:1524-1699 [ ] 0% > Processing Locus bur_0_2025286_0:1808-2504 [ ] 0% > Processing Locus bur_0_2025286_0:2736-2814 [ ] 0% > Processing Locus bur_0_2032354_0:23-2009 [ ] 1% > Processing Locus can_0_3076940_0:5-132 [ ] 1% > Processing Locus can_0_3189753_0:0-204 [ ] 2% > Processing Locus can_0_3217045_0:28-736 [ ] 2% > Processing Locus can_0_3218459_0:4-871 [ ] 2% > Processing Locus can_0_3270131_0:9-87 [ ] 3% > Processing Locus can_0_3270131_0:321-531 [ ] 3% > Processing Locus can_0_3270131_0:811-1101 [ ] 3% > Processing Locus can_0_3270131_0:1244-2050 [ ] 3% > Processing Locus ct_1_3082021_0:2-127 [ ] 3% > Processing Locus ct_1_3132277_0:0-171 [* ] 4% > Processing Locus ct_1_3133451_0:21-179 [* ] 4% > Processing Locus ct_1_3133995_0:58-195 [* ] 5% > Processing Locus ct_1_3241157_0:13-739 [* ] 5% > Processing Locus ct_1_3247037_0:194-510 [* ] 5% > Processing Locus ct_1_3302721_0:1261-1339 [* ] 6% > Processing Locus edi_0_2744702_0:0-157 [* ] 6% > Processing Locus edi_0_2871668_0:165-522 [* ] 7% > Processing Locus edi_0_2889434_0:39-136 [* ] 7% > Processing Locus edi_0_2889434_0:418-684 [* ] 7% > Processing Locus edi_0_2918156_0:77-582 [* ] 7% > Processing Locus edi_0_2932438_0:28-288 [** ] 8% > Processing Locus hi_0_2773206_0:22-155 [** ] 8% > Processing Locus hi_0_2778596_0:12-166 [** ] 9% > Processing Locus hi_0_2939638_0:18-637 [** ] 9% > Processing Locus kn_0_3613403_0:12-171 [** ] 10% > Processing Locus kn_0_3819922_1:13-331 [** ] 10% > Processing Locus kn_0_3819922_1:614-2016 [** ] 10% > Processing Locus ler_0_3998410_0:5-163 [** ] 10% > Processing Locus ler_0_4018856_0:7-183 [** ] 11% > Processing Locus mt_0_4217716_0:0-181 [** ] 11% > Processing Locus mt_0_4229662_0:0-197 [*** ] 12% > Processing Locus mt_0_4231054_0:4-188 [*** ] 12% > Processing Locus mt_0_4528444_1:561-1183 [*** ] 13% > Processing Locus no_0_2885444_0:25-107 [*** ] 13% > Processing Locus no_0_2905273_0:13-118 [*** ] 13% > Processing Locus no_0_2936769_0:4-152 [*** ] 14% > Processing Locus no_0_2956652_0:1-169 [*** ] 14% > Processing Locus no_0_3113578_1:318-832 [*** ] 15% > Processing Locus no_0_3116640_0:664-841 [*** ] 15% > Processing Locus no_0_3116640_0:1387-1837 [*** ] 15% > Processing Locus no_0_3128142_0:25-360 [*** ] 15% > Processing Locus no_0_3128142_0:565-824 [*** ] 15% > Processing Locus no_0_3128142_0:1149-1227 [*** ] 15% > Processing Locus no_0_3128142_0:1758-2107 [*** ] 15% > Processing Locus no_0_3128142_0:2482-2920 [*** ] 15% > Processing Locus oy_0_2966542_0:0-90 [**** ] 16% > Processing Locus oy_0_3001818_0:22-154 [**** ] 16% > Processing Locus oy_0_3098144_0:4-324 [**** ] 17% > Processing Locus oy_0_3121110_0:53-552 [**** ] 17% > Processing Locus oy_0_3148368_0:952-1030 [**** ] 18% > Processing Locus oy_0_3162092_0:171-1984 [**** ] 18% > Processing Locus po_0_3293868_0:0-117 [**** ] 18% > Processing Locus po_0_3299272_0:2-119 [**** ] 19% > Processing Locus po_0_3324652_0:0-132 [**** ] 19% > Processing Locus po_0_3330421_0:4-130 [***** ] 20% > Processing Locus po_0_3332479_0:0-136 [***** ] 20% > Processing Locus po_0_3340213_0:5-86 [***** ] 21% > Processing Locus po_0_3372769_0:2-165 [***** ] 21% > Processing Locus po_0_3382155_0:1-133 [***** ] 21% > Processing Locus po_0_3507160_0:16-427 [***** ] 22% > Processing Locus po_0_3573778_0:350-1264 [***** ] 22% > Processing Locus po_0_3606391_0:946-1122 [***** ] 23% > Processing Locus po_0_3606391_0:1263-1580 [***** ] 23% > Processing Locus po_0_3606391_0:1711-1789 [***** ] 23% > Processing Locus po_0_3606391_0:2012-2401 [***** ] 23% > Processing Locus po_0_3606391_0:2572-2651 [***** ] 23% > Processing Locus po_0_3606391_0:2771-2849 [***** ] 23% > Processing Locus po_0_3606391_1:113-191 [***** ] 23% > Processing Locus po_0_3606391_1:293-497 [***** ] 23% > Processing Locus po_0_3606391_1:791-1003 [***** ] 23% > Processing Locus rsch_4_4032032_0:0-84 [***** ] 23% > Processing Locus rsch_4_4055167_0:0-108 [****** ] 24% > Processing Locus rsch_4_4110791_0:5-155 [****** ] 24% > Processing Locus rsch_4_4214541_0:3-223 [****** ] 25% > Processing Locus rsch_4_4219071_0:34-436 [****** ] 25% > Processing Locus rsch_4_4255532_0:3-287 [****** ] 26% > Processing Locus rsch_4_4266550_0:6-1148 [****** ] 26% > Processing Locus rsch_4_4292194_1:5-1133 [****** ] 26% > Processing Locus rsch_4_4297142_0:42-233 [****** ] 27% > Processing Locus sf_2_2459023_0:3-110 [****** ] 27% > Processing Locus sf_2_2486157_0:0-118 [******* ] 28% > Processing Locus sf_2_2524453_0:1-164 [******* ] 28% > Processing Locus sf_2_2680171_0:9-1095 [******* ] 28% > Processing Locus sf_2_2682779_0:593-991 [******* ] 29% > Processing Locus sf_2_2701328_0:482-608 [******* ] 29% > Processing Locus tsu_0_3036945_0:21-119 [******* ] 30% > Processing Locus tsu_0_3211741_0:3-787 [******* ] 30% > Processing Locus tsu_0_3215671_0:29-418 [******* ] 31% > Processing Locus tsu_0_3215671_0:539-869 [******* ] 31% > Processing Locus tsu_0_3229935_0:28-1235 [******* ] 31% > Processing Locus wil_2_2834553_0:1-97 [******* ] 31% > Processing Locus wil_2_2915899_0:15-94 [******** ] 32% > Processing Locus wil_2_2925323_0:0-104 [******** ] 32% > Processing Locus wil_2_3079625_0:11-604 [******** ] 33% > Processing Locus wil_2_3090237_0:260-494 [******** ] 33% > Processing Locus wil_2_3092619_0:1119-1197 [******** ] 34% > Processing Locus ws_0_3182508_0:4-180 [******** ] 34% > Processing Locus ws_0_3190963_0:49-127 [******** ] 34% > Processing Locus ws_0_3326342_0:193-408 [******** ] 35% > Processing Locus ws_0_3340488_0:210-1139 [******** ] 35% > Processing Locus ws_0_3347582_0:157-573 [********* ] 36% > Processing Locus ws_0_3347582_0:692-1306 [********* ] 36% > Processing Locus ws_0_3372048_0:28-976 [********* ] 36% > Processing Locus ws_0_3372048_0:1104-1235 [********* ] 36% > Processing Locus ws_0_3381390_0:142-1279 [********* ] 36% > Processing Locus ws_0_3381390_0:1604-1682 [********* ] 36% > Processing Locus wu_0_2654219_0:18-147 [********* ] 37% > Processing Locus wu_0_2678387_0:7-182 [********* ] 37% > Processing Locus wu_0_2687576_0:15-170 [********* ] 38% > Processing Locus wu_0_2824308_0:17-95 [********* ] 38% > Processing Locus wu_0_2824308_0:269-797 [********* ] 38% > Processing Locus zu_0_3118546_0:4-164 [********* ] 39% > Processing Locus zu_0_3190435_0:20-303 [********* ] 39% > Processing Locus zu_0_3238769_0:142-220 [********* ] 39% > Processing Locus zu_0_3242889_0:12-213 [********** ] 40% > Processing Locus zu_0_3255169_0:55-133 [********** ] 40% > Processing Locus zu_0_3255169_0:409-1089 [********** ] 40% > Processing Locus zu_0_3255503_0:1066-1394 [********** ] 41% > Processing Locus zu_0_3259399_1:88-317 [********** ] 41% > Processing Locus zu_0_3260131_0:166-400 [********** ] 42% > Processing Locus zu_0_3277661_0:334-911 [********** ] 42% > Processing Locus zu_0_3278243_0:24-102 [********** ] 42% > Processing Locus zu_0_3280213_0:764-922 [********** ] 43% > Processing Locus zu_0_3280213_0:1378-1500 [********** ] 43% > Processing Locus zu_0_3289907_1:271-826 [********** ] 43% > Processing Locus zu_0_3289907_1:1171-1262 [********** ] 43% > Processing Locus zu_0_3289907_1:1382-1826 [********** ] 43% > Processing Locus zu_0_3289907_1:1931-2668 [********** ] 43% > Processing Locus zu_0_3289907_1:2825-3698 [********** ] 43% > Processing Locus zu_0_3289907_1:3827-4516 [********** ] 43% > Processed 139 loci. [*************************] 100% > Map Properties: > Total Map Mass: 4923.62 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:12:29] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:9-113 [ ] 0% > Processing Locus bur_0_2020452_0:1-1386 [ ] 0% > Processing Locus bur_0_2020452_0:2100-2306 [ ] 1% > Processing Locus bur_0_2025286_0:118-888 [ ] 2% > Processing Locus bur_0_2025286_0:1186-1388 [ ] 2% > Processing Locus bur_0_2025286_0:1524-1699 [ ] 3% > Processing Locus bur_0_2025286_0:1808-2504 [* ] 4% > Processing Locus bur_0_2025286_0:2736-2814 [* ] 5% > Processing Locus bur_0_2032354_0:23-2009 [* ] 5% > Processing Locus can_0_3076940_0:5-132 [* ] 6% > Processing Locus can_0_3189753_0:0-204 [* ] 7% > Processing Locus can_0_3217045_0:28-736 [* ] 7% > Processing Locus can_0_3218459_0:4-871 [** ] 8% > Processing Locus can_0_3270131_0:9-87 [** ] 9% > Processing Locus can_0_3270131_0:321-531 [** ] 10% > Processing Locus can_0_3270131_0:811-1101 [** ] 10% > Processing Locus can_0_3270131_0:1244-2050 [** ] 11% > Processing Locus ct_1_3082021_0:2-127 [*** ] 12% > Processing Locus ct_1_3132277_0:0-171 [*** ] 12% > Processing Locus ct_1_3133451_0:21-179 [*** ] 13% > Processing Locus ct_1_3133995_0:58-195 [*** ] 14%[Mon Apr 4 14:12:29 2011] Retrieving sequences for splices > Processing Locus ct_1_3241157_0:13-739 [*** ] 15% > Processing Locus ct_1_3247037_0:194-510 [*** ] 15% > Processing Locus ct_1_3302721_0:1261-1339 [**** ] 16% > Processing Locus edi_0_2744702_0:0-157 [**** ] 17% > Processing Locus edi_0_2871668_0:165-522 [**** ] 17% > Processing Locus edi_0_2889434_0:39-136 [**** ] 18% > Processing Locus edi_0_2889434_0:418-684 [**** ] 19% > Processing Locus edi_0_2918156_0:77-582 [***** ] 20% > Processing Locus edi_0_2932438_0:28-288 [***** ] 20% > Processing Locus hi_0_2773206_0:22-155 [***** ] 21% > Processing Locus hi_0_2778596_0:12-166 [***** ] 22% > Processing Locus hi_0_2939638_0:18-637 [***** ] 23% > Processing Locus kn_0_3613403_0:12-171 [***** ] 23% > Processing Locus kn_0_3819922_1:13-331 [****** ] 24% > Processing Locus kn_0_3819922_1:614-2016 [****** ] 25% > Processing Locus ler_0_3998410_0:5-163 [****** ] 25% > Processing Locus ler_0_4018856_0:7-183 [****** ] 26% > Processing Locus mt_0_4217716_0:0-181 [****** ] 27% > Processing Locus mt_0_4229662_0:0-197 [******* ] 28% > Processing Locus mt_0_4231054_0:4-188 [******* ] 28% > Processing Locus mt_0_4528444_1:561-1183 [******* ] 29% > Processing Locus no_0_2885444_0:25-107 [******* ] 30% > Processing Locus no_0_2905273_0:13-118 [******* ] 30% > Processing Locus no_0_2936769_0:4-152 [******* ] 31% > Processing Locus no_0_2956652_0:1-169 [******** ] 32% > Processing Locus no_0_3113578_1:318-832 [******** ] 33% > Processing Locus no_0_3116640_0:664-841 [******** ] 33% > Processing Locus no_0_3116640_0:1387-1837 [******** ] 34% > Processing Locus no_0_3128142_0:25-360 > Processing Locus no_0_3128142_0:565-824 [******** ] 35% > Processing Locus no_0_3128142_0:1149-1227 [********* ] 36% > Processing Locus no_0_3128142_0:1758-2107 [********* ] 37% > Processing Locus no_0_3128142_0:2482-2920 [********* ] 38% > Processing Locus oy_0_2966542_0:0-90 [********* ] 38% > Processing Locus oy_0_3001818_0:22-154 [********* ] 39% > Processing Locus oy_0_3098144_0:4-324 [********** ] 40% > Processing Locus oy_0_3121110_0:53-552 [********** ] 41% > Processing Locus oy_0_3148368_0:952-1030 [********** ] 41% > Processing Locus oy_0_3162092_0:171-1984 [********** ] 42% > Processing Locus po_0_3293868_0:0-117 [********** ] 43% > Processing Locus po_0_3299272_0:2-119 [********** ] 43% > Processing Locus po_0_3324652_0:0-132 [*********** ] 44% > Processing Locus po_0_3330421_0:4-130 [*********** ] 45% > Processing Locus po_0_3332479_0:0-136 [*********** ] 46% > Processing Locus po_0_3340213_0:5-86 [*********** ] 46% > Processing Locus po_0_3372769_0:2-165 [*********** ] 47% > Processing Locus po_0_3382155_0:1-133 [************ ] 48% > Processing Locus po_0_3507160_0:16-427 [************ ] 48% > Processing Locus po_0_3573778_0:350-1264 [************ ] 49% > Processing Locus po_0_3606391_0:946-1122 [************ ] 50% > Processing Locus po_0_3606391_0:1263-1580 [************ ] 51% > Processing Locus po_0_3606391_0:1711-1789 [************ ] 51% > Processing Locus po_0_3606391_0:2012-2401 [************* ] 52% > Processing Locus po_0_3606391_0:2572-2651 [************* ] 53% > Processing Locus po_0_3606391_0:2771-2849 [************* ] 53% > Processing Locus po_0_3606391_1:113-191 [************* ] 54% > Processing Locus po_0_3606391_1:293-497 [************* ] 55% > Processing Locus po_0_3606391_1:791-1003 [************** ] 56% > Processing Locus rsch_4_4032032_0:0-84 [************** ] 56% > Processing Locus rsch_4_4055167_0:0-108 [************** ] 57% > Processing Locus rsch_4_4110791_0:5-155 [************** ] 58% > Processing Locus rsch_4_4214541_0:3-223 [************** ] 58% > Processing Locus rsch_4_4219071_0:34-436 [************** ] 59% > Processing Locus rsch_4_4255532_0:3-287 [*************** ] 60% > Processing Locus rsch_4_4266550_0:6-1148 [*************** ] 61% > Processing Locus rsch_4_4292194_1:5-1133 [*************** ] 61% > Processing Locus rsch_4_4297142_0:42-233 [*************** ] 62% > Processing Locus sf_2_2459023_0:3-110 [*************** ] 63% > Processing Locus sf_2_2486157_0:0-118 [**************** ] 64% > Processing Locus sf_2_2524453_0:1-164 [**************** ] 64% > Processing Locus sf_2_2680171_0:9-1095 [**************** ] 65% > Processing Locus sf_2_2682779_0:593-991 [**************** ] 66% > Processing Locus sf_2_2701328_0:482-608 [**************** ] 66% > Processing Locus tsu_0_3036945_0:21-119 [**************** ] 67% > Processing Locus tsu_0_3211741_0:3-787 [***************** ] 68% > Processing Locus tsu_0_3215671_0:29-418 [***************** ] 69% > Processing Locus tsu_0_3215671_0:539-869 [***************** ] 69% > Processing Locus tsu_0_3229935_0:28-1235 [***************** ] 70% > Processing Locus wil_2_2834553_0:1-97 [***************** ] 71% > Processing Locus wil_2_2915899_0:15-94 [***************** ] 71% > Processing Locus wil_2_2925323_0:0-104 [****************** ] 72% > Processing Locus wil_2_3079625_0:11-604 [****************** ] 73% > Processing Locus wil_2_3090237_0:260-494 [****************** ] 74% > Processing Locus wil_2_3092619_0:1119-1197 [****************** ] 74% > Processing Locus ws_0_3182508_0:4-180 [****************** ] 75% > Processing Locus ws_0_3190963_0:49-127 [******************* ] 76% > Processing Locus ws_0_3326342_0:193-408 [******************* ] 76% > Processing Locus ws_0_3340488_0:210-1139 [******************* ] 77% > Processing Locus ws_0_3347582_0:157-573 [******************* ] 78% > Processing Locus ws_0_3347582_0:692-1306 [******************* ] 79% > Processing Locus ws_0_3372048_0:28-976 [******************* ] 79% > Processing Locus ws_0_3372048_0:1104-1235 [******************** ] 80% > Processing Locus ws_0_3381390_0:142-1279 [******************** ] 81% > Processing Locus ws_0_3381390_0:1604-1682 [******************** ] 82% > Processing Locus wu_0_2654219_0:18-147 [******************** ] 82% > Processing Locus wu_0_2678387_0:7-182 [******************** ] 83% > Processing Locus wu_0_2687576_0:15-170 [********************* ] 84% > Processing Locus wu_0_2824308_0:17-95 [********************* ] 84% > Processing Locus wu_0_2824308_0:269-797 [********************* ] 85% > Processing Locus zu_0_3118546_0:4-164 [********************* ] 86% > Processing Locus zu_0_3190435_0:20-303 [********************* ] 87% > Processing Locus zu_0_3238769_0:142-220 [********************* ] 87% > Processing Locus zu_0_3242889_0:12-213 [********************** ] 88% > Processing Locus zu_0_3255169_0:55-133 [********************** ] 89% > Processing Locus zu_0_3255169_0:409-1089 [********************** ] 89% > Processing Locus zu_0_3255503_0:1066-1394 [********************** ] 90% > Processing Locus zu_0_3259399_1:88-317 [********************** ] 91% > Processing Locus zu_0_3260131_0:166-400 [*********************** ] 92% > Processing Locus zu_0_3277661_0:334-911 [*********************** ] 92% > Processing Locus zu_0_3278243_0:24-102 [*********************** ] 93% > Processing Locus zu_0_3280213_0:764-922 [*********************** ] 94% > Processing Locus zu_0_3280213_0:1378-1500 [*********************** ] 94% > Processing Locus zu_0_3289907_1:271-826 [*********************** ] 95% > Processing Locus zu_0_3289907_1:1171-1262 [************************ ] 96% > Processing Locus zu_0_3289907_1:1382-1826 [************************ ] 97% > Processing Locus zu_0_3289907_1:1931-2668 [************************ ] 97% > Processing Locus zu_0_3289907_1:2825-3698 [************************ ] 98% > Processing Locus zu_0_3289907_1:3827-4516 [************************ ] 99% > Processed 139 loci. [*************************] 100% [14:12:29] Loading reference annotation and sequence [14:12:29] Learning bias parameters. > Processing Locus bur_0_1804399_0:9-113 [ ] 0% > Processing Locus bur_0_2020452_0:1-1386 [ ] 0% > Processing Locus bur_0_2025286_0:118-888 [ ] 1% > Processing Locus bur_0_2025286_0:1808-2504 [ ] 2% > Processing Locus bur_0_2032354_0:23-2009 [ ] 2% > Processing Locus can_0_3076940_0:5-132 [ ] 3% > Processing Locus can_0_3189753_0:0-204 [* ] 4% > Processing Locus can_0_3217045_0:28-736 [* ] 5% > Processing Locus can_0_3218459_0:4-871 [* ] 5% > Processing Locus ct_1_3082021_0:2-127 [* ] 6% > Processing Locus ct_1_3132277_0:0-171 [* ] 7% > Processing Locus ct_1_3133995_0:58-195 [* ] 7% > Processing Locus ct_1_3241157_0:13-739 [** ] 8% > Processing Locus edi_0_2744702_0:0-157 [** ] 9% > Processing Locus edi_0_2871668_0:165-522 [** ] 10% > Processing Locus edi_0_2918156_0:77-582 [** ] 10% > Processing Locus edi_0_2932438_0:28-288 [** ] 11% > Processing Locus hi_0_2778596_0:12-166 [*** ] 12% > Processing Locus hi_0_2939638_0:18-637 [*** ] 12% > Processing Locus kn_0_3819922_1:614-2016 [*** ] 13% > Processing Locus ler_0_4018856_0:7-183 [*** ] 14% > Processing Locus mt_0_4217716_0:0-181 [*** ] 15% > Processing Locus mt_0_4229662_0:0-197 [*** ] 15% > Processing Locus mt_0_4528444_1:633-1183 [**** ] 16% > Processing Locus no_0_2905273_0:13-118 [**** ] 17% > Processing Locus no_0_2936769_0:4-152 [**** ] 17% > Processing Locus no_0_2956652_0:1-169 [**** ] 18% > Processing Locus no_0_3113578_1:318-832 [**** ] 19% > Processing Locus oy_0_2966542_0:0-90 [***** ] 20% > Processing Locus oy_0_3001818_0:22-154 [***** ] 20% > Processing Locus oy_0_3098144_0:4-324 [***** ] 21% > Processing Locus oy_0_3121110_0:53-552 [***** ] 22% > Processing Locus oy_0_3162092_0:171-1984 [***** ] 23% > Processing Locus po_0_3293868_0:0-117 [***** ] 23% > Processing Locus po_0_3299272_0:2-119 [****** ] 24% > Processing Locus po_0_3324652_0:0-132 [****** ] 25% > Processing Locus po_0_3330421_0:4-130 [****** ] 25% > Processing Locus po_0_3332479_0:0-136 [****** ] 26% > Processing Locus po_0_3372769_0:2-165 [****** ] 27% > Processing Locus po_0_3382155_0:1-133 [******* ] 28% > Processing Locus po_0_3507160_0:23-427 [******* ] 28% > Processing Locus po_0_3573778_0:350-1264 [******* ] 29% > Processing Locus rsch_4_4055167_0:0-108 [******* ] 30% > Processing Locus rsch_4_4110791_0:5-155 [******* ] 30% > Processing Locus rsch_4_4214541_0:3-223 [******* ] 31% > Processing Locus rsch_4_4219071_0:34-436 [******** ] 32% > Processing Locus rsch_4_4255532_0:3-287 [******** ] 33% > Processing Locus rsch_4_4266550_0:6-1148 [******** ] 33% > Processing Locus rsch_4_4292194_1:5-1133 [******** ] 34% > Processing Locus rsch_4_4297142_0:42-233 [******** ] 35% > Processing Locus sf_2_2459023_0:3-110 [******** ] 35% > Processing Locus sf_2_2486157_0:0-118 [********* ] 36% > Processing Locus sf_2_2524453_0:1-164 [********* ] 37% > Processing Locus sf_2_2680171_0:9-1095 [********* ] 38% > Processing Locus tsu_0_3211741_0:3-787 [********* ] 38% > Processing Locus tsu_0_3215671_0:29-418 [********* ] 39% > Processing Locus tsu_0_3215671_0:539-869 [********** ] 40% > Processing Locus wil_2_2925323_0:0-104 [********** ] 41% > Processing Locus wil_2_3079625_0:11-604 [********** ] 41% > Processing Locus ws_0_3182508_0:4-180 [********** ] 42% > Processing Locus ws_0_3340488_0:210-1139 [********** ] 43% > Processing Locus ws_0_3347582_0:157-573 [********** ] 43% > Processing Locus ws_0_3347582_0:692-1306 [*********** ] 44% > Processing Locus ws_0_3381390_0:142-1279 [*********** ] 45% > Processing Locus wu_0_2654219_0:18-147 [*********** ] 46% > Processing Locus wu_0_2687576_0:15-170 [*********** ] 46% > Processing Locus wu_0_2824308_0:269-797 [*********** ] 47% > Processing Locus zu_0_3118546_0:4-164 [************ ] 48% > Processing Locus zu_0_3190435_0:20-303 [************ ] 48% > Processing Locus zu_0_3242889_0:12-213 [************ ] 49% > Processing Locus zu_0_3255169_0:409-1089 [************ ] 50% > Processing Locus zu_0_3255503_0:1066-1394 [************ ] 51% > Processing Locus zu_0_3259399_1:88-317 [************ ] 51% > Processing Locus zu_0_3277661_0:334-911 [************* ] 52% > Processing Locus zu_0_3289907_1:1382-1826 [************* ] 53% > Processing Locus zu_0_3289907_1:1931-2668 [************* ] 53% > Processing Locus zu_0_3289907_1:2825-3698 [************* ] 54% > Processing Locus zu_0_3289907_1:3827-4516 [************* ] 55% > Processed 78 loci. [*************************] 100% [14:12:29] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:9-113 [ ] 0% > Processing Locus bur_0_2020452_0:1-1386 [ ] 0% > Processing Locus bur_0_2025286_0:118-888 [ ] 1% > Processing Locus bur_0_2025286_0:1808-2504 [ ] 2% > Processing Locus bur_0_2032354_0:23-2009 [ ] 2% > Processing Locus can_0_3076940_0:5-132 [ ] 3% > Processing Locus can_0_3189753_0:0-204 [* ] 4% > Processing Locus can_0_3217045_0:28-736 [* ] 5% > Processing Locus can_0_3218459_0:4-871 [* ] 5% > Processing Locus ct_1_3082021_0:2-127 [* ] 6% > Processing Locus ct_1_3132277_0:0-171 [* ] 7% > Processing Locus ct_1_3133995_0:58-195 [* ] 7% > Processing Locus ct_1_3241157_0:13-739 [** ] 8% > Processing Locus edi_0_2744702_0:0-157 [** ] 9% > Processing Locus edi_0_2871668_0:165-522 [** ] 10% > Processing Locus edi_0_2918156_0:77-582 [** ] 10% > Processing Locus edi_0_2932438_0:28-288 [** ] 11% > Processing Locus hi_0_2778596_0:12-166 [*** ] 12% > Processing Locus hi_0_2939638_0:18-637 [*** ] 12% > Processing Locus kn_0_3819922_1:614-2016 [*** ] 13% > Processing Locus ler_0_4018856_0:7-183 [*** ] 14% > Processing Locus mt_0_4217716_0:0-181 [*** ] 15% > Processing Locus mt_0_4229662_0:0-197 [*** ] 15% > Processing Locus mt_0_4528444_1:633-1183 [**** ] 16% > Processing Locus no_0_2905273_0:13-118 [**** ] 17% > Processing Locus no_0_2936769_0:4-152 [**** ] 17% > Processing Locus no_0_2956652_0:1-169 [**** ] 18% > Processing Locus no_0_3113578_1:318-832 [**** ] 19% > Processing Locus oy_0_2966542_0:0-90 [***** ] 20% > Processing Locus oy_0_3001818_0:22-154 [***** ] 20% > Processing Locus oy_0_3098144_0:4-324 [***** ] 21% > Processing Locus oy_0_3121110_0:53-552 [***** ] 22% > Processing Locus oy_0_3162092_0:171-1984 [***** ] 23% > Processing Locus po_0_3293868_0:0-117 [***** ] 23% > Processing Locus po_0_3299272_0:2-119 [****** ] 24% > Processing Locus po_0_3324652_0:0-132 [****** ] 25% > Processing Locus po_0_3330421_0:4-130 [****** ] 25% > Processing Locus po_0_3332479_0:0-136 [****** ] 26% > Processing Locus po_0_3372769_0:2-165 [****** ] 27% > Processing Locus po_0_3382155_0:1-133 [******* ] 28% > Processing Locus po_0_3507160_0:23-427 [******* ] 28% > Processing Locus po_0_3573778_0:350-1264 [******* ] 29% > Processing Locus rsch_4_4055167_0:0-108 [******* ] 30% > Processing Locus rsch_4_4110791_0:5-155 [******* ] 30% > Processing Locus rsch_4_4214541_0:3-223 [******* ] 31% > Processing Locus rsch_4_4219071_0:34-436 [******** ] 32% > Processing Locus rsch_4_4255532_0:3-287 [******** ] 33% > Processing Locus rsch_4_4266550_0:6-1148 [******** ] 33% > Processing Locus rsch_4_4292194_1:5-1133 [******** ] 34% > Processing Locus rsch_4_4297142_0:42-233 [******** ] 35% > Processing Locus sf_2_2459023_0:3-110 [******** ] 35% > Processing Locus sf_2_2486157_0:0-118 [********* ] 36% > Processing Locus sf_2_2524453_0:1-164 [********* ] 37% > Processing Locus sf_2_2680171_0:9-1095 [********* ] 38% > Processing Locus tsu_0_3211741_0:3-787 [********* ] 38% > Processing Locus tsu_0_3215671_0:29-418 [********* ] 39% > Processing Locus tsu_0_3215671_0:539-869 [********** ] 40% > Processing Locus wil_2_2925323_0:0-104 [********** ] 41% > Processing Locus wil_2_3079625_0:11-604 [********** ] 41% > Processing Locus ws_0_3182508_0:4-180 [********** ] 42% > Processing Locus ws_0_3340488_0:210-1139 [********** ] 43% > Processing Locus ws_0_3347582_0:157-573 [********** ] 43% > Processing Locus ws_0_3347582_0:692-1306 [*********** ] 44% > Processing Locus ws_0_3381390_0:142-1279 [*********** ] 45% > Processing Locus wu_0_2654219_0:18-147 [*********** ] 46% > Processing Locus wu_0_2687576_0:15-170 [*********** ] 46% > Processing Locus wu_0_2824308_0:269-797 [*********** ] 47% > Processing Locus zu_0_3118546_0:4-164 [************ ] 48% > Processing Locus zu_0_3190435_0:20-303 [************ ] 48% > Processing Locus zu_0_3242889_0:12-213 [************ ] 49% > Processing Locus zu_0_3255169_0:409-1089 [************ ] 50% > Processing Locus zu_0_3255503_0:1066-1394 [************ ] 51% > Processing Locus zu_0_3259399_1:88-317 [************ ] 51% > Processing Locus zu_0_3277661_0:334-911 [************* ] 52% > Processing Locus zu_0_3289907_1:1382-1826 [************* ] 53% > Processing Locus zu_0_3289907_1:1931-2668 [************* ] 53% > Processing Locus zu_0_3289907_1:2825-3698 [************* ] 54% > Processing Locus zu_0_3289907_1:3827-4516 [************* ] 55% > Processed 78 loci. [*************************] 100% [Mon Apr 4 14:12:29 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:12:29 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:12:31 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:12:31 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:12:33 2011] Mapping reads against segment_juncs with Bowtie cufflinks -p 4 -o ./Rsch_4 -r it2.fa ./Rsch_4/accepted_hits.bam [14:12:34] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1863298_0:31-138 [ ] 0% > Processing Locus bur_0_1873494_0:1-187 [ ] 0% > Processing Locus bur_0_2025286_0:42-142 [ ] 0% > Processing Locus bur_0_2025286_0:254-1354 [ ] 0% > Processing Locus bur_0_2025286_0:1523-2624 [ ] 0% > Processing Locus can_0_3093852_0:6-116 [ ] 1% > Processing Locus can_0_3122480_0:2-143 [ ] 1% > Processing Locus can_0_3233581_0:38-459 [ ] 2% > Processing Locus can_0_3270131_0:22-286 [ ] 2% > Processing Locus can_0_3270131_0:484-730 [ ] 2% > Processing Locus can_0_3270131_0:838-920 [ ] 2% > Processing Locus can_0_3270131_0:1146-2229 [ ] 2% > Processing Locus ct_1_3082021_0:2-126 [ ] 2% > Processing Locus ct_1_3132277_0:61-166 [ ] 3% > Processing Locus ct_1_3241157_0:2-769 [ ] 3% > Processing Locus edi_0_2859720_0:143-525 [* ] 4% > Processing Locus edi_0_2871668_0:199-533 [* ] 4% > Processing Locus edi_0_2888586_0:7-1047 [* ] 5% > Processing Locus edi_0_2918156_0:11-582 [* ] 5% > Processing Locus edi_0_2932438_0:38-288 [* ] 5% > Processing Locus edi_0_2934714_0:229-308 [* ] 6% > Processing Locus edi_0_2934714_0:481-3363 [* ] 6% > Processing Locus edi_0_2934714_0:3757-4555 [* ] 6% > Processing Locus edi_0_2934714_0:4776-5139 [* ] 6% > Processing Locus edi_0_2934714_0:5270-5810 [* ] 6% > Processing Locus hi_0_2778596_0:29-161 [* ] 6% > Processing Locus hi_0_2795398_0:1-190 [* ] 7% > Processing Locus hi_0_2939638_0:9-639 [* ] 7% > Processing Locus kn_0_3594465_0:14-144 [* ] 7% > Processing Locus kn_0_3605300_0:2-80 [** ] 8% > Processing Locus kn_0_3613403_0:0-130 [** ] 8% > Processing Locus kn_0_3617271_0:22-180 [** ] 9% > Processing Locus kn_0_3626969_0:6-141 [** ] 9% > Processing Locus kn_0_3819922_1:24-344 [** ] 10% > Processing Locus kn_0_3819922_1:918-1901 [** ] 10% > Processing Locus ler_0_3998410_0:11-163 [** ] 10% > Processing Locus ler_0_4018856_0:2-186 [** ] 10% > Processing Locus mt_0_4193196_0:47-166 [** ] 11% > Processing Locus mt_0_4217716_0:0-186 [** ] 11% > Processing Locus mt_0_4229662_0:9-194 [*** ] 12% > Processing Locus mt_0_4230874_0:26-189 [*** ] 12% > Processing Locus mt_0_4528444_1:553-1234 [*** ] 13% > Processing Locus no_0_2885444_0:3-108 [*** ] 13% > Processing Locus no_0_2905273_0:9-119 [*** ] 13% > Processing Locus no_0_2934639_0:23-124 [*** ] 14% > Processing Locus no_0_2936769_0:0-152 [*** ] 14% > Processing Locus no_0_2951521_0:1-141 [*** ] 15% > Processing Locus no_0_2956652_0:0-178 [*** ] 15% > Processing Locus no_0_2959683_0:5-180 [*** ] 15% > Processing Locus no_0_3116640_0:472-1885 [**** ] 16% > Processing Locus no_0_3128142_0:10-1060 [**** ] 16% > Processing Locus no_0_3128142_0:1192-1392 [**** ] 16% > Processing Locus no_0_3128142_0:1671-2198 [**** ] 16% > Processing Locus no_0_3128142_0:2509-2882 [**** ] 16% > Processing Locus oy_0_3148368_0:195-273 [**** ] 17% > Processing Locus oy_0_3148368_0:638-716 [**** ] 17% > Processing Locus oy_0_3148368_0:1123-1201 [**** ] 17% > Processing Locus oy_0_3162092_0:249-1985 [**** ] 17% > Processing Locus po_0_3299272_0:8-119 [**** ] 18% > Processing Locus po_0_3332479_0:0-136 [**** ] 18% > Processing Locus po_0_3372769_0:1-163 [**** ] 18% > Processing Locus po_0_3382155_0:71-172 [**** ] 19% > Processing Locus rsch_4_4032032_0:2-86 [**** ] 19% > Processing Locus rsch_4_4034850_0:0-100 [***** ] 20% > Processing Locus rsch_4_4055167_0:4-110 [***** ] 20% > Processing Locus rsch_4_4085063_0:0-120 [***** ] 21% > Processing Locus rsch_4_4091241_0:3-124 [***** ] 21% > Processing Locus rsch_4_4107621_0:4-155 [***** ] 21% > Processing Locus rsch_4_4110791_0:5-155 [***** ] 22% > Processing Locus rsch_4_4118145_0:5-156 [***** ] 22% > Processing Locus rsch_4_4214541_0:1-234 [***** ] 23% > Processing Locus rsch_4_4219071_0:0-429 [***** ] 23% > Processing Locus rsch_4_4255532_0:15-287 [***** ] 23% > Processing Locus rsch_4_4266550_0:5-1157 [****** ] 24% > Processing Locus rsch_4_4275442_0:6-347 [****** ] 24% > Processing Locus rsch_4_4275442_0:516-594 [****** ] 24% > Processing Locus rsch_4_4277288_0:7-1339 [****** ] 25% > Processing Locus rsch_4_4292194_1:2-1129 [****** ] 25% > Processing Locus rsch_4_4297142_0:37-297 [****** ] 26% > Processing Locus sf_2_2459023_0:1-110 [****** ] 26% > Processing Locus sf_2_2488391_0:0-127 [****** ] 26% > Processing Locus sf_2_2524453_0:0-165 [****** ] 27% > Processing Locus sf_2_2680171_0:75-694 [****** ] 27% > Processing Locus sf_2_2680171_0:1058-1167 [****** ] 27% > Processing Locus sf_2_2687774_0:625-819 [******* ] 28% > Processing Locus wil_2_2834553_0:0-78 [******* ] 28% > Processing Locus wil_2_3050523_0:53-231 [******* ] 28% > Processing Locus wil_2_3054893_0:27-570 [******* ] 29% > Processing Locus wil_2_3063473_0:640-718 [******* ] 29% > Processing Locus wil_2_3087183_0:547-625 [******* ] 30% > Processing Locus wil_2_3092619_0:364-442 [******* ] 30% > Processing Locus wil_2_3092619_0:805-883 [******* ] 30% > Processing Locus wil_2_3092619_0:1290-1368 [******* ] 30% > Processing Locus ws_0_3190679_0:2-146 [******* ] 31% > Processing Locus ws_0_3326342_0:0-408 [******* ] 31% > Processing Locus ws_0_3340488_0:205-1139 [******* ] 31% > Processing Locus ws_0_3371988_0:14-99 [******** ] 32% > Processing Locus ws_0_3371988_0:1259-1337 [******** ] 32% > Processing Locus ws_0_3371988_0:2192-2270 [******** ] 32% > Processing Locus ws_0_3380934_0:2-211 [******** ] 32% > Processing Locus ws_0_3381390_0:8-1722 [******** ] 33% > Processing Locus wu_0_2654219_0:0-149 [******** ] 33% > Processing Locus wu_0_2678387_0:8-171 [******** ] 34% > Processing Locus wu_0_2679395_0:1-133 [******** ] 34% > Processing Locus wu_0_2687576_0:23-170 [******** ] 34% > Processing Locus zu_0_3022629_0:4-82 [******** ] 35% > Processing Locus zu_0_3082201_0:1-143 [******** ] 35% > Processing Locus zu_0_3118546_0:3-169 [********* ] 36% > Processing Locus zu_0_3238769_0:185-263 [********* ] 36% > Processing Locus zu_0_3242889_0:20-213 [********* ] 36% > Processing Locus zu_0_3255503_0:1140-1379 [********* ] 37% > Processing Locus zu_0_3277661_0:261-910 [********* ] 37% > Processed 112 loci. [*************************] 100% > Map Properties: > Total Map Mass: 4686.79 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:12:34] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1863298_0:31-138 [ ] 0% > Processing Locus bur_0_1873494_0:1-187 [ ] 0% > Processing Locus bur_0_2025286_0:42-142 [ ] 1% > Processing Locus bur_0_2025286_0:254-1354 [ ] 2% > Processing Locus bur_0_2025286_0:1523-2624 [ ] 3% > Processing Locus can_0_3093852_0:6-116 [* ] 4% > Processing Locus can_0_3122480_0:2-143 [* ] 5% > Processing Locus can_0_3233581_0:38-459 [* ] 6% > Processing Locus can_0_3270131_0:22-286 [* ] 7% > Processing Locus can_0_3270131_0:484-730 [** ] 8% > Processing Locus can_0_3270131_0:838-920 [** ] 8% > Processing Locus can_0_3270131_0:1146-2229 [** ] 9% > Processing Locus ct_1_3082021_0:2-126 [** ] 10% > Processing Locus ct_1_3132277_0:61-166 [** ] 11% > Processing Locus ct_1_3241157_0:2-769 [*** ] 12% > Processing Locus edi_0_2859720_0:143-525 [*** ] 13% > Processing Locus edi_0_2871668_0:199-533 [*** ] 14% > Processing Locus edi_0_2888586_0:7-1047 [*** ] 15% > Processing Locus edi_0_2918156_0:11-582 [**** ] 16% > Processing Locus edi_0_2932438_0:38-288 [**** ] 16% > Processing Locus edi_0_2934714_0:229-308 [**** ] 17% > Processing Locus edi_0_2934714_0:481-3363 [**** ] 18% > Processing Locus edi_0_2934714_0:3757-4555 [**** ] 19% > Processing Locus edi_0_2934714_0:4776-5139 [***** ] 20% > Processing Locus edi_0_2934714_0:5270-5810 [***** ] 21% > Processing Locus hi_0_2778596_0:29-161 [***** ] 22% > Processing Locus hi_0_2795398_0:1-190 [***** ] 23%[Mon Apr 4 14:12:34 2011] Joining segment hits > Processing Locus hi_0_2939638_0:9-639 [****** ] 24% > Processing Locus kn_0_3594465_0:14-144 [****** ] 25% > Processing Locus kn_0_3605300_0:2-80 [****** ] 25% > Processing Locus kn_0_3613403_0:0-130 [****** ] 26% > Processing Locus kn_0_3617271_0:22-180 [****** ] 27% > Processing Locus kn_0_3626969_0:6-141 [******* ] 28% > Processing Locus kn_0_3819922_1:24-344 [******* ] 29% > Processing Locus kn_0_3819922_1:918-1901 [******* ] 30% > Processing Locus ler_0_3998410_0:11-163 [******* ] 31% > Processing Locus ler_0_4018856_0:2-186 [******** ] 32% > Processing Locus mt_0_4193196_0:47-166 [******** ] 33% > Processing Locus mt_0_4217716_0:0-186 [******** ] 33% > Processing Locus mt_0_4229662_0:9-194 [******** ] 34% > Processing Locus mt_0_4230874_0:26-189 [******** ] 35% > Processing Locus mt_0_4528444_1:553-1234 [********* ] 36% > Processing Locus no_0_2885444_0:3-108 [********* ] 37% > Processing Locus no_0_2905273_0:9-119 [********* ] 38% > Processing Locus no_0_2934639_0:23-124 [********* ] 39% > Processing Locus no_0_2936769_0:0-152 [********** ] 40% > Processing Locus no_0_2951521_0:1-141 [********** ] 41% > Processing Locus no_0_2956652_0:0-178 [********** ] 41% > Processing Locus no_0_2959683_0:5-180 [********** ] 42% > Processing Locus no_0_3116640_0:472-1885 [********** ] 43% > Processing Locus no_0_3128142_0:10-1060 [*********** ] 44% > Processing Locus no_0_3128142_0:1192-1392 [*********** ] 45% > Processing Locus no_0_3128142_0:1671-2198 [*********** ] 46% > Processing Locus no_0_3128142_0:2509-2882 [*********** ] 47% > Processing Locus oy_0_3148368_0:195-273 [************ ] 48% > Processing Locus oy_0_3148368_0:638-716 [************ ] 49% > Processing Locus oy_0_3148368_0:1123-1201 [************ ] 50% > Processing Locus oy_0_3162092_0:249-1985 [************ ] 50% > Processing Locus po_0_3299272_0:8-119 [************ ] 51% > Processing Locus po_0_3332479_0:0-136 [************* ] 52% > Processing Locus po_0_3372769_0:1-163 [************* ] 53% > Processing Locus po_0_3382155_0:71-172 [************* ] 54% > Processing Locus rsch_4_4032032_0:2-86 [************* ] 55% > Processing Locus rsch_4_4034850_0:0-100 [************** ] 56% > Processing Locus rsch_4_4055167_0:4-110 [************** ] 57% > Processing Locus rsch_4_4085063_0:0-120 [************** ] 58% > Processing Locus rsch_4_4091241_0:3-124 [************** ] 58% > Processing Locus rsch_4_4107621_0:4-155 [************** ] 59% > Processing Locus rsch_4_4110791_0:5-155 [*************** ] 60% > Processing Locus rsch_4_4118145_0:5-156 [*************** ] 61% > Processing Locus rsch_4_4214541_0:1-234 [*************** ] 62% > Processing Locus rsch_4_4219071_0:0-429 [*************** ] 63% > Processing Locus rsch_4_4255532_0:15-287 [**************** ] 64% > Processing Locus rsch_4_4266550_0:5-1157 [**************** ] 65% > Processing Locus rsch_4_4275442_0:6-347 [**************** ] 66% > Processing Locus rsch_4_4275442_0:516-594 [**************** ] 66% > Processing Locus rsch_4_4277288_0:7-1339 [**************** ] 67% > Processing Locus rsch_4_4292194_1:2-1129 [***************** ] 68% > Processing Locus rsch_4_4297142_0:37-297 [***************** ] 69% > Processing Locus sf_2_2459023_0:1-110 [***************** ] 70% > Processing Locus sf_2_2488391_0:0-127 [***************** ] 71% > Processing Locus sf_2_2524453_0:0-165 [****************** ] 72% > Processing Locus sf_2_2680171_0:75-694 [****************** ] 73% > Processing Locus sf_2_2680171_0:1058-1167 [****************** ] 74% > Processing Locus sf_2_2687774_0:625-819 [****************** ] 75% > Processing Locus wil_2_2834553_0:0-78 [****************** ] 75% > Processing Locus wil_2_3050523_0:53-231 [******************* ] 76% > Processing Locus wil_2_3054893_0:27-570 [******************* ] 77% > Processing Locus wil_2_3063473_0:640-718 [******************* ] 78% > Processing Locus wil_2_3087183_0:547-625 [******************* ] 79% > Processing Locus wil_2_3092619_0:364-442 [******************** ] 80% > Processing Locus wil_2_3092619_0:805-883 [******************** ] 81% > Processing Locus wil_2_3092619_0:1290-1368 [******************** ] 82% > Processing Locus ws_0_3190679_0:2-146 [******************** ] 83% > Processing Locus ws_0_3326342_0:0-408 [******************** ] 83% > Processing Locus ws_0_3340488_0:205-1139 [********************* ] 84% > Processing Locus ws_0_3371988_0:14-99 [********************* ] 85% > Processing Locus ws_0_3371988_0:1259-1337 [********************* ] 86% > Processing Locus ws_0_3371988_0:2192-2270 [********************* ] 87% > Processing Locus ws_0_3380934_0:2-211 [********************** ] 88% > Processing Locus ws_0_3381390_0:8-1722 [********************** ] 89% > Processing Locus wu_0_2654219_0:0-149 [********************** ] 90% > Processing Locus wu_0_2678387_0:8-171 [********************** ] 91% > Processing Locus wu_0_2679395_0:1-133 [********************** ] 91% > Processing Locus wu_0_2687576_0:23-170 [*********************** ] 92% > Processing Locus zu_0_3022629_0:4-82 [*********************** ] 93% > Processing Locus zu_0_3082201_0:1-143 [*********************** ] 94% > Processing Locus zu_0_3118546_0:3-169 [*********************** ] 95% > Processing Locus zu_0_3238769_0:185-263 [************************ ] 96% > Processing Locus zu_0_3242889_0:20-213 [************************ ] 97% > Processing Locus zu_0_3255503_0:1140-1379 [************************ ] 98% > Processing Locus zu_0_3277661_0:261-910 [************************ ] 99% > Processed 112 loci. [*************************] 100% [14:12:34] Loading reference annotation and sequence [14:12:34] Learning bias parameters. > Processing Locus bur_0_1863298_0:31-138 [ ] 0% > Processing Locus bur_0_1873494_0:1-187 [ ] 0% > Processing Locus bur_0_2025286_0:254-1354 [ ] 1% > Processing Locus bur_0_2025286_0:1523-2624 [ ] 2% > Processing Locus can_0_3122480_0:2-143 [ ] 3% > Processing Locus can_0_3233581_0:38-459 [* ] 4% > Processing Locus can_0_3270131_0:1146-2229 [* ] 5% > Processing Locus ct_1_3082021_0:2-126 [* ] 6% > Processing Locus ct_1_3132277_0:61-166 [* ] 7% > Processing Locus ct_1_3241157_0:22-769 [** ] 8% > Processing Locus edi_0_2859720_0:143-525 [** ] 8% > Processing Locus edi_0_2871668_0:199-533 [** ] 9% > Processing Locus edi_0_2888586_0:7-1047 [** ] 10% > Processing Locus edi_0_2918156_0:11-582 [** ] 11% > Processing Locus edi_0_2932438_0:38-288 [*** ] 12% > Processing Locus edi_0_2934714_0:481-3363 [*** ] 13% > Processing Locus edi_0_2934714_0:3757-4555 [*** ] 14% > Processing Locus edi_0_2934714_0:5270-5810 [*** ] 15% > Processing Locus hi_0_2795398_0:1-190 [**** ] 16% > Processing Locus hi_0_2939638_0:9-639 [**** ] 16% > Processing Locus kn_0_3613403_0:0-130 [**** ] 17% > Processing Locus kn_0_3617271_0:22-180 [**** ] 18% > Processing Locus kn_0_3819922_1:918-1901 [**** ] 19% > Processing Locus ler_0_3998410_0:11-163 [***** ] 20% > Processing Locus ler_0_4018856_0:2-186 [***** ] 21% > Processing Locus mt_0_4193196_0:47-166 [***** ] 22% > Processing Locus mt_0_4217716_0:0-186 [***** ] 23% > Processing Locus mt_0_4229662_0:9-194 [****** ] 24% > Processing Locus mt_0_4230874_0:26-189 [****** ] 25% > Processing Locus mt_0_4528444_1:553-1234 [****** ] 25% > Processing Locus no_0_2885444_0:3-108 [****** ] 26% > Processing Locus no_0_2905273_0:9-119 [****** ] 27% > Processing Locus no_0_2934639_0:23-124 [******* ] 28% > Processing Locus no_0_2936769_0:0-152 [******* ] 29% > Processing Locus no_0_2956652_0:0-178 [******* ] 30% > Processing Locus no_0_2959683_0:5-180 [******* ] 31% > Processing Locus no_0_3116640_0:472-1885 [******** ] 32% > Processing Locus no_0_3128142_0:10-1060 [******** ] 33% > Processing Locus no_0_3128142_0:1671-2198 [******** ] 33% > Processing Locus no_0_3128142_0:2509-2882 [******** ] 34% > Processing Locus oy_0_3162092_0:249-1985 [******** ] 35% > Processing Locus po_0_3299272_0:8-119 [********* ] 36% > Processing Locus po_0_3332479_0:0-136 [********* ] 37% > Processing Locus po_0_3372769_0:1-163 [********* ] 38% > Processing Locus rsch_4_4032032_0:2-86 [********* ] 39% > Processing Locus rsch_4_4034850_0:0-100 [********** ] 40% > Processing Locus rsch_4_4055167_0:4-110 [********** ] 41% > Processing Locus rsch_4_4085063_0:0-120 [********** ] 41% > Processing Locus rsch_4_4107621_0:4-155 [********** ] 42% > Processing Locus rsch_4_4110791_0:5-155 [********** ] 43% > Processing Locus rsch_4_4214541_0:1-234 [*********** ] 44% > Processing Locus rsch_4_4255532_0:15-287 [*********** ] 45% > Processing Locus rsch_4_4266550_0:5-1157 [*********** ] 46% > Processing Locus rsch_4_4277288_0:7-1339 [*********** ] 47% > Processing Locus rsch_4_4292194_1:2-1129 [************ ] 48% > Processing Locus rsch_4_4297142_0:37-297 [************ ] 49% > Processing Locus sf_2_2459023_0:1-110 [************ ] 50% > Processing Locus sf_2_2488391_0:0-127 [************ ] 50% > Processing Locus sf_2_2524453_0:0-165 [************ ] 51% > Processing Locus sf_2_2680171_0:75-694 [************* ] 52% > Processing Locus wil_2_3054893_0:27-570 [************* ] 53% > Processing Locus ws_0_3340488_0:206-1139 [************* ] 54% > Processing Locus ws_0_3380934_0:2-211 [************* ] 55% > Processing Locus ws_0_3381390_0:8-1722 [************** ] 56% > Processing Locus wu_0_2654219_0:0-149 [************** ] 57% > Processing Locus wu_0_2679395_0:1-133 [************** ] 58% > Processing Locus wu_0_2687576_0:23-170 [************** ] 58% > Processing Locus zu_0_3082201_0:1-143 [************** ] 59% > Processing Locus zu_0_3118546_0:3-169 [*************** ] 60% > Processing Locus zu_0_3242889_0:20-213 [*************** ] 61% > Processing Locus zu_0_3255503_0:1140-1379 [*************** ] 62% > Processing Locus zu_0_3277661_0:261-910 [*************** ] 63% > Processed 72 loci. [*************************] 100% [14:12:34] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1863298_0:31-138 [ ] 0% > Processing Locus bur_0_1873494_0:1-187 [ ] 0% > Processing Locus bur_0_2025286_0:254-1354 [ ] 1% > Processing Locus bur_0_2025286_0:1523-2624 [ ] 2% > Processing Locus can_0_3122480_0:2-143 [ ] 3% > Processing Locus can_0_3233581_0:38-459 [* ] 4% > Processing Locus can_0_3270131_0:1146-2229 [* ] 5% > Processing Locus ct_1_3082021_0:2-126 [* ] 6% > Processing Locus ct_1_3132277_0:61-166 [* ] 7% > Processing Locus ct_1_3241157_0:22-769 [** ] 8% > Processing Locus edi_0_2859720_0:143-525 [** ] 8% > Processing Locus edi_0_2871668_0:199-533 [** ] 9% > Processing Locus edi_0_2888586_0:7-1047 [** ] 10% > Processing Locus edi_0_2918156_0:11-582 [** ] 11% > Processing Locus edi_0_2932438_0:38-288 [*** ] 12% > Processing Locus edi_0_2934714_0:481-3363 [*** ] 13% > Processing Locus edi_0_2934714_0:3757-4555 [*** ] 14% > Processing Locus edi_0_2934714_0:5270-5810 [*** ] 15% > Processing Locus hi_0_2795398_0:1-190 [**** ] 16% > Processing Locus hi_0_2939638_0:9-639 [**** ] 16% > Processing Locus kn_0_3613403_0:0-130 [**** ] 17% > Processing Locus kn_0_3617271_0:22-180 [**** ] 18% > Processing Locus kn_0_3819922_1:918-1901 [**** ] 19% > Processing Locus ler_0_3998410_0:11-163 [***** ] 20% > Processing Locus ler_0_4018856_0:2-186 [***** ] 21% > Processing Locus mt_0_4193196_0:47-166 [***** ] 22% > Processing Locus mt_0_4217716_0:0-186 [***** ] 23% > Processing Locus mt_0_4229662_0:9-194 [****** ] 24% > Processing Locus mt_0_4230874_0:26-189 [****** ] 25% > Processing Locus mt_0_4528444_1:553-1234 [****** ] 25% > Processing Locus no_0_2885444_0:3-108 [****** ] 26% > Processing Locus no_0_2905273_0:9-119 [****** ] 27% > Processing Locus no_0_2934639_0:23-124 [******* ] 28% > Processing Locus no_0_2936769_0:0-152 [******* ] 29% > Processing Locus no_0_2956652_0:0-178 [******* ] 30% > Processing Locus no_0_2959683_0:5-180 [******* ] 31% > Processing Locus no_0_3116640_0:472-1885 [******** ] 32% > Processing Locus no_0_3128142_0:10-1060 [******** ] 33% > Processing Locus no_0_3128142_0:1671-2198 [******** ] 33% > Processing Locus no_0_3128142_0:2509-2882 [******** ] 34% > Processing Locus oy_0_3162092_0:249-1985 [******** ] 35% > Processing Locus po_0_3299272_0:8-119 [********* ] 36% > Processing Locus po_0_3332479_0:0-136 [********* ] 37% > Processing Locus po_0_3372769_0:1-163 [********* ] 38% > Processing Locus rsch_4_4032032_0:2-86 [********* ] 39% > Processing Locus rsch_4_4034850_0:0-100 [********** ] 40% > Processing Locus rsch_4_4055167_0:4-110 [********** ] 41% > Processing Locus rsch_4_4085063_0:0-120 [********** ] 41% > Processing Locus rsch_4_4107621_0:4-155 [********** ] 42% > Processing Locus rsch_4_4110791_0:5-155 [********** ] 43% > Processing Locus rsch_4_4214541_0:1-234 [*********** ] 44% > Processing Locus rsch_4_4255532_0:15-287 [*********** ] 45% > Processing Locus rsch_4_4266550_0:5-1157 [*********** ] 46% > Processing Locus rsch_4_4277288_0:7-1339 [*********** ] 47% > Processing Locus rsch_4_4292194_1:2-1129 [************ ] 48% > Processing Locus rsch_4_4297142_0:37-297 [************ ] 49% > Processing Locus sf_2_2459023_0:1-110 [************ ] 50% > Processing Locus sf_2_2488391_0:0-127 [************ ] 50% > Processing Locus sf_2_2524453_0:0-165 [************ ] 51% > Processing Locus sf_2_2680171_0:75-694 [************* ] 52% > Processing Locus wil_2_3054893_0:27-570 [************* ] 53% > Processing Locus ws_0_3340488_0:206-1139 [************* ] 54% > Processing Locus ws_0_3380934_0:2-211 [************* ] 55% > Processing Locus ws_0_3381390_0:8-1722 [************** ] 56% > Processing Locus wu_0_2654219_0:0-149 [************** ] 57% > Processing Locus wu_0_2679395_0:1-133 [************** ] 58% > Processing Locus wu_0_2687576_0:23-170 [************** ] 58% > Processing Locus zu_0_3082201_0:1-143 [************** ] 59% > Processing Locus zu_0_3118546_0:3-169 [*************** ] 60% > Processing Locus zu_0_3242889_0:20-213 [*************** ] 61% > Processing Locus zu_0_3255503_0:1140-1379 [*************** ] 62% > Processing Locus zu_0_3277661_0:261-910 [*************** ] 63% > Processed 72 loci. [*************************] 100% [Mon Apr 4 14:12:35 2011] Joining segment hits [Mon Apr 4 14:12:35 2011] Reporting output tracks [Mon Apr 4 14:12:36 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:12:36 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:11 elapsed] ----------------------------------------------- Run complete [00:01:06 elapsed] [Mon Apr 4 14:12:39 2011] Mapping reads against it2.fa with Bowtie(2/3) cufflinks -p 4 -o ./Tsu_0 -r it2.fa ./Tsu_0/accepted_hits.bam [14:12:41] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:0-113 [ ] 0% > Processing Locus bur_0_1856286_0:22-100 [ ] 0% > Processing Locus bur_0_1873494_0:14-188 [ ] 0% > Processing Locus bur_0_2020452_0:2-1305 [ ] 1% > Processing Locus bur_0_2020452_0:1501-1579 [ ] 1% > Processing Locus bur_0_2020452_0:1891-1969 [ ] 1% > Processing Locus bur_0_2020452_0:2093-2245 [ ] 1% > Processing Locus can_0_3076940_0:0-140 [ ] 1% > Processing Locus can_0_3270131_0:357-531 [ ] 2% > Processing Locus can_0_3270131_0:1616-1694 [ ] 2% > Processing Locus can_0_3270131_0:1857-2260 [ ] 2% > Processing Locus ct_1_3082021_0:1-129 [ ] 2% > Processing Locus ct_1_3241157_0:4-734 [ ] 2% > Processing Locus ct_1_3247037_0:426-504 [ ] 3% > Processing Locus ct_1_3302721_0:1261-1339 [ ] 3% > Processing Locus edi_0_2859720_0:136-523 [* ] 4% > Processing Locus edi_0_2871668_0:156-529 [* ] 4% > Processing Locus edi_0_2891226_0:728-806 [* ] 5% > Processing Locus edi_0_2918156_0:78-582 [* ] 5% > Processing Locus edi_0_2932438_0:9-289 [* ] 5% > Processing Locus hi_0_2778596_0:17-168 [* ] 6% > Processing Locus hi_0_2795398_0:0-188 [* ] 6% > Processing Locus kn_0_3613403_0:4-121 [* ] 7% > Processing Locus ler_0_3998410_0:11-163 [* ] 7% > Processing Locus ler_0_4018856_0:36-183 [* ] 7% > Processing Locus ler_0_4224097_0:1212-1290 [** ] 8% > Processing Locus mt_0_4213448_0:13-181 [** ] 8% > Processing Locus mt_0_4217716_0:9-183 [** ] 9% > Processing Locus mt_0_4229662_0:1-197 [** ] 9% > Processing Locus mt_0_4230874_0:30-198 [** ] 10% > Processing Locus mt_0_4231054_0:0-198 [** ] 10% > Processing Locus no_0_2885444_0:24-105 [** ] 10% > Processing Locus no_0_2905273_0:26-121 [** ] 11% > Processing Locus no_0_2956652_0:7-172 [** ] 11% > Processing Locus no_0_3101262_0:250-732 [*** ] 12% > Processing Locus oy_0_2965192_0:18-123 [*** ] 12% > Processing Locus oy_0_3001818_0:50-154 [*** ] 13% > Processing Locus oy_0_3121110_0:373-451 [*** ] 13% > Processing Locus oy_0_3148368_0:585-663 [*** ] 13% > Processing Locus oy_0_3162092_0:1560-1638 [*** ] 14% > Processing Locus po_0_3299272_0:0-119 [*** ] 14% > Processing Locus po_0_3372769_0:1-165 [*** ] 15% > Processing Locus po_0_3507160_0:2-438 [*** ] 15% > Processing Locus po_0_3606391_0:1125-1289 [*** ] 15% > Processing Locus po_0_3606391_0:1408-1753 [*** ] 15% > Processing Locus po_0_3606391_0:1976-2892 [*** ] 15% > Processing Locus po_0_3606391_1:29-119 [**** ] 16% > Processing Locus po_0_3606391_1:686-976 [**** ] 16% > Processing Locus rsch_4_4032032_0:0-84 [**** ] 16% > Processing Locus rsch_4_4034850_0:0-100 [**** ] 17% > Processing Locus rsch_4_4055167_0:0-110 [**** ] 17% > Processing Locus rsch_4_4214541_0:3-233 [**** ] 18% > Processing Locus rsch_4_4255532_0:0-287 [**** ] 18% > Processing Locus rsch_4_4275442_0:33-624 [**** ] 18% > Processing Locus rsch_4_4277288_0:3-1369 [**** ] 19% > Processing Locus rsch_4_4277566_0:317-535 [**** ] 19% > Processing Locus rsch_4_4277566_0:1008-1110 [**** ] 19% > Processing Locus rsch_4_4292194_1:1-1115 [***** ] 20% > Processing Locus rsch_4_4297142_0:31-300 [***** ] 20% > Processing Locus sf_2_2459023_0:3-110 [***** ] 21% > Processing Locus sf_2_2486157_0:0-118 [***** ] 21% > Processing Locus sf_2_2524453_0:1-159 [***** ] 21% > Processing Locus sf_2_2687786_0:17-2176 [***** ] 22% > Processing Locus sf_2_2701328_0:484-594 [***** ] 22% > Processing Locus tsu_0_2970253_0:2-102 [***** ] 23% > Processing Locus tsu_0_3036945_0:15-120 [***** ] 23% > Processing Locus tsu_0_3135135_0:117-195 [***** ] 23% > Processing Locus tsu_0_3175121_0:23-426 [****** ] 24% > Processing Locus tsu_0_3175121_0:595-704 [****** ] 24% > Processing Locus tsu_0_3208747_0:13-401 [****** ] 24% > Processing Locus tsu_0_3211741_0:3-780 [****** ] 25% > Processing Locus tsu_0_3212935_0:0-1034 [****** ] 25% > Processing Locus tsu_0_3215671_0:25-500 [****** ] 26% > Processing Locus tsu_0_3215671_0:644-855 [****** ] 26% > Processing Locus tsu_0_3215737_0:6-1108 [****** ] 26% > Processing Locus tsu_0_3215821_0:188-1104 [****** ] 26% > Processing Locus tsu_0_3242833_1:29-912 [****** ] 27% > Processing Locus wil_2_2834553_0:25-103 [****** ] 27% > Processing Locus wil_2_2915899_0:45-166 [******* ] 28% > Processing Locus wil_2_3050523_0:15-273 [******* ] 28% > Processing Locus wil_2_3054893_0:454-543 [******* ] 28% > Processing Locus wil_2_3088151_0:31-181 [******* ] 29% > Processing Locus wil_2_3088151_0:645-1637 [******* ] 29% > Processing Locus wil_2_3088151_0:1838-1916 [******* ] 29% > Processing Locus wil_2_3092619_0:752-830 [******* ] 29% > Processing Locus ws_0_3182508_0:3-130 [******* ] 30% > Processing Locus ws_0_3373604_0:1594-2858 [******* ] 30% > Processing Locus ws_0_3381390_0:11-1727 [******* ] 31% > Processing Locus wu_0_2654219_0:0-137 [******* ] 31% > Processing Locus wu_0_2678387_0:6-169 [******* ] 31% > Processing Locus wu_0_2687576_0:21-170 [******** ] 32% > Processing Locus zu_0_3075813_0:17-97 [******** ] 32% > Processing Locus zu_0_3082201_0:0-148 [******** ] 33% > Processing Locus zu_0_3092045_0:4-146 [******** ] 33% > Processing Locus zu_0_3190435_0:25-103 [******** ] 34% > Processing Locus zu_0_3242889_0:3-330 [******** ] 34% > Processing Locus zu_0_3255503_0:1081-1359 [******** ] 34% > Processing Locus zu_0_3277661_0:331-910 [******** ] 35% > Processing Locus zu_0_3280213_0:257-1196 [******** ] 35% > Processing Locus zu_0_3280213_0:1342-2096 [******** ] 35% > Processed 100 loci. [*************************] 100% > Map Properties: > Total Map Mass: 6363.83 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:12:42] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:0-113 [ ] 0% > Processing Locus bur_0_1856286_0:22-100 [ ] 1% > Processing Locus bur_0_1873494_0:14-188 [ ] 2% > Processing Locus bur_0_2020452_0:2-1305 [ ] 3% > Processing Locus bur_0_2020452_0:1501-1579 [* ] 4% > Processing Locus bur_0_2020452_0:1891-1969 [* ] 5% > Processing Locus bur_0_2020452_0:2093-2245 [* ] 6% > Processing Locus can_0_3076940_0:0-140 [* ] 7% > Processing Locus can_0_3270131_0:357-531 [** ] 8% > Processing Locus can_0_3270131_0:1616-1694 [** ] 9% > Processing Locus can_0_3270131_0:1857-2260 [** ] 10% > Processing Locus ct_1_3082021_0:1-129 [** ] 11% > Processing Locus ct_1_3241157_0:4-734 [*** ] 12% > Processing Locus ct_1_3247037_0:426-504 [*** ] 13% > Processing Locus ct_1_3302721_0:1261-1339 [*** ] 14% > Processing Locus edi_0_2859720_0:136-523 [*** ] 15% > Processing Locus edi_0_2871668_0:156-529 [**** ] 16% > Processing Locus edi_0_2891226_0:728-806 [**** ] 17% > Processing Locus edi_0_2918156_0:78-582 [**** ] 18% > Processing Locus edi_0_2932438_0:9-289 [**** ] 19% > Processing Locus hi_0_2778596_0:17-168 [***** ] 20% > Processing Locus hi_0_2795398_0:0-188 [***** ] 21% > Processing Locus kn_0_3613403_0:4-121 [***** ] 22% > Processing Locus ler_0_3998410_0:11-163 [***** ] 23% > Processing Locus ler_0_4018856_0:36-183 [****** ] 24% > Processing Locus ler_0_4224097_0:1212-1290 [****** ] 25% > Processing Locus mt_0_4213448_0:13-181 [****** ] 26% > Processing Locus mt_0_4217716_0:9-183 [****** ] 27% > Processing Locus mt_0_4229662_0:1-197 [******* ] 28% > Processing Locus mt_0_4230874_0:30-198 [******* ] 29% > Processing Locus mt_0_4231054_0:0-198 [******* ] 30% > Processing Locus no_0_2885444_0:24-105 [******* ] 31% > Processing Locus no_0_2905273_0:26-121 [******** ] 32% > Processing Locus no_0_2956652_0:7-172 [******** ] 33% > Processing Locus no_0_3101262_0:250-732 [******** ] 34% > Processing Locus oy_0_2965192_0:18-123 [******** ] 35% > Processing Locus oy_0_3001818_0:50-154 [********* ] 36% > Processing Locus oy_0_3121110_0:373-451 [********* ] 37% > Processing Locus oy_0_3148368_0:585-663 [********* ] 38% > Processing Locus oy_0_3162092_0:1560-1638 [********* ] 39% > Processing Locus po_0_3299272_0:0-119 [********** ] 40% > Processing Locus po_0_3372769_0:1-165 [********** ] 41% > Processing Locus po_0_3507160_0:2-438 [********** ] 42% > Processing Locus po_0_3606391_0:1125-1289 [********** ] 43% > Processing Locus po_0_3606391_0:1408-1753 [*********** ] 44% > Processing Locus po_0_3606391_0:1976-2892 [*********** ] 45% > Processing Locus po_0_3606391_1:29-119 [*********** ] 46% > Processing Locus po_0_3606391_1:686-976 [*********** ] 47% > Processing Locus rsch_4_4032032_0:0-84 [************ ] 48% > Processing Locus rsch_4_4034850_0:0-100 [************ ] 49% > Processing Locus rsch_4_4055167_0:0-110 [************ ] 50% > Processing Locus rsch_4_4214541_0:3-233 [************ ] 51% > Processing Locus rsch_4_4255532_0:0-287 [************* ] 52% > Processing Locus rsch_4_4275442_0:33-624 [************* ] 53% > Processing Locus rsch_4_4277288_0:3-1369 [************* ] 54% > Processing Locus rsch_4_4277566_0:317-535 [************* ] 55% > Processing Locus rsch_4_4277566_0:1008-1110 [************** ] 56% > Processing Locus rsch_4_4292194_1:1-1115 [************** ] 57% > Processing Locus rsch_4_4297142_0:31-300 [************** ] 58% > Processing Locus sf_2_2459023_0:3-110 [************** ] 59% > Processing Locus sf_2_2486157_0:0-118 [*************** ] 60% > Processing Locus sf_2_2524453_0:1-159 [*************** ] 61% > Processing Locus sf_2_2687786_0:17-2176 [*************** ] 62% > Processing Locus sf_2_2701328_0:484-594 [*************** ] 63% > Processing Locus tsu_0_2970253_0:2-102 [**************** ] 64% > Processing Locus tsu_0_3036945_0:15-120 [**************** ] 65% > Processing Locus tsu_0_3135135_0:117-195 [**************** ] 66% > Processing Locus tsu_0_3175121_0:23-426 [**************** ] 67% > Processing Locus tsu_0_3175121_0:595-704 [***************** ] 68% > Processing Locus tsu_0_3208747_0:13-401 [***************** ] 69% > Processing Locus tsu_0_3211741_0:3-780 [***************** ] 70% > Processing Locus tsu_0_3212935_0:0-1034 [***************** ] 71% > Processing Locus tsu_0_3215671_0:25-500 [****************** ] 72% > Processing Locus tsu_0_3215671_0:644-855 [****************** ] 73% > Processing Locus tsu_0_3215737_0:6-1108 [****************** ] 74% > Processing Locus tsu_0_3215821_0:188-1104 [****************** ] 75% > Processing Locus tsu_0_3242833_1:29-912 [******************* ] 76% > Processing Locus wil_2_2834553_0:25-103 [******************* ] 77% > Processing Locus wil_2_2915899_0:45-166 [******************* ] 78% > Processing Locus wil_2_3050523_0:15-273 [******************* ] 79% > Processing Locus wil_2_3054893_0:454-543 [******************** ] 80% > Processing Locus wil_2_3088151_0:31-181 [******************** ] 81% > Processing Locus wil_2_3088151_0:645-1637 [******************** ] 82% > Processing Locus wil_2_3088151_0:1838-1916 [******************** ] 83% > Processing Locus wil_2_3092619_0:752-830 [********************* ] 84% > Processing Locus ws_0_3182508_0:3-130 [********************* ] 85% > Processing Locus ws_0_3373604_0:1594-2858 [********************* ] 86% > Processing Locus ws_0_3381390_0:11-1727 [********************* ] 87% > Processing Locus wu_0_2654219_0:0-137 [********************** ] 88% > Processing Locus wu_0_2678387_0:6-169 [********************** ] 89% > Processing Locus wu_0_2687576_0:21-170 [********************** ] 90% > Processing Locus zu_0_3075813_0:17-97 [********************** ] 91% > Processing Locus zu_0_3082201_0:0-148 [*********************** ] 92% > Processing Locus zu_0_3092045_0:4-146 [*********************** ] 93% > Processing Locus zu_0_3190435_0:25-103 [*********************** ] 94% > Processing Locus zu_0_3242889_0:3-330 [*********************** ] 95% > Processing Locus zu_0_3255503_0:1081-1359 [************************ ] 96% > Processing Locus zu_0_3277661_0:331-910 [************************ ] 97% > Processing Locus zu_0_3280213_0:257-1196 [************************ ] 98% > Processing Locus zu_0_3280213_0:1342-2096 [************************ ] 99% > Processed 100 loci. [*************************] 100% [14:12:42] Loading reference annotation and sequence [14:12:42] Learning bias parameters. > Processing Locus bur_0_1804399_0:0-113 [ ] 0% > Processing Locus bur_0_1873494_0:14-188 [ ] 1% > Processing Locus bur_0_2020452_0:2-1305 [ ] 2% > Processing Locus can_0_3076940_0:0-140 [ ] 3% > Processing Locus ct_1_3082021_0:1-129 [* ] 4% > Processing Locus ct_1_3241157_0:4-734 [* ] 5% > Processing Locus edi_0_2859720_0:136-523 [* ] 6% > Processing Locus edi_0_2871668_0:156-529 [* ] 7% > Processing Locus edi_0_2918156_0:78-582 [** ] 8% > Processing Locus edi_0_2932438_0:9-289 [** ] 9% > Processing Locus hi_0_2778596_0:17-168 [** ] 10% > Processing Locus hi_0_2795398_0:0-188 [** ] 11% > Processing Locus ler_0_4018856_0:36-183 [*** ] 12% > Processing Locus mt_0_4213448_0:13-181 [*** ] 13% > Processing Locus mt_0_4217716_0:9-183 [*** ] 14% > Processing Locus mt_0_4229662_0:1-197 [*** ] 15% > Processing Locus mt_0_4230874_0:30-198 [**** ] 16% > Processing Locus mt_0_4231054_0:0-198 [**** ] 17% > Processing Locus no_0_3101262_0:250-732 [**** ] 18% > Processing Locus oy_0_2965192_0:18-123 [**** ] 19% > Processing Locus oy_0_3001818_0:50-154 [***** ] 20% > Processing Locus po_0_3299272_0:0-119 [***** ] 21% > Processing Locus po_0_3372769_0:1-165 [***** ] 22% > Processing Locus po_0_3507160_0:2-438 [***** ] 23% > Processing Locus rsch_4_4034850_0:0-100 [****** ] 24% > Processing Locus rsch_4_4055167_0:0-110 [****** ] 25% > Processing Locus rsch_4_4214541_0:3-233 [****** ] 26% > Processing Locus rsch_4_4255532_0:0-287 [****** ] 27% > Processing Locus rsch_4_4275442_0:33-624 [******* ] 28% > Processing Locus rsch_4_4277288_0:3-1369 [******* ] 29% > Processing Locus rsch_4_4277566_0:317-535 [******* ] 30% > Processing Locus rsch_4_4277566_0:1008-1110 [******* ] 31% > Processing Locus rsch_4_4292194_1:1-1115 [******** ] 32% > Processing Locus rsch_4_4297142_0:31-300 [******** ] 33% > Processing Locus sf_2_2459023_0:3-110 [******** ] 34% > Processing Locus sf_2_2486157_0:0-118 [******** ] 35% > Processing Locus sf_2_2524453_0:1-159 [********* ] 36% > Processing Locus sf_2_2687786_0:17-2176 [********* ] 37% > Processing Locus tsu_0_2970253_0:2-102 [********* ] 38% > Processing Locus tsu_0_3175121_0:23-426 [********* ] 39% > Processing Locus tsu_0_3208747_0:13-401 [********** ] 40% > Processing Locus tsu_0_3211741_0:3-780 [********** ] 41% > Processing Locus tsu_0_3212935_0:0-1034 [********** ] 42% > Processing Locus tsu_0_3215671_0:25-500 [********** ] 43% > Processing Locus tsu_0_3215671_0:644-855 [*********** ] 44% > Processing Locus tsu_0_3215737_0:6-1108 [*********** ] 45% > Processing Locus tsu_0_3215821_0:188-1104 [*********** ] 46% > Processing Locus tsu_0_3242833_1:29-912 [*********** ] 47% > Processing Locus wil_2_3050523_0:15-273 [************ ] 48% > Processing Locus wil_2_3088151_0:645-1637 [************ ] 49% > Processing Locus ws_0_3373604_0:1594-2858 [************ ] 50% > Processing Locus ws_0_3381390_0:11-1727 [************ ] 51% > Processing Locus wu_0_2654219_0:0-137 [************* ] 52% > Processing Locus wu_0_2687576_0:21-170 [************* ] 53% > Processing Locus zu_0_3082201_0:0-148 [************* ] 54% > Processing Locus zu_0_3242889_0:3-330 [************* ] 55% > Processing Locus zu_0_3255503_0:1081-1359 [************** ] 56% > Processing Locus zu_0_3277661_0:331-910 [************** ] 57% > Processing Locus zu_0_3280213_0:257-1196 [************** ] 58% > Processing Locus zu_0_3280213_0:1342-2096 [************** ] 59% > Processed 60 loci. [*************************] 100% [14:12:42] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:0-113 [ ] 0% > Processing Locus bur_0_1873494_0:14-188 [ ] 1% > Processing Locus bur_0_2020452_0:2-1305 [ ] 2% > Processing Locus can_0_3076940_0:0-140 [ ] 3% > Processing Locus ct_1_3082021_0:1-129 [* ] 4% > Processing Locus ct_1_3241157_0:4-734 [* ] 5% > Processing Locus edi_0_2859720_0:136-523 [* ] 6% > Processing Locus edi_0_2871668_0:156-529 [* ] 7% > Processing Locus edi_0_2918156_0:78-582 [** ] 8% > Processing Locus edi_0_2932438_0:9-289 [** ] 9% > Processing Locus hi_0_2778596_0:17-168 [** ] 10% > Processing Locus hi_0_2795398_0:0-188 [** ] 11% > Processing Locus ler_0_4018856_0:36-183 [*** ] 12% > Processing Locus mt_0_4213448_0:13-181 [*** ] 13% > Processing Locus mt_0_4217716_0:9-183 [*** ] 14% > Processing Locus mt_0_4229662_0:1-197 [*** ] 15% > Processing Locus mt_0_4230874_0:30-198 [**** ] 16% > Processing Locus mt_0_4231054_0:0-198 [**** ] 17% > Processing Locus no_0_3101262_0:250-732 [**** ] 18% > Processing Locus oy_0_2965192_0:18-123 [**** ] 19% > Processing Locus oy_0_3001818_0:50-154 [***** ] 20% > Processing Locus po_0_3299272_0:0-119 [***** ] 21% > Processing Locus po_0_3372769_0:1-165 [***** ] 22% > Processing Locus po_0_3507160_0:2-438 [***** ] 23% > Processing Locus rsch_4_4034850_0:0-100 [****** ] 24% > Processing Locus rsch_4_4055167_0:0-110 [****** ] 25% > Processing Locus rsch_4_4214541_0:3-233 [****** ] 26% > Processing Locus rsch_4_4255532_0:0-287 [****** ] 27% > Processing Locus rsch_4_4275442_0:33-624 [******* ] 28% > Processing Locus rsch_4_4277288_0:3-1369 [******* ] 29% > Processing Locus rsch_4_4277566_0:317-535 [******* ] 30% > Processing Locus rsch_4_4277566_0:1008-1110 [******* ] 31% > Processing Locus rsch_4_4292194_1:1-1115 [******** ] 32% > Processing Locus rsch_4_4297142_0:31-300 [******** ] 33% > Processing Locus sf_2_2459023_0:3-110 [******** ] 34% > Processing Locus sf_2_2486157_0:0-118 [******** ] 35% > Processing Locus sf_2_2524453_0:1-159 [********* ] 36% > Processing Locus sf_2_2687786_0:17-2176 [********* ] 37% > Processing Locus tsu_0_2970253_0:2-102 [********* ] 38% > Processing Locus tsu_0_3175121_0:23-426 [********* ] 39% > Processing Locus tsu_0_3208747_0:13-401 [********** ] 40% > Processing Locus tsu_0_3211741_0:3-780 [********** ] 41% > Processing Locus tsu_0_3212935_0:0-1034 [********** ] 42% > Processing Locus tsu_0_3215671_0:25-500 [********** ] 43% > Processing Locus tsu_0_3215671_0:644-855 [*********** ] 44% > Processing Locus tsu_0_3215737_0:6-1108 [*********** ] 45% > Processing Locus tsu_0_3215821_0:188-1104 [*********** ] 46% > Processing Locus tsu_0_3242833_1:29-912 [*********** ] 47% > Processing Locus wil_2_3050523_0:15-273 [************ ] 48% > Processing Locus wil_2_3088151_0:645-1637 [************ ] 49% > Processing Locus ws_0_3373604_0:1594-2858 [************ ] 50% > Processing Locus ws_0_3381390_0:11-1727 [************ ] 51% > Processing Locus wu_0_2654219_0:0-137 [************* ] 52% > Processing Locus wu_0_2687576_0:21-170 [************* ] 53% > Processing Locus zu_0_3082201_0:0-148 [************* ] 54% > Processing Locus zu_0_3242889_0:3-330 [************* ] 55% > Processing Locus zu_0_3255503_0:1081-1359 [************** ] 56% > Processing Locus zu_0_3277661_0:331-910 [************** ] 57% > Processing Locus zu_0_3280213_0:257-1196 [************** ] 58% > Processing Locus zu_0_3280213_0:1342-2096 [************** ] 59% > Processed 60 loci. [*************************] 100% [Mon Apr 4 14:12:42 2011] Mapping reads against it2.fa with Bowtie(3/3) cufflinks -p 4 -o ./Sf_2 -r it2.fa ./Sf_2/accepted_hits.bam [14:12:42] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1873494_0:1-187 [ ] 0% > Processing Locus can_0_3076940_0:0-136 [ ] 0% > Processing Locus can_0_3122480_0:0-151 [ ] 0% > Processing Locus can_0_3189753_0:1-204 [ ] 1% > Processing Locus can_0_3218459_0:0-893 [ ] 1% > Processing Locus can_0_3258779_0:48-126 [ ] 2% > Processing Locus can_0_3258779_0:248-326 [ ] 2% > Processing Locus can_0_3258779_0:443-649 [ ] 2% > Processing Locus can_0_3270131_0:24-569 [ ] 2% > Processing Locus can_0_3270131_0:863-949 [ ] 2% > Processing Locus can_0_3270131_0:1600-2264 [ ] 2% > Processing Locus ct_1_3082021_0:0-123 [ ] 2% > Processing Locus ct_1_3125173_0:88-179 [ ] 3% > Processing Locus ct_1_3133451_0:81-159 [ ] 3% > Processing Locus ct_1_3133995_0:80-195 [* ] 4% > Processing Locus ct_1_3247037_0:209-546 [* ] 4% > Processing Locus edi_0_2744702_0:0-158 [* ] 5% > Processing Locus edi_0_2871668_0:263-534 [* ] 5% > Processing Locus edi_0_2891226_0:647-725 [* ] 5% > Processing Locus edi_0_2934714_0:895-973 [* ] 6% > Processing Locus hi_0_2778596_0:12-168 [* ] 6% > Processing Locus hi_0_2939638_0:45-624 [* ] 7% > Processing Locus kn_0_3605300_0:1-168 [* ] 7% > Processing Locus kn_0_3613403_0:1-174 [* ] 7% > Processing Locus kn_0_3819922_1:1378-1456 [** ] 8% > Processing Locus ler_0_3998410_0:1-163 [** ] 8% > Processing Locus ler_0_4018856_0:1-161 [** ] 9% > Processing Locus mt_0_4217716_0:0-182 [** ] 9% > Processing Locus mt_0_4229662_0:9-196 [** ] 10% > Processing Locus mt_0_4231054_0:0-83 [** ] 10% > Processing Locus mt_0_4528444_1:554-1205 [** ] 10% > Processing Locus no_0_2885444_0:27-110 [** ] 11% > Processing Locus no_0_2905273_0:22-121 [** ] 11% > Processing Locus no_0_2936769_0:14-92 [*** ] 12% > Processing Locus no_0_2956652_0:5-169 [*** ] 12% > Processing Locus no_0_3088052_0:0-939 [*** ] 13% > Processing Locus oy_0_3098144_0:15-302 [*** ] 13% > Processing Locus po_0_3306688_0:15-121 [*** ] 13% > Processing Locus po_0_3330421_0:0-131 [*** ] 14% > Processing Locus po_0_3332479_0:0-136 [*** ] 14% > Processing Locus po_0_3382155_0:2-80 [*** ] 15% > Processing Locus rsch_4_4032032_0:0-86 [*** ] 15% > Processing Locus rsch_4_4055167_0:0-111 [*** ] 15% > Processing Locus rsch_4_4214541_0:72-150 [**** ] 16% > Processing Locus rsch_4_4219071_0:79-413 [**** ] 16% > Processing Locus rsch_4_4275442_0:96-600 [**** ] 17% > Processing Locus rsch_4_4277566_0:318-533 [**** ] 17% > Processing Locus rsch_4_4277566_0:1020-1111 [**** ] 17% > Processing Locus sf_2_2459023_0:2-110 [**** ] 18% > Processing Locus sf_2_2486157_0:1-113 [**** ] 18% > Processing Locus sf_2_2488391_0:1-126 [**** ] 18% > Processing Locus sf_2_2504999_0:4-145 [**** ] 19% > Processing Locus sf_2_2524453_0:1-165 [**** ] 19% > Processing Locus sf_2_2532172_0:6-180 [***** ] 20% > Processing Locus sf_2_2653966_0:3-695 [***** ] 20% > Processing Locus sf_2_2671632_0:0-986 [***** ] 21% > Processing Locus sf_2_2676583_0:1-948 [***** ] 21% > Processing Locus sf_2_2680171_0:0-1162 [***** ] 21% > Processing Locus sf_2_2682779_0:614-991 [***** ] 22% > Processing Locus sf_2_2687774_0:82-195 [***** ] 22% > Processing Locus sf_2_2687774_0:588-1427 [***** ] 22% > Processing Locus sf_2_2687786_0:92-2152 [***** ] 23% > Processing Locus sf_2_2701328_0:0-728 [***** ] 23% > Processing Locus tsu_0_3175121_0:0-416 [***** ] 23% > Processing Locus tsu_0_3175121_0:598-701 [***** ] 23% > Processing Locus tsu_0_3215671_0:150-275 [****** ] 24% > Processing Locus tsu_0_3215671_0:764-843 [****** ] 24% > Processing Locus tsu_0_3215821_0:246-1154 [****** ] 24% > Processing Locus tsu_0_3243273_0:579-3159 [****** ] 25% > Processing Locus tsu_0_3243273_0:3566-4034 [****** ] 25% > Processing Locus tsu_0_3243273_0:4566-4725 [****** ] 25% > Processing Locus wil_2_2834553_0:0-104 [****** ] 25% > Processing Locus wil_2_3050523_0:57-267 [****** ] 26% > Processing Locus wil_2_3052273_0:28-1111 [****** ] 26% > Processing Locus wil_2_3054893_0:25-559 [****** ] 26% > Processing Locus wil_2_3087183_0:238-316 [****** ] 27% > Processing Locus wil_2_3088151_0:17-586 [****** ] 27% > Processing Locus wil_2_3088151_0:726-872 [****** ] 27% > Processing Locus wil_2_3088151_0:1137-1366 [****** ] 27% > Processing Locus ws_0_3182508_0:2-159 [******* ] 28% > Processing Locus ws_0_3190963_0:26-157 [******* ] 28% > Processing Locus ws_0_3326342_0:32-428 [******* ] 28% > Processing Locus ws_0_3340488_0:210-1137 [******* ] 29% > Processing Locus ws_0_3373604_0:1593-2804 [******* ] 29% > Processing Locus ws_0_3382500_0:115-1129 [******* ] 30% > Processing Locus ws_0_3382500_0:1229-1668 [******* ] 30% > Processing Locus ws_0_3382500_0:1825-2361 [******* ] 30% > Processing Locus ws_0_3382500_0:2572-2853 [******* ] 30% > Processing Locus ws_0_3382500_0:3094-3452 [******* ] 30% > Processing Locus wu_0_2654219_0:68-147 [******* ] 30% > Processing Locus wu_0_2678387_0:51-173 [******* ] 31% > Processing Locus wu_0_2687576_0:29-171 [******* ] 31% > Processing Locus zu_0_3022629_0:0-113 [******* ] 31% > Processing Locus zu_0_3082201_0:1-147 [******** ] 32% > Processing Locus zu_0_3118546_0:4-169 [******** ] 32% > Processing Locus zu_0_3255169_0:38-1095 [******** ] 33% > Processing Locus zu_0_3278243_0:412-760 [******** ] 33% > Processed 97 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5377.83 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:12:42] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1873494_0:1-187 [ ] 0% > Processing Locus can_0_3076940_0:0-136 [ ] 1% > Processing Locus can_0_3122480_0:0-151 [ ] 2% > Processing Locus can_0_3189753_0:1-204 [ ] 3% > Processing Locus can_0_3218459_0:0-893 [* ] 4% > Processing Locus can_0_3258779_0:48-126 [* ] 5% > Processing Locus can_0_3258779_0:248-326 [* ] 6% > Processing Locus can_0_3258779_0:443-649 [* ] 7% > Processing Locus can_0_3270131_0:24-569 [** ] 8% > Processing Locus can_0_3270131_0:863-949 [** ] 9% > Processing Locus can_0_3270131_0:1600-2264 [** ] 10% > Processing Locus ct_1_3082021_0:0-123 [** ] 11% > Processing Locus ct_1_3125173_0:88-179 [*** ] 12% > Processing Locus ct_1_3133451_0:81-159 [*** ] 13% > Processing Locus ct_1_3133995_0:80-195 [*** ] 14% > Processing Locus ct_1_3247037_0:209-546 [*** ] 15% > Processing Locus edi_0_2744702_0:0-158 [**** ] 16% > Processing Locus edi_0_2871668_0:263-534 [**** ] 17% > Processing Locus edi_0_2891226_0:647-725 [**** ] 18% > Processing Locus edi_0_2934714_0:895-973 [**** ] 19% > Processing Locus hi_0_2778596_0:12-168 [***** ] 20% > Processing Locus hi_0_2939638_0:45-624 [***** ] 21% > Processing Locus kn_0_3605300_0:1-168 [***** ] 22% > Processing Locus kn_0_3613403_0:1-174 [***** ] 23% > Processing Locus kn_0_3819922_1:1378-1456 [****** ] 24% > Processing Locus ler_0_3998410_0:1-163 [****** ] 25% > Processing Locus ler_0_4018856_0:1-161 [****** ] 26% > Processing Locus mt_0_4217716_0:0-182 [****** ] 27% > Processing Locus mt_0_4229662_0:9-196 [******* ] 28% > Processing Locus mt_0_4231054_0:0-83 [******* ] 29% > Processing Locus mt_0_4528444_1:554-1205 [******* ] 30% > Processing Locus no_0_2885444_0:27-110 [******* ] 31% > Processing Locus no_0_2905273_0:22-121 [******** ] 32% > Processing Locus no_0_2936769_0:14-92 [******** ] 34% > Processing Locus no_0_2956652_0:5-169 [******** ] 35% > Processing Locus no_0_3088052_0:0-939 [********* ] 36% > Processing Locus oy_0_3098144_0:15-302 [********* ] 37% > Processing Locus po_0_3306688_0:15-121 [********* ] 38% > Processing Locus po_0_3330421_0:0-131 [********* ] 39% > Processing Locus po_0_3332479_0:0-136 [********** ] 40% > Processing Locus po_0_3382155_0:2-80 [********** ] 41% > Processing Locus rsch_4_4032032_0:0-86 [********** ] 42% > Processing Locus rsch_4_4055167_0:0-111 [********** ] 43% > Processing Locus rsch_4_4214541_0:72-150 [*********** ] 44% > Processing Locus rsch_4_4219071_0:79-413 [*********** ] 45% > Processing Locus rsch_4_4275442_0:96-600 [*********** ] 46% > Processing Locus rsch_4_4277566_0:318-533 [*********** ] 47% > Processing Locus rsch_4_4277566_0:1020-1111 [************ ] 48% > Processing Locus sf_2_2459023_0:2-110 [************ ] 49% > Processing Locus sf_2_2486157_0:1-113 [************ ] 50% > Processing Locus sf_2_2488391_0:1-126 [************ ] 51% > Processing Locus sf_2_2504999_0:4-145 [************* ] 52% > Processing Locus sf_2_2524453_0:1-165 [************* ] 53% > Processing Locus sf_2_2532172_0:6-180 [************* ] 54% > Processing Locus sf_2_2653966_0:3-695 [************* ] 55% > Processing Locus sf_2_2671632_0:0-986 [************** ] 56% > Processing Locus sf_2_2676583_0:1-948 [************** ] 57% > Processing Locus sf_2_2680171_0:0-1162 [************** ] 58% > Processing Locus sf_2_2682779_0:614-991 [************** ] 59% > Processing Locus sf_2_2687774_0:82-195 [*************** ] 60% > Processing Locus sf_2_2687774_0:588-1427 [*************** ] 61% > Processing Locus sf_2_2687786_0:92-2152 [*************** ] 62% > Processing Locus sf_2_2701328_0:0-728 [*************** ] 63% > Processing Locus tsu_0_3175121_0:0-416 [**************** ] 64% > Processing Locus tsu_0_3175121_0:598-701 [**************** ] 65% > Processing Locus tsu_0_3215671_0:150-275 [**************** ] 67% > Processing Locus tsu_0_3215671_0:764-843 [***************** ] 68% > Processing Locus tsu_0_3215821_0:246-1154 [***************** ] 69% > Processing Locus tsu_0_3243273_0:579-3159 [***************** ] 70% > Processing Locus tsu_0_3243273_0:3566-4034 [***************** ] 71% > Processing Locus tsu_0_3243273_0:4566-4725 [****************** ] 72% > Processing Locus wil_2_2834553_0:0-104 [****************** ] 73% > Processing Locus wil_2_3050523_0:57-267 [****************** ] 74% > Processing Locus wil_2_3052273_0:28-1111 [****************** ] 75% > Processing Locus wil_2_3054893_0:25-559 [******************* ] 76% > Processing Locus wil_2_3087183_0:238-316 [******************* ] 77% > Processing Locus wil_2_3088151_0:17-586 [******************* ] 78% > Processing Locus wil_2_3088151_0:726-872 [******************* ] 79% > Processing Locus wil_2_3088151_0:1137-1366 [******************** ] 80% > Processing Locus ws_0_3182508_0:2-159 [******************** ] 81% > Processing Locus ws_0_3190963_0:26-157 [******************** ] 82% > Processing Locus ws_0_3326342_0:32-428 [******************** ] 83% > Processing Locus ws_0_3340488_0:210-1137 [********************* ] 84% > Processing Locus ws_0_3373604_0:1593-2804 [********************* ] 85% > Processing Locus ws_0_3382500_0:115-1129 [********************* ] 86% > Processing Locus ws_0_3382500_0:1229-1668 [********************* ] 87% > Processing Locus ws_0_3382500_0:1825-2361 [********************** ] 88% > Processing Locus ws_0_3382500_0:2572-2853 [********************** ] 89% > Processing Locus ws_0_3382500_0:3094-3452 [********************** ] 90% > Processing Locus wu_0_2654219_0:68-147 [********************** ] 91% > Processing Locus wu_0_2678387_0:51-173 [*********************** ] 92% > Processing Locus wu_0_2687576_0:29-171 [*********************** ] 93% > Processing Locus zu_0_3022629_0:0-113 [*********************** ] 94% > Processing Locus zu_0_3082201_0:1-147 [*********************** ] 95% > Processing Locus zu_0_3118546_0:4-169 [************************ ] 96% > Processing Locus zu_0_3255169_0:38-1095 [************************ ] 97% > Processing Locus zu_0_3278243_0:412-760 [************************ ] 98% > Processed 97 loci. [*************************] 100% [14:12:42] Loading reference annotation and sequence [14:12:42] Learning bias parameters. > Processing Locus bur_0_1873494_0:1-187 [ ] 0% > Processing Locus can_0_3076940_0:0-136 [ ] 1% > Processing Locus can_0_3122480_0:0-151 [ ] 2% > Processing Locus can_0_3189753_0:1-204 [ ] 3% > Processing Locus can_0_3218459_0:0-893 [* ] 4% > Processing Locus can_0_3270131_0:1600-2264 [* ] 5% > Processing Locus ct_1_3125173_0:88-179 [* ] 6% > Processing Locus ct_1_3133995_0:80-195 [* ] 7% > Processing Locus edi_0_2744702_0:0-158 [** ] 8% > Processing Locus edi_0_2871668_0:263-534 [** ] 9% > Processing Locus hi_0_2778596_0:12-168 [** ] 10% > Processing Locus hi_0_2939638_0:45-624 [** ] 11% > Processing Locus kn_0_3605300_0:1-168 [*** ] 12% > Processing Locus kn_0_3613403_0:1-174 [*** ] 13% > Processing Locus ler_0_4018856_0:1-161 [*** ] 14% > Processing Locus mt_0_4217716_0:0-182 [*** ] 15% > Processing Locus mt_0_4229662_0:9-196 [**** ] 16% > Processing Locus mt_0_4231054_0:0-83 [**** ] 17% > Processing Locus mt_0_4528444_1:554-1205 [**** ] 18% > Processing Locus no_0_2956652_0:5-169 [**** ] 19% > Processing Locus no_0_3088052_0:0-939 [***** ] 20% > Processing Locus oy_0_3098144_0:15-302 [***** ] 21% > Processing Locus po_0_3306688_0:15-121 [***** ] 22% > Processing Locus po_0_3330421_0:0-131 [***** ] 23% > Processing Locus po_0_3332479_0:0-136 [****** ] 24% > Processing Locus rsch_4_4032032_0:0-86 [****** ] 25% > Processing Locus rsch_4_4055167_0:0-111 [****** ] 26% > Processing Locus rsch_4_4275442_0:96-600 [****** ] 27% > Processing Locus rsch_4_4277566_0:318-533 [******* ] 28% > Processing Locus rsch_4_4277566_0:1020-1111 [******* ] 29% > Processing Locus sf_2_2459023_0:2-110 [******* ] 30% > Processing Locus sf_2_2486157_0:1-113 [******* ] 31% > Processing Locus sf_2_2488391_0:1-126 [******** ] 32% > Processing Locus sf_2_2504999_0:4-145 [******** ] 34% > Processing Locus sf_2_2524453_0:1-165 [******** ] 35% > Processing Locus sf_2_2532172_0:6-180 [********* ] 36% > Processing Locus sf_2_2653966_0:3-695 [********* ] 37% > Processing Locus sf_2_2671632_0:0-986 [********* ] 38% > Processing Locus sf_2_2676583_0:1-948 [********* ] 39% > Processing Locus sf_2_2680171_0:0-1162 [********** ] 40% > Processing Locus sf_2_2682779_0:614-991 [********** ] 41% > Processing Locus sf_2_2687774_0:795-1427 [********** ] 42% > Processing Locus sf_2_2687786_0:92-2152 [********** ] 43% > Processing Locus sf_2_2701328_0:0-728 [*********** ] 44% > Processing Locus tsu_0_3175121_0:0-416 [*********** ] 45% > Processing Locus tsu_0_3215821_0:246-1154 [*********** ] 46% > Processing Locus tsu_0_3243273_0:579-3159 [*********** ] 47% > Processing Locus tsu_0_3243273_0:3566-4034 [************ ] 48% > Processing Locus wil_2_2834553_0:0-104 [************ ] 49% > Processing Locus wil_2_3050523_0:57-267 [************ ] 50% > Processing Locus wil_2_3052273_0:28-1111 [************ ] 51% > Processing Locus wil_2_3054893_0:25-559 [************* ] 52% > Processing Locus wil_2_3088151_0:17-586 [************* ] 53% > Processing Locus ws_0_3182508_0:2-159 [************* ] 54% > Processing Locus ws_0_3190963_0:26-157 [************* ] 55% > Processing Locus ws_0_3340488_0:210-1137 [************** ] 56% > Processing Locus ws_0_3373604_0:1593-2804 [************** ] 57% > Processing Locus ws_0_3382500_0:115-1129 [************** ] 58% > Processing Locus ws_0_3382500_0:1825-2361 [************** ] 59% > Processing Locus wu_0_2687576_0:29-171 [*************** ] 60% > Processing Locus zu_0_3022629_0:0-113 [*************** ] 61% > Processing Locus zu_0_3082201_0:1-147 [*************** ] 62% > Processing Locus zu_0_3118546_0:4-169 [*************** ] 63% > Processing Locus zu_0_3255169_0:38-1095 [**************** ] 64% > Processed 64 loci. [*************************] 100% [14:12:42] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1873494_0:1-187 [ ] 0% > Processing Locus can_0_3076940_0:0-136 [ ] 1% > Processing Locus can_0_3122480_0:0-151 [ ] 2% > Processing Locus can_0_3189753_0:1-204 [ ] 3% > Processing Locus can_0_3218459_0:0-893 [* ] 4% > Processing Locus can_0_3270131_0:1600-2264 [* ] 5% > Processing Locus ct_1_3125173_0:88-179 [* ] 6% > Processing Locus ct_1_3133995_0:80-195 [* ] 7% > Processing Locus edi_0_2744702_0:0-158 [** ] 8% > Processing Locus edi_0_2871668_0:263-534 [** ] 9% > Processing Locus hi_0_2778596_0:12-168 [** ] 10% > Processing Locus hi_0_2939638_0:45-624 [** ] 11% > Processing Locus kn_0_3605300_0:1-168 [*** ] 12% > Processing Locus kn_0_3613403_0:1-174 [*** ] 13% > Processing Locus ler_0_4018856_0:1-161 [*** ] 14% > Processing Locus mt_0_4217716_0:0-182 [*** ] 15% > Processing Locus mt_0_4229662_0:9-196 [**** ] 16% > Processing Locus mt_0_4231054_0:0-83 [**** ] 17% > Processing Locus mt_0_4528444_1:554-1205 [**** ] 18% > Processing Locus no_0_2956652_0:5-169 [**** ] 19% > Processing Locus no_0_3088052_0:0-939 [***** ] 20% > Processing Locus oy_0_3098144_0:15-302 [***** ] 21% > Processing Locus po_0_3306688_0:15-121 [***** ] 22% > Processing Locus po_0_3330421_0:0-131 [***** ] 23% > Processing Locus po_0_3332479_0:0-136 [****** ] 24% > Processing Locus rsch_4_4032032_0:0-86 [****** ] 25% > Processing Locus rsch_4_4055167_0:0-111 [****** ] 26% > Processing Locus rsch_4_4275442_0:96-600 [****** ] 27% > Processing Locus rsch_4_4277566_0:318-533 [******* ] 28% > Processing Locus rsch_4_4277566_0:1020-1111 [******* ] 29% > Processing Locus sf_2_2459023_0:2-110 [******* ] 30% > Processing Locus sf_2_2486157_0:1-113 [******* ] 31% > Processing Locus sf_2_2488391_0:1-126 [******** ] 32% > Processing Locus sf_2_2504999_0:4-145 [******** ] 34% > Processing Locus sf_2_2524453_0:1-165 [******** ] 35% > Processing Locus sf_2_2532172_0:6-180 [********* ] 36% > Processing Locus sf_2_2653966_0:3-695 [********* ] 37% > Processing Locus sf_2_2671632_0:0-986 [********* ] 38% > Processing Locus sf_2_2676583_0:1-948 [********* ] 39% > Processing Locus sf_2_2680171_0:0-1162 [********** ] 40% > Processing Locus sf_2_2682779_0:614-991 [********** ] 41% > Processing Locus sf_2_2687774_0:795-1427 [********** ] 42% > Processing Locus sf_2_2687786_0:92-2152 [********** ] 43% > Processing Locus sf_2_2701328_0:0-728 [*********** ] 44% > Processing Locus tsu_0_3175121_0:0-416 [*********** ] 45% > Processing Locus tsu_0_3215821_0:246-1154 [*********** ] 46% > Processing Locus tsu_0_3243273_0:579-3159 [*********** ] 47% > Processing Locus tsu_0_3243273_0:3566-4034 [************ ] 48% > Processing Locus wil_2_2834553_0:0-104 [************ ] 49% > Processing Locus wil_2_3050523_0:57-267 [************ ] 50% > Processing Locus wil_2_3052273_0:28-1111 [************ ] 51% > Processing Locus wil_2_3054893_0:25-559 [************* ] 52% > Processing Locus wil_2_3088151_0:17-586 [************* ] 53% > Processing Locus ws_0_3182508_0:2-159 [************* ] 54% > Processing Locus ws_0_3190963_0:26-157 [************* ] 55% > Processing Locus ws_0_3340488_0:210-1137 [************** ] 56% > Processing Locus ws_0_3373604_0:1593-2804 [************** ] 57% > Processing Locus ws_0_3382500_0:115-1129 [************** ] 58% > Processing Locus ws_0_3382500_0:1825-2361 [************** ] 59% > Processing Locus wu_0_2687576_0:29-171 [*************** ] 60% > Processing Locus zu_0_3022629_0:0-113 [*************** ] 61% > Processing Locus zu_0_3082201_0:1-147 [*************** ] 62% > Processing Locus zu_0_3118546_0:4-169 [*************** ] 63% > Processing Locus zu_0_3255169_0:38-1095 [**************** ] 64% > Processed 64 loci. [*************************] 100% [Mon Apr 4 14:12:45 2011] Searching for junctions via segment mapping [Mon Apr 4 14:12:59 2011] Retrieving sequences for splices [Mon Apr 4 14:12:59 2011] Indexing splices [Mon Apr 4 14:12:59 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:13:01 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:13:03 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:13:05 2011] Joining segment hits [Mon Apr 4 14:13:06 2011] Reporting output tracks ----------------------------------------------- Run complete [00:01:09 elapsed] 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 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 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 ./Ws_0 -n it2.fa Ws_0.Toit2.merge.fq reference: it2.fa cufflinks -p 4 -o ./Wil_2 -r it2.fa ./Wil_2/accepted_hits.bam $RNAGI/rnagi.sh -o ./Wu_0 -n it2.fa Wu_0.Toit2.merge.fq reference: it2.fa [14:13:12] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:0-108 [ ] 0% > Processing Locus bur_0_1873494_0:6-186 [ ] 0% > Processing Locus can_0_3076940_0:5-141 [ ] 0% > Processing Locus can_0_3189753_0:0-205 [ ] 1% > Processing Locus can_0_3223655_0:84-442 [ ] 1% > Processing Locus can_0_3231205_0:13-890 [ ] 2% > Processing Locus can_0_3270131_0:33-111 [ ] 2% > Processing Locus can_0_3270131_0:222-855 [ ] 2% > Processing Locus can_0_3270131_0:1079-2095 [ ] 2% > Processing Locus ct_1_3082021_0:4-128 [ ] 2% > Processing Locus ct_1_3132277_0:88-175 [ ] 3% > Processing Locus ct_1_3302721_0:1261-1339 [ ] 3% > Processing Locus edi_0_2723255_0:62-140 [* ] 4% > Processing Locus edi_0_2859720_0:154-525 [* ] 4% > Processing Locus edi_0_2871668_0:189-523 [* ] 5% > Processing Locus hi_0_2755116_0:4-82 [* ] 5% > Processing Locus hi_0_2773206_0:7-158 [* ] 5% > Processing Locus hi_0_2778596_0:35-156 [* ] 6% > Processing Locus hi_0_2795398_0:0-190 [* ] 6% > Processing Locus hi_0_2961678_0:251-1503 [* ] 7% > Processing Locus kn_0_3605300_0:1-168 [* ] 7% > Processing Locus kn_0_3613403_0:4-174 [* ] 7% > Processing Locus ler_0_3998410_0:0-164 [** ] 8% > Processing Locus ler_0_4018856_0:1-184 [** ] 8% > Processing Locus ler_0_4224097_0:924-1703 [** ] 9% > Processing Locus mt_0_4193196_0:2-165 [** ] 9% > Processing Locus mt_0_4217716_0:5-185 [** ] 10% > Processing Locus mt_0_4229662_0:4-197 [** ] 10% > Processing Locus mt_0_4230874_0:17-95 [** ] 10% > Processing Locus mt_0_4231054_0:0-83 [** ] 11% > Processing Locus mt_0_4528444_1:409-1205 [** ] 11% > Processing Locus no_0_2885444_0:3-113 [*** ] 12% > Processing Locus no_0_2905273_0:7-121 [*** ] 12% > Processing Locus no_0_2956652_0:5-176 [*** ] 13% > Processing Locus oy_0_3001818_0:56-154 [*** ] 13% > Processing Locus oy_0_3148368_0:662-740 [*** ] 13% > Processing Locus oy_0_3162092_0:759-837 [*** ] 14% > Processing Locus oy_0_3162092_0:1569-1664 [*** ] 14% > Processing Locus rsch_4_4032032_0:0-89 [*** ] 14% > Processing Locus rsch_4_4055167_0:0-109 [*** ] 15% > Processing Locus rsch_4_4110791_0:1-79 [*** ] 15% > Processing Locus rsch_4_4214541_0:1-234 [*** ] 15% > Processing Locus rsch_4_4219071_0:11-413 [**** ] 16% > Processing Locus rsch_4_4255532_0:0-287 [**** ] 16% > Processing Locus rsch_4_4266550_0:15-1157 [**** ] 17% > Processing Locus rsch_4_4292194_1:0-1127 [**** ] 17% > Processing Locus rsch_4_4297142_0:37-297 [**** ] 18% > Processing Locus sf_2_2486157_0:1-127 [**** ] 18% > Processing Locus sf_2_2524453_0:2-161 [**** ] 18% > Processing Locus sf_2_2532172_0:8-176 [**** ] 19% > Processing Locus sf_2_2687774_0:25-202 [**** ] 19% > Processing Locus sf_2_2687774_0:535-1429 [**** ] 19% > Processing Locus sf_2_2701328_0:1-728 [***** ] 20% > Processing Locus tsu_0_3036945_0:10-150 [***** ] 20% > Processing Locus tsu_0_3135135_0:28-169 [***** ] 21% > Processing Locus tsu_0_3215671_0:149-275 [***** ] 21% > Processing Locus tsu_0_3215671_0:767-845 [***** ] 21% > Processing Locus wil_2_2834553_0:0-104 [***** ] 21% > Processing Locus wil_2_2892485_0:55-133 [***** ] 22% > Processing Locus wil_2_2906137_0:12-147 [***** ] 22% > Processing Locus wil_2_2915899_0:37-158 [***** ] 23% > Processing Locus wil_2_2920529_0:0-183 [***** ] 23% > Processing Locus wil_2_2925323_0:12-185 [***** ] 23% > Processing Locus wil_2_2945095_0:60-204 [****** ] 24% > Processing Locus wil_2_3008461_1:2-360 [****** ] 24% > Processing Locus wil_2_3050523_0:32-268 [****** ] 25% > Processing Locus wil_2_3052273_0:36-1026 [****** ] 25% > Processing Locus wil_2_3052951_0:5-913 [****** ] 26% > Processing Locus wil_2_3054893_0:43-561 [****** ] 26% > Processing Locus wil_2_3063473_0:0-756 [****** ] 26% > Processing Locus wil_2_3066229_0:1-761 [****** ] 27% > Processing Locus wil_2_3068737_0:358-1768 [****** ] 27% > Processing Locus wil_2_3077447_0:1-1244 [******* ] 28% > Processing Locus wil_2_3087183_0:9-819 [******* ] 28% > Processing Locus wil_2_3088151_0:7-955 [******* ] 28% > Processing Locus wil_2_3088151_0:1075-1589 [******* ] 28% > Processing Locus wil_2_3089541_0:2-445 [******* ] 29% > Processing Locus wil_2_3090237_0:259-493 [******* ] 29% > Processing Locus wil_2_3092619_0:829-907 [******* ] 30% > Processing Locus ws_0_3182508_0:6-182 [******* ] 30% > Processing Locus ws_0_3190679_0:65-195 [******* ] 31% > Processing Locus ws_0_3298283_0:18-512 [******* ] 31% > Processing Locus ws_0_3326342_0:11-440 [******* ] 31% > Processing Locus ws_0_3340488_0:31-1139 [******** ] 32% > Processing Locus ws_0_3347582_0:170-248 [******** ] 32% > Processing Locus ws_0_3347582_0:395-500 [******** ] 32% > Processing Locus ws_0_3347582_0:1053-1379 [******** ] 32% > Processing Locus ws_0_3371988_0:0-112 [******** ] 33% > Processing Locus ws_0_3371988_0:1898-2052 [******** ] 33% > Processing Locus ws_0_3380934_0:3-207 [******** ] 33% > Processing Locus ws_0_3381390_0:16-1691 [******** ] 34% > Processing Locus wu_0_2654219_0:40-143 [******** ] 34% > Processing Locus wu_0_2678387_0:7-173 [******** ] 34% > Processing Locus wu_0_2687576_0:14-171 [******** ] 35% > Processing Locus wu_0_2824308_0:436-514 [******** ] 35% > Processing Locus zu_0_3075813_0:4-93 [********* ] 36% > Processing Locus zu_0_3082201_0:1-149 [********* ] 36% > Processing Locus zu_0_3092045_0:13-139 [********* ] 36% > Processing Locus zu_0_3118546_0:4-165 [********* ] 37% > Processing Locus zu_0_3119698_0:72-182 [********* ] 37% > Processing Locus zu_0_3190435_0:15-271 [********* ] 38% > Processing Locus zu_0_3238769_0:114-192 [********* ] 38% > Processing Locus zu_0_3242889_0:2-390 [********* ] 39% > Processing Locus zu_0_3243571_0:187-801 [********* ] 39% > Processing Locus zu_0_3255503_0:1066-1369 [********* ] 39% > Processing Locus zu_0_3260131_0:165-399 [********** ] 40% > Processing Locus zu_0_3277661_0:309-910 [********** ] 40% > Processed 107 loci. [*************************] 100% > Map Properties: > Total Map Mass: 9740.52 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:13:12] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:0-108 [ ] 0% > Processing Locus bur_0_1873494_0:6-186 [ ] 0% > Processing Locus can_0_3076940_0:5-141 [ ] 1% > Processing Locus can_0_3189753_0:0-205 [ ] 2% > Processing Locus can_0_3223655_0:84-442 [ ] 3% > Processing Locus can_0_3231205_0:13-890 [* ] 4% > Processing Locus can_0_3270131_0:33-111 [* ] 5% > Processing Locus can_0_3270131_0:222-855 [* ] 6% > Processing Locus can_0_3270131_0:1079-2095 [* ] 7% > Processing Locus ct_1_3082021_0:4-128 [** ] 8% > Processing Locus ct_1_3132277_0:88-175 [** ] 9% > Processing Locus ct_1_3302721_0:1261-1339 [** ] 10% > Processing Locus edi_0_2723255_0:62-140 [** ] 11% > Processing Locus edi_0_2859720_0:154-525 [*** ] 12% > Processing Locus edi_0_2871668_0:189-523 [*** ] 13% > Processing Locus hi_0_2755116_0:4-82 [*** ] 14% > Processing Locus hi_0_2773206_0:7-158 [*** ] 14% > Processing Locus hi_0_2778596_0:35-156 [*** ] 15% > Processing Locus hi_0_2795398_0:0-190 [**** ] 16% > Processing Locus hi_0_2961678_0:251-1503 [**** ] 17% > Processing Locus kn_0_3605300_0:1-168 [**** ] 18% > Processing Locus kn_0_3613403_0:4-174 [**** ] 19% > Processing Locus ler_0_3998410_0:0-164 [***** ] 20% > Processing Locus ler_0_4018856_0:1-184 [***** ] 21% > Processing Locus ler_0_4224097_0:924-1703 [***** ] 22% > Processing Locus mt_0_4193196_0:2-165 [***** ] 23% > Processing Locus mt_0_4217716_0:5-185 [****** ] 24% > Processing Locus mt_0_4229662_0:4-197 [****** ] 25% > Processing Locus mt_0_4230874_0:17-95 [****** ] 26% > Processing Locus mt_0_4231054_0:0-83 [****** ] 27% > Processing Locus mt_0_4528444_1:409-1205 [******* ] 28% > Processing Locus no_0_2885444_0:3-113 [******* ] 28% > Processing Locus no_0_2905273_0:7-121 [******* ] 29% > Processing Locus no_0_2956652_0:5-176 [******* ] 30% > Processing Locus oy_0_3001818_0:56-154 [******* ] 31% > Processing Locus oy_0_3148368_0:662-740 [******** ] 32% > Processing Locus oy_0_3162092_0:759-837 [******** ] 33% > Processing Locus oy_0_3162092_0:1569-1664 [******** ] 34% > Processing Locus rsch_4_4032032_0:0-89 [******** ] 35% > Processing Locus rsch_4_4055167_0:0-109 [********* ] 36% > Processing Locus rsch_4_4110791_0:1-79 [********* ] 37% > Processing Locus rsch_4_4214541_0:1-234 [********* ] 38% > Processing Locus rsch_4_4219071_0:11-413 [********* ] 39% > Processing Locus rsch_4_4255532_0:0-287 [********** ] 40% > Processing Locus rsch_4_4266550_0:15-1157 [********** ] 41% > Processing Locus rsch_4_4292194_1:0-1127 [********** ] 42% > Processing Locus rsch_4_4297142_0:37-297 [********** ] 42% > Processing Locus sf_2_2486157_0:1-127 [********** ] 43% > Processing Locus sf_2_2524453_0:2-161 [*********** ] 44% > Processing Locus sf_2_2532172_0:8-176 [*********** ] 45% > Processing Locus sf_2_2687774_0:25-202 [*********** ] 46% > Processing Locus sf_2_2687774_0:535-1429 [*********** ] 47% > Processing Locus sf_2_2701328_0:1-728 [************ ] 48% > Processing Locus tsu_0_3036945_0:10-150 [************ ] 49% > Processing Locus tsu_0_3135135_0:28-169 [************ ] 50% > Processing Locus tsu_0_3215671_0:149-275 [************ ] 51% > Processing Locus tsu_0_3215671_0:767-845 [************* ] 52% > Processing Locus wil_2_2834553_0:0-104 [************* ] 53% > Processing Locus wil_2_2892485_0:55-133 [************* ] 54% > Processing Locus wil_2_2906137_0:12-147 [************* ] 55% > Processing Locus wil_2_2915899_0:37-158 [************** ] 56% > Processing Locus wil_2_2920529_0:0-183 [************** ] 57% > Processing Locus wil_2_2925323_0:12-185 [************** ] 57% > Processing Locus wil_2_2945095_0:60-204 [************** ] 58% > Processing Locus wil_2_3008461_1:2-360 [************** ] 59% > Processing Locus wil_2_3050523_0:32-268 [*************** ] 60% > Processing Locus wil_2_3052273_0:36-1026 [*************** ] 61% > Processing Locus wil_2_3052951_0:5-913 [*************** ] 62% > Processing Locus wil_2_3054893_0:43-561 [*************** ] 63% > Processing Locus wil_2_3063473_0:0-756 [**************** ] 64% > Processing Locus wil_2_3066229_0:1-761 [**************** ] 65% > Processing Locus wil_2_3068737_0:358-1768 [**************** ] 66% > Processing Locus wil_2_3077447_0:1-1244 [**************** ] 67% > Processing Locus wil_2_3087183_0:9-819 [***************** ] 68% > Processing Locus wil_2_3088151_0:7-955 [***************** ] 69% > Processing Locus wil_2_3088151_0:1075-1589 [***************** ] 70% > Processing Locus wil_2_3089541_0:2-445 [***************** ] 71% > Processing Locus wil_2_3090237_0:259-493 [***************** ] 71% > Processing Locus wil_2_3092619_0:829-907 [****************** ] 72% > Processing Locus ws_0_3182508_0:6-182 [****************** ] 73% > Processing Locus ws_0_3190679_0:65-195 [****************** ] 74% > Processing Locus ws_0_3298283_0:18-512 [****************** ] 75% > Processing Locus ws_0_3326342_0:11-440 [******************* ] 76% > Processing Locus ws_0_3340488_0:31-1139 [******************* ] 77% > Processing Locus ws_0_3347582_0:170-248 [******************* ] 78% > Processing Locus ws_0_3347582_0:395-500 [******************* ] 79% > Processing Locus ws_0_3347582_0:1053-1379 [******************** ] 80% > Processing Locus ws_0_3371988_0:0-112 [******************** ] 81% > Processing Locus ws_0_3371988_0:1898-2052 [******************** ] 82% > Processing Locus ws_0_3380934_0:3-207 [******************** ] 83% > Processing Locus ws_0_3381390_0:16-1691 [********************* ] 84% > Processing Locus wu_0_2654219_0:40-143 [********************* ] 85% > Processing Locus wu_0_2678387_0:7-173 [********************* ] 85% > Processing Locus wu_0_2687576_0:14-171 [********************* ] 86% > Processing Locus wu_0_2824308_0:436-514 [********************* ] 87% > Processing Locus zu_0_3075813_0:4-93 [********************** ] 88%$RNAGI/rnagi.sh -o ./Zu_0 -n it2.fa Zu_0.Toit2.merge.fq > Processing Locus zu_0_3082201_0:1-149 [********************** ] 89% > Processing Locus zu_0_3092045_0:13-139 [********************** ] 90% > Processing Locus zu_0_3118546_0:4-165 [********************** ] 91% > Processing Locus zu_0_3119698_0:72-182 [*********************** ] 92% > Processing Locus zu_0_3190435_0:15-271 [*********************** ] 93% > Processing Locus zu_0_3238769_0:114-192 [*********************** ] 94%reference: it2.fa > Processing Locus zu_0_3242889_0:2-390 [*********************** ] 95% > Processing Locus zu_0_3243571_0:187-801 [************************ ] 96% > Processing Locus zu_0_3255503_0:1066-1369 [************************ ] 97% > Processing Locus zu_0_3260131_0:165-399 [************************ ] 98% > Processing Locus zu_0_3277661_0:309-910 [************************ ] 99% > Processed 107 loci. [*************************] 100% [14:13:12] Loading reference annotation and sequence [14:13:12] Learning bias parameters. > Processing Locus bur_0_1804399_0:0-108 [ ] 0% > Processing Locus bur_0_1873494_0:6-186 [ ] 0% > Processing Locus can_0_3076940_0:5-141 [ ] 1% > Processing Locus can_0_3189753_0:0-205 [ ] 2% > Processing Locus can_0_3223655_0:84-442 [ ] 3% > Processing Locus can_0_3231205_0:13-890 [* ] 4% > Processing Locus can_0_3270131_0:1079-2095 [* ] 5% > Processing Locus ct_1_3082021_0:4-128 [* ] 6% > Processing Locus ct_1_3132277_0:88-175 [* ] 7% > Processing Locus edi_0_2859720_0:154-525 [** ] 8% > Processing Locus edi_0_2871668_0:189-523 [** ] 9% > Processing Locus hi_0_2773206_0:7-158 [** ] 10% > Processing Locus hi_0_2795398_0:0-190 [** ] 11% > Processing Locus hi_0_2961678_0:251-1503 [*** ] 12% > Processing Locus kn_0_3605300_0:1-168 [*** ] 13% > Processing Locus kn_0_3613403_0:4-174 [*** ] 14% > Processing Locus ler_0_3998410_0:0-164 [*** ] 14% > Processing Locus ler_0_4018856_0:1-184 [*** ] 15% > Processing Locus ler_0_4224097_0:924-1703 [**** ] 16% > Processing Locus mt_0_4193196_0:2-165 [**** ] 17% > Processing Locus mt_0_4217716_0:5-185 [**** ] 18% > Processing Locus mt_0_4229662_0:4-197 [**** ] 19% > Processing Locus mt_0_4231054_0:0-83 [***** ] 20% > Processing Locus mt_0_4528444_1:409-1205 [***** ] 21% > Processing Locus no_0_2885444_0:3-113 [***** ] 22% > Processing Locus no_0_2905273_0:7-121 [***** ] 23% > Processing Locus no_0_2956652_0:5-176 [****** ] 24% > Processing Locus oy_0_3001818_0:56-154 [****** ] 25% > Processing Locus rsch_4_4032032_0:0-89 [****** ] 26% > Processing Locus rsch_4_4055167_0:0-109 [****** ] 27% > Processing Locus rsch_4_4214541_0:1-234 [******* ] 28% > Processing Locus rsch_4_4255532_0:0-287 [******* ] 28% > Processing Locus rsch_4_4266550_0:15-1157 [******* ] 29% > Processing Locus rsch_4_4292194_1:0-1127 [******* ] 30% > Processing Locus rsch_4_4297142_0:37-297 [******* ] 31% > Processing Locus sf_2_2486157_0:1-127 [******** ] 32% > Processing Locus sf_2_2524453_0:2-161 [******** ] 33% > Processing Locus sf_2_2532172_0:8-176 [******** ] 34% > Processing Locus sf_2_2687774_0:535-1429 [******** ] 35% > Processing Locus sf_2_2701328_0:1-728 [********* ] 36% > Processing Locus wil_2_2834553_0:0-104 [********* ] 37% > Processing Locus wil_2_2906137_0:12-147 [********* ] 38% > Processing Locus wil_2_2920529_0:0-183 [********* ] 39% > Processing Locus wil_2_2925323_0:12-185 [********** ] 40% > Processing Locus wil_2_2945095_0:60-204 [********** ] 41% > Processing Locus wil_2_3008461_1:2-360 [********** ] 42% > Processing Locus wil_2_3050523_0:32-268 [********** ] 42% > Processing Locus wil_2_3052273_0:36-1026 [********** ] 43% > Processing Locus wil_2_3052951_0:5-913 [*********** ] 44% > Processing Locus wil_2_3054893_0:43-561 [*********** ] 45% > Processing Locus wil_2_3063473_0:0-756 [*********** ] 46% > Processing Locus wil_2_3066229_0:1-761 [*********** ] 47% > Processing Locus wil_2_3068737_0:358-1768 [************ ] 48% > Processing Locus wil_2_3077447_0:1-1244 [************ ] 49% > Processing Locus wil_2_3087183_0:9-819 [************ ] 50% > Processing Locus wil_2_3088151_0:7-955 [************ ] 51% > Processing Locus wil_2_3088151_0:1075-1589 [************* ] 52% > Processing Locus wil_2_3089541_0:2-445 [************* ] 53% > Processing Locus ws_0_3182508_0:6-182 [************* ] 54% > Processing Locus ws_0_3298283_0:18-512 [************* ] 55% > Processing Locus ws_0_3340488_0:31-1139 [************** ] 56% > Processing Locus ws_0_3371988_0:0-112 [************** ] 57% > Processing Locus ws_0_3380934_0:3-207 [************** ] 57% > Processing Locus ws_0_3381390_0:16-1691 [************** ] 58% > Processing Locus wu_0_2654219_0:40-143 [************** ] 59% > Processing Locus wu_0_2678387_0:7-173 [*************** ] 60% > Processing Locus wu_0_2687576_0:14-171 [*************** ] 61% > Processing Locus zu_0_3082201_0:1-149 [*************** ] 62% > Processing Locus zu_0_3118546_0:4-165 [*************** ] 63% > Processing Locus zu_0_3190435_0:15-271 [**************** ] 64% > Processing Locus zu_0_3242889_0:2-390 [**************** ] 65% > Processing Locus zu_0_3243571_0:187-801 [**************** ] 66% > Processing Locus zu_0_3255503_0:1066-1369 [**************** ] 67% > Processing Locus zu_0_3277661_0:309-910 [***************** ] 68% > Processed 74 loci. [*************************] 100% [14:13:12] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:0-108 [ ] 0% > Processing Locus bur_0_1873494_0:6-186 [ ] 0% > Processing Locus can_0_3076940_0:5-141 [ ] 1% > Processing Locus can_0_3189753_0:0-205 [ ] 2% > Processing Locus can_0_3223655_0:84-442 [ ] 3% > Processing Locus can_0_3231205_0:13-890 [* ] 4% > Processing Locus can_0_3270131_0:1079-2095 [* ] 5% > Processing Locus ct_1_3082021_0:4-128 [* ] 6% > Processing Locus ct_1_3132277_0:88-175 [* ] 7% > Processing Locus edi_0_2859720_0:154-525 [** ] 8% > Processing Locus edi_0_2871668_0:189-523 [** ] 9% > Processing Locus hi_0_2773206_0:7-158 [** ] 10% > Processing Locus hi_0_2795398_0:0-190 [** ] 11% > Processing Locus hi_0_2961678_0:251-1503 [*** ] 12% > Processing Locus kn_0_3605300_0:1-168 [*** ] 13% > Processing Locus kn_0_3613403_0:4-174 [*** ] 14% > Processing Locus ler_0_3998410_0:0-164 [*** ] 14% > Processing Locus ler_0_4018856_0:1-184 [*** ] 15% > Processing Locus ler_0_4224097_0:924-1703 [**** ] 16% > Processing Locus mt_0_4193196_0:2-165 [**** ] 17% > Processing Locus mt_0_4217716_0:5-185 [**** ] 18% > Processing Locus mt_0_4229662_0:4-197 [**** ] 19% > Processing Locus mt_0_4231054_0:0-83 [***** ] 20% > Processing Locus mt_0_4528444_1:409-1205 [***** ] 21% > Processing Locus no_0_2885444_0:3-113 [***** ] 22% > Processing Locus no_0_2905273_0:7-121 [***** ] 23% > Processing Locus no_0_2956652_0:5-176 [****** ] 24% > Processing Locus oy_0_3001818_0:56-154 [****** ] 25% > Processing Locus rsch_4_4032032_0:0-89 [****** ] 26% > Processing Locus rsch_4_4055167_0:0-109 [****** ] 27% > Processing Locus rsch_4_4214541_0:1-234 [******* ] 28% > Processing Locus rsch_4_4255532_0:0-287 [******* ] 28% > Processing Locus rsch_4_4266550_0:15-1157 [******* ] 29% > Processing Locus rsch_4_4292194_1:0-1127 [******* ] 30% > Processing Locus rsch_4_4297142_0:37-297 [******* ] 31% > Processing Locus sf_2_2486157_0:1-127 [******** ] 32% > Processing Locus sf_2_2524453_0:2-161 [******** ] 33% > Processing Locus sf_2_2532172_0:8-176 [******** ] 34% > Processing Locus sf_2_2687774_0:535-1429 [******** ] 35% > Processing Locus sf_2_2701328_0:1-728 [********* ] 36% > Processing Locus wil_2_2834553_0:0-104 [********* ] 37% > Processing Locus wil_2_2906137_0:12-147 [********* ] 38% > Processing Locus wil_2_2920529_0:0-183 [********* ] 39% > Processing Locus wil_2_2925323_0:12-185 [********** ] 40% > Processing Locus wil_2_2945095_0:60-204 [********** ] 41% > Processing Locus wil_2_3008461_1:2-360 [********** ] 42% > Processing Locus wil_2_3050523_0:32-268 [********** ] 42% > Processing Locus wil_2_3052273_0:36-1026 [********** ] 43% > Processing Locus wil_2_3052951_0:5-913 [*********** ] 44% > Processing Locus wil_2_3054893_0:43-561 [*********** ] 45% > Processing Locus wil_2_3063473_0:0-756 [*********** ] 46% > Processing Locus wil_2_3066229_0:1-761 [*********** ] 47% > Processing Locus wil_2_3068737_0:358-1768 [************ ] 48% > Processing Locus wil_2_3077447_0:1-1244 [************ ] 49% > Processing Locus wil_2_3087183_0:9-819 [************ ] 50% > Processing Locus wil_2_3088151_0:7-955 [************ ] 51% > Processing Locus wil_2_3088151_0:1075-1589 [************* ] 52% > Processing Locus wil_2_3089541_0:2-445 [************* ] 53% > Processing Locus ws_0_3182508_0:6-182 [************* ] 54% > Processing Locus ws_0_3298283_0:18-512 [************* ] 55% > Processing Locus ws_0_3340488_0:31-1139 [************** ] 56% > Processing Locus ws_0_3371988_0:0-112 [************** ] 57% > Processing Locus ws_0_3380934_0:3-207 [************** ] 57% > Processing Locus ws_0_3381390_0:16-1691 [************** ] 58% > Processing Locus wu_0_2654219_0:40-143 [************** ] 59% > Processing Locus wu_0_2678387_0:7-173 [*************** ] 60% > Processing Locus wu_0_2687576_0:14-171 [*************** ] 61% > Processing Locus zu_0_3082201_0:1-149 [*************** ] 62% > Processing Locus zu_0_3118546_0:4-165 [*************** ] 63% > Processing Locus zu_0_3190435_0:15-271 [**************** ] 64% > Processing Locus zu_0_3242889_0:2-390 [**************** ] 65% > Processing Locus zu_0_3243571_0:187-801 [**************** ] 66% > Processing Locus zu_0_3255503_0:1066-1369 [**************** ] 67% > Processing Locus zu_0_3277661_0:309-910 [***************** ] 68% > Processed 74 loci. [*************************] 100% tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Ws_0 it2.fa ./Ws_0/Ws_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:13:19 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:13:19 2011] Preparing output location ./Ws_0// [Mon Apr 4 14:13:19 2011] Checking for Bowtie index files [Mon Apr 4 14:13:19 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:13:19 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:13:19 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:13:19 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:13:19 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Zu_0 it2.fa ./Zu_0/Zu_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:13:22 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:13:22 2011] Preparing output location ./Zu_0// [Mon Apr 4 14:13:22 2011] Checking for Bowtie index files [Mon Apr 4 14:13:22 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:13:22 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:13:22 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:13:22 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:13:22 2011] Checking reads tophat --num-threads 4 --max-multihits 10 --coverage-search --microexon-search -o ./Wu_0 it2.fa ./Wu_0/Wu_0.Toit2.merge.flt_1.fq [Mon Apr 4 14:13:23 2011] Beginning TopHat run (v1.1.4) ----------------------------------------------- [Mon Apr 4 14:13:23 2011] Preparing output location ./Wu_0// [Mon Apr 4 14:13:23 2011] Checking for Bowtie index files [Mon Apr 4 14:13:23 2011] Checking for reference FASTA file Warning: Could not find FASTA file it2.fa.fa [Mon Apr 4 14:13:23 2011] Reconstituting reference FASTA file from Bowtie index [Mon Apr 4 14:13:23 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Apr 4 14:13:23 2011] Checking for Samtools Samtools version: 0.1.7.0 [Mon Apr 4 14:13:24 2011] Checking reads min read length: 78bp, max read length: 78bp format: fastq quality scale: phred33 (default) [Mon Apr 4 14:13:27 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:13:30 2011] Joining segment hits 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 14:13:34 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:13:35 2011] Mapping reads against it2.fa with Bowtie [Mon Apr 4 14:13:37 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:13:38 2011] Joining segment hits [Mon Apr 4 14:13:40 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:13:40 2011] Joining segment hits [Mon Apr 4 14:13:42 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:13:44 2011] Searching for junctions via segment mapping [Mon Apr 4 14:13:49 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:13:49 2011] Mapping reads against it2.fa with Bowtie(1/3) [Mon Apr 4 14:13:53 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:13:53 2011] Mapping reads against it2.fa with Bowtie(2/3) [Mon Apr 4 14:13:56 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:13:56 2011] Retrieving sequences for splices [Mon Apr 4 14:13:56 2011] Indexing splices [Mon Apr 4 14:13:56 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:13:57 2011] Mapping reads against it2.fa with Bowtie(3/3) [Mon Apr 4 14:13:58 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:14:00 2011] Searching for junctions via segment mapping [Mon Apr 4 14:14:00 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:14:01 2011] Searching for junctions via segment mapping [Mon Apr 4 14:14:02 2011] Joining segment hits [Mon Apr 4 14:14:03 2011] Reporting output tracks ----------------------------------------------- Run complete [00:00:45 elapsed] cufflinks -p 4 -o ./Ws_0 -r it2.fa ./Ws_0/accepted_hits.bam [14:14:07] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1804399_0:0-108 [ ] 0% > Processing Locus bur_0_1856286_0:51-129 [ ] 0% > Processing Locus bur_0_1863298_0:63-141 [ ] 0% > Processing Locus bur_0_1873494_0:24-181 [ ] 1% > Processing Locus can_0_3076940_0:0-139 [ ] 1% > Processing Locus can_0_3122480_0:2-147 [ ] 2% > Processing Locus can_0_3189753_0:42-203 [ ] 2% > Processing Locus can_0_3270131_0:34-112 [ ] 2% > Processing Locus can_0_3270131_0:218-1237 [ ] 2% > Processing Locus can_0_3270131_0:1509-2269 [ ] 2% > Processing Locus ct_1_3082021_0:3-129 [ ] 3% > Processing Locus ct_1_3125173_0:28-106 [ ] 3% > Processing Locus ct_1_3132277_0:0-174 [* ] 4% > Processing Locus ct_1_3133451_0:20-189 [* ] 4% > Processing Locus ct_1_3247037_0:61-552 [* ] 5% > Processing Locus edi_0_2723255_0:61-140 [* ] 5% > Processing Locus edi_0_2871668_0:9-115 [* ] 5% > Processing Locus edi_0_2871668_0:241-527 [* ] 5% > Processing Locus hi_0_2755116_0:1-84 [* ] 6% > Processing Locus hi_0_2778596_0:20-163 [* ] 6% > Processing Locus hi_0_2939638_0:1-632 [* ] 7% > Processing Locus hi_0_2961678_0:86-1505 [* ] 7% > Processing Locus hi_0_2964064_0:131-209 [* ] 7% > Processing Locus hi_0_2964064_0:644-722 [* ] 7% > Processing Locus kn_0_3594465_0:7-140 [** ] 8% > Processing Locus kn_0_3613403_0:8-154 [** ] 8% > Processing Locus kn_0_3617271_0:86-164 [** ] 9% > Processing Locus ler_0_3967940_0:15-135 [** ] 9% > Processing Locus ler_0_3998132_0:47-125 [** ] 10% > Processing Locus ler_0_3998410_0:4-164 [** ] 10% > Processing Locus ler_0_4018856_0:1-183 [** ] 10% > Processing Locus ler_0_4165287_0:34-737 [** ] 11% > Processing Locus ler_0_4224097_0:1026-1636 [** ] 11% > Processing Locus mt_0_4193196_0:3-166 [*** ] 12% > Processing Locus mt_0_4217716_0:6-183 [*** ] 12% > Processing Locus mt_0_4229662_0:0-195 [*** ] 13% > Processing Locus mt_0_4230874_0:45-192 [*** ] 13% > Processing Locus mt_0_4231054_0:1-80 [*** ] 13% > Processing Locus mt_0_4528444_1:572-789 [*** ] 14% > Processing Locus mt_0_4528444_1:1047-1230 [*** ] 14% > Processing Locus no_0_2885444_0:21-109 [*** ] 14% > Processing Locus no_0_2905273_0:9-112 [*** ] 15% > Processing Locus no_0_2956652_0:0-174 [*** ] 15% > Processing Locus no_0_3113578_1:318-834 [*** ] 15% > Processing Locus no_0_3116640_0:474-1885 [**** ] 16% > Processing Locus no_0_3128142_0:26-824 [**** ] 16% > Processing Locus no_0_3128142_0:1533-1611 [**** ] 16% > Processing Locus no_0_3128142_0:1736-2923 [**** ] 16% > Processing Locus oy_0_3001818_0:56-155 [**** ] 17% > Processing Locus oy_0_3148368_0:897-975 [**** ] 17% > Processing Locus po_0_3324652_0:0-126 [**** ] 18% > Processing Locus po_0_3382155_0:1-141 [**** ] 18% > Processing Locus rsch_4_4032032_0:0-89 [**** ] 18% > Processing Locus rsch_4_4034850_0:1-96 [**** ] 19% > Processing Locus rsch_4_4055167_0:0-107 [**** ] 19% > Processing Locus rsch_4_4219071_0:1-79 [***** ] 20% > Processing Locus rsch_4_4219071_0:183-413 [***** ] 20% > Processing Locus rsch_4_4275442_0:68-602 [***** ] 20% > Processing Locus sf_2_2459023_0:2-110 [***** ] 21% > Processing Locus sf_2_2524453_0:1-163 [***** ] 21% > Processing Locus tsu_0_3135135_0:116-211 [***** ] 21% > Processing Locus wil_2_2834553_0:19-97 [***** ] 22% > Processing Locus wil_2_2925323_0:53-185 [***** ] 22% > Processing Locus wil_2_2945095_0:102-180 [***** ] 23% > Processing Locus wil_2_3054893_0:26-574 [***** ] 23% > Processing Locus wil_2_3077447_0:655-778 [***** ] 23% > Processing Locus wil_2_3079625_0:5-628 [****** ] 24% > Processing Locus wil_2_3088151_0:5-533 [****** ] 24% > Processing Locus wil_2_3088151_0:653-1547 [****** ] 24% > Processing Locus ws_0_3181530_0:2-182 [****** ] 25% > Processing Locus ws_0_3182508_0:8-153 [****** ] 25% > Processing Locus ws_0_3326342_0:1-434 [****** ] 26% > Processing Locus ws_0_3339092_0:2-657 [****** ] 26% > Processing Locus ws_0_3340488_0:162-1132 [****** ] 26% > Processing Locus ws_0_3344070_0:14-915 [****** ] 27% > Processing Locus ws_0_3347582_0:157-485 [****** ] 27% > Processing Locus ws_0_3347582_0:766-856 [****** ] 27% > Processing Locus ws_0_3347582_0:964-1042 [****** ] 27% > Processing Locus ws_0_3347582_0:1188-1326 [****** ] 27% > Processing Locus ws_0_3349444_1:574-750 [******* ] 28% > Processing Locus ws_0_3371988_0:0-160 [******* ] 28% > Processing Locus ws_0_3371988_0:1582-1869 [******* ] 28% > Processing Locus ws_0_3371988_0:2126-2204 [******* ] 28% > Processing Locus ws_0_3373604_0:1594-2760 [******* ] 28% > Processing Locus ws_0_3380934_0:4-211 [******* ] 29% > Processing Locus ws_0_3381390_0:0-586 [******* ] 29% > Processing Locus ws_0_3381390_0:693-1636 [******* ] 29% > Processing Locus ws_0_3382500_0:145-3781 [******* ] 30% > Processing Locus ws_0_3382728_0:47-643 [******* ] 30% > Processing Locus ws_0_3382728_0:954-3077 [******* ] 30% > Processing Locus wu_0_2654219_0:40-142 [******* ] 31% > Processing Locus wu_0_2678387_0:6-167 [******* ] 31% > Processing Locus wu_0_2679395_0:23-101 [******* ] 31% > Processing Locus wu_0_2687576_0:89-167 [******** ] 32% > Processing Locus zu_0_3082201_0:1-79 [******** ] 32% > Processing Locus zu_0_3118546_0:4-143 [******** ] 33% > Processing Locus zu_0_3243571_0:571-649 [******** ] 33% > Processed 97 loci. [*************************] 100% > Map Properties: > Total Map Mass: 3940.92 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:14:07] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1804399_0:0-108 [ ] 0% > Processing Locus bur_0_1856286_0:51-129 [ ] 1% > Processing Locus bur_0_1863298_0:63-141 [ ] 2% > Processing Locus bur_0_1873494_0:24-181 [ ] 3% > Processing Locus can_0_3076940_0:0-139 [* ] 4% > Processing Locus can_0_3122480_0:2-147 [* ] 5% > Processing Locus can_0_3189753_0:42-203 [* ] 6% > Processing Locus can_0_3270131_0:34-112 [* ] 7% > Processing Locus can_0_3270131_0:218-1237 [** ] 8% > Processing Locus can_0_3270131_0:1509-2269 [** ] 9% > Processing Locus ct_1_3082021_0:3-129 [** ] 10% > Processing Locus ct_1_3125173_0:28-106 [** ] 11% > Processing Locus ct_1_3132277_0:0-174 [*** ] 12% > Processing Locus ct_1_3133451_0:20-189 [*** ] 13% > Processing Locus ct_1_3247037_0:61-552 [*** ] 14% > Processing Locus edi_0_2723255_0:61-140 [*** ] 15% > Processing Locus edi_0_2871668_0:9-115 [**** ] 16% > Processing Locus edi_0_2871668_0:241-527 [**** ] 17% > Processing Locus hi_0_2755116_0:1-84 [**** ] 18% > Processing Locus hi_0_2778596_0:20-163 [**** ] 19% > Processing Locus hi_0_2939638_0:1-632 [***** ] 20% > Processing Locus hi_0_2961678_0:86-1505 [***** ] 21% > Processing Locus hi_0_2964064_0:131-209 [***** ] 22% > Processing Locus hi_0_2964064_0:644-722 [***** ] 23% > Processing Locus kn_0_3594465_0:7-140 [****** ] 24% > Processing Locus kn_0_3613403_0:8-154 [****** ] 25% > Processing Locus kn_0_3617271_0:86-164 [****** ] 26% > Processing Locus ler_0_3967940_0:15-135 [****** ] 27% > Processing Locus ler_0_3998132_0:47-125 [******* ] 28% > Processing Locus ler_0_3998410_0:4-164 [******* ] 29% > Processing Locus ler_0_4018856_0:1-183 [******* ] 30% > Processing Locus ler_0_4165287_0:34-737 [******* ] 31% > Processing Locus ler_0_4224097_0:1026-1636 [******** ] 32% > Processing Locus mt_0_4193196_0:3-166 [******** ] 34% > Processing Locus mt_0_4217716_0:6-183 [******** ] 35% > Processing Locus mt_0_4229662_0:0-195 [********* ] 36% > Processing Locus mt_0_4230874_0:45-192 [********* ] 37% > Processing Locus mt_0_4231054_0:1-80 [********* ] 38% > Processing Locus mt_0_4528444_1:572-789 [********* ] 39% > Processing Locus mt_0_4528444_1:1047-1230 [********** ] 40% > Processing Locus no_0_2885444_0:21-109 [********** ] 41% > Processing Locus no_0_2905273_0:9-112 [********** ] 42% > Processing Locus no_0_2956652_0:0-174 [********** ] 43% > Processing Locus no_0_3113578_1:318-834 [*********** ] 44% > Processing Locus no_0_3116640_0:474-1885 [*********** ] 45% > Processing Locus no_0_3128142_0:26-824 [*********** ] 46% > Processing Locus no_0_3128142_0:1533-1611 [*********** ] 47% > Processing Locus no_0_3128142_0:1736-2923 [************ ] 48% > Processing Locus oy_0_3001818_0:56-155 [************ ] 49% > Processing Locus oy_0_3148368_0:897-975 [************ ] 50% > Processing Locus po_0_3324652_0:0-126 [************ ] 51% > Processing Locus po_0_3382155_0:1-141 [************* ] 52% > Processing Locus rsch_4_4032032_0:0-89 [************* ] 53% > Processing Locus rsch_4_4034850_0:1-96 [************* ] 54% > Processing Locus rsch_4_4055167_0:0-107 [************* ] 55% > Processing Locus rsch_4_4219071_0:1-79 [************** ] 56% > Processing Locus rsch_4_4219071_0:183-413 [************** ] 57% > Processing Locus rsch_4_4275442_0:68-602 [************** ] 58% > Processing Locus sf_2_2459023_0:2-110 [************** ] 59% > Processing Locus sf_2_2524453_0:1-163 [*************** ] 60% > Processing Locus tsu_0_3135135_0:116-211 [*************** ] 61% > Processing Locus wil_2_2834553_0:19-97 [*************** ] 62% > Processing Locus wil_2_2925323_0:53-185 [*************** ] 63% > Processing Locus wil_2_2945095_0:102-180 [**************** ] 64% > Processing Locus wil_2_3054893_0:26-574 [**************** ] 65% > Processing Locus wil_2_3077447_0:655-778 [**************** ] 67% > Processing Locus wil_2_3079625_0:5-628 [***************** ] 68% > Processing Locus wil_2_3088151_0:5-533 [***************** ] 69% > Processing Locus wil_2_3088151_0:653-1547 [***************** ] 70% > Processing Locus ws_0_3181530_0:2-182 [***************** ] 71% > Processing Locus ws_0_3182508_0:8-153 [****************** ] 72% > Processing Locus ws_0_3326342_0:1-434 [****************** ] 73% > Processing Locus ws_0_3339092_0:2-657 [****************** ] 74% > Processing Locus ws_0_3340488_0:162-1132 [****************** ] 75% > Processing Locus ws_0_3344070_0:14-915 [******************* ] 76% > Processing Locus ws_0_3347582_0:157-485 [******************* ] 77% > Processing Locus ws_0_3347582_0:766-856 [******************* ] 78% > Processing Locus ws_0_3347582_0:964-1042 [******************* ] 79% > Processing Locus ws_0_3347582_0:1188-1326 [******************** ] 80% > Processing Locus ws_0_3349444_1:574-750 [******************** ] 81% > Processing Locus ws_0_3371988_0:0-160 [******************** ] 82% > Processing Locus ws_0_3371988_0:1582-1869 [******************** ] 83% > Processing Locus ws_0_3371988_0:2126-2204 [********************* ] 84% > Processing Locus ws_0_3373604_0:1594-2760 [********************* ] 85% > Processing Locus ws_0_3380934_0:4-211 [********************* ] 86% > Processing Locus ws_0_3381390_0:0-586 [********************* ] 87% > Processing Locus ws_0_3381390_0:693-1636 [********************** ] 88% > Processing Locus ws_0_3382500_0:145-3781 [********************** ] 89% > Processing Locus ws_0_3382728_0:47-643 [********************** ] 90% > Processing Locus ws_0_3382728_0:954-3077 [********************** ] 91% > Processing Locus wu_0_2654219_0:40-142 [*********************** ] 92% > Processing Locus wu_0_2678387_0:6-167 [*********************** ] 93% > Processing Locus wu_0_2679395_0:23-101 [*********************** ] 94% > Processing Locus wu_0_2687576_0:89-167 [*********************** ] 95% > Processing Locus zu_0_3082201_0:1-79 [************************ ] 96% > Processing Locus zu_0_3118546_0:4-143 [************************ ] 97% > Processing Locus zu_0_3243571_0:571-649 [************************ ] 98% > Processed 97 loci. [*************************] 100% [14:14:07] Loading reference annotation and sequence [14:14:07] Learning bias parameters. > Processing Locus bur_0_1873494_0:24-181 [ ] 0% > Processing Locus can_0_3076940_0:0-139 [ ] 1% > Processing Locus can_0_3122480_0:2-147 [ ] 2% > Processing Locus can_0_3189753_0:42-203 [ ] 3% > Processing Locus can_0_3270131_0:218-1237 [* ] 4% > Processing Locus can_0_3270131_0:1509-2269 [* ] 5% > Processing Locus ct_1_3082021_0:3-129 [* ] 6% > Processing Locus ct_1_3132277_0:0-174 [* ] 7% > Processing Locus ct_1_3133451_0:20-189 [** ] 8% > Processing Locus edi_0_2723255_0:61-140 [** ] 9% > Processing Locus edi_0_2871668_0:241-527 [** ] 10% > Processing Locus hi_0_2778596_0:20-163 [** ] 11% > Processing Locus hi_0_2939638_0:1-632 [*** ] 12% > Processing Locus hi_0_2961678_0:86-1505 [*** ] 13% > Processing Locus kn_0_3613403_0:8-154 [*** ] 14% > Processing Locus ler_0_3967940_0:15-135 [*** ] 15% > Processing Locus ler_0_3998410_0:4-164 [**** ] 16% > Processing Locus ler_0_4018856_0:1-183 [**** ] 17% > Processing Locus ler_0_4165287_0:34-737 [**** ] 18% > Processing Locus ler_0_4224097_0:1026-1636 [**** ] 19% > Processing Locus mt_0_4193196_0:3-166 [***** ] 20% > Processing Locus mt_0_4217716_0:6-183 [***** ] 21% > Processing Locus mt_0_4229662_0:0-195 [***** ] 22% > Processing Locus mt_0_4230874_0:45-192 [***** ] 23% > Processing Locus no_0_2905273_0:9-112 [****** ] 24% > Processing Locus no_0_2956652_0:0-174 [****** ] 25% > Processing Locus no_0_3113578_1:318-834 [****** ] 26% > Processing Locus no_0_3116640_0:474-1885 [****** ] 27% > Processing Locus no_0_3128142_0:26-824 [******* ] 28% > Processing Locus no_0_3128142_0:1736-2923 [******* ] 29% > Processing Locus oy_0_3001818_0:56-155 [******* ] 30% > Processing Locus po_0_3324652_0:0-126 [******* ] 31% > Processing Locus po_0_3382155_0:1-141 [******** ] 32% > Processing Locus rsch_4_4032032_0:0-89 [******** ] 34% > Processing Locus rsch_4_4055167_0:0-107 [******** ] 35% > Processing Locus rsch_4_4275442_0:68-602 [********* ] 36% > Processing Locus sf_2_2459023_0:2-110 [********* ] 37% > Processing Locus sf_2_2524453_0:1-163 [********* ] 38% > Processing Locus wil_2_2925323_0:53-185 [********* ] 39% > Processing Locus wil_2_3054893_0:26-574 [********** ] 40% > Processing Locus wil_2_3079625_0:16-628 [********** ] 41% > Processing Locus wil_2_3088151_0:5-533 [********** ] 42% > Processing Locus wil_2_3088151_0:653-1547 [********** ] 43% > Processing Locus ws_0_3181530_0:2-182 [*********** ] 44% > Processing Locus ws_0_3339092_0:2-657 [*********** ] 45% > Processing Locus ws_0_3344070_0:14-915 [*********** ] 46% > Processing Locus ws_0_3349444_1:574-750 [*********** ] 47% > Processing Locus ws_0_3371988_0:0-160 [************ ] 48% > Processing Locus ws_0_3373604_0:1594-2760 [************ ] 49% > Processing Locus ws_0_3380934_0:4-211 [************ ] 50% > Processing Locus ws_0_3381390_0:0-586 [************ ] 51% > Processing Locus ws_0_3381390_0:693-1636 [************* ] 52% > Processing Locus ws_0_3382500_0:145-3781 [************* ] 53% > Processing Locus ws_0_3382728_0:47-643 [************* ] 54% > Processing Locus ws_0_3382728_0:954-3077 [************* ] 55% > Processing Locus zu_0_3118546_0:4-143 [************** ] 56% > Processed 56 loci. [*************************] 100% [14:14:07] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1873494_0:24-181 [ ] 0% > Processing Locus can_0_3076940_0:0-139 [ ] 1% > Processing Locus can_0_3122480_0:2-147 [ ] 2% > Processing Locus can_0_3189753_0:42-203 [ ] 3% > Processing Locus can_0_3270131_0:218-1237 [* ] 4% > Processing Locus can_0_3270131_0:1509-2269 [* ] 5% > Processing Locus ct_1_3082021_0:3-129 [* ] 6% > Processing Locus ct_1_3132277_0:0-174 [* ] 7% > Processing Locus ct_1_3133451_0:20-189 [** ] 8% > Processing Locus edi_0_2723255_0:61-140 [** ] 9% > Processing Locus edi_0_2871668_0:241-527 [** ] 10% > Processing Locus hi_0_2778596_0:20-163 [** ] 11% > Processing Locus hi_0_2939638_0:1-632 [*** ] 12% > Processing Locus hi_0_2961678_0:86-1505 [*** ] 13% > Processing Locus kn_0_3613403_0:8-154 [*** ] 14% > Processing Locus ler_0_3967940_0:15-135 [*** ] 15% > Processing Locus ler_0_3998410_0:4-164 [**** ] 16% > Processing Locus ler_0_4018856_0:1-183 [**** ] 17% > Processing Locus ler_0_4165287_0:34-737 [**** ] 18% > Processing Locus ler_0_4224097_0:1026-1636 [**** ] 19% > Processing Locus mt_0_4193196_0:3-166 [***** ] 20% > Processing Locus mt_0_4217716_0:6-183 [***** ] 21% > Processing Locus mt_0_4229662_0:0-195 [***** ] 22% > Processing Locus mt_0_4230874_0:45-192 [***** ] 23% > Processing Locus no_0_2905273_0:9-112 [****** ] 24% > Processing Locus no_0_2956652_0:0-174 [****** ] 25% > Processing Locus no_0_3113578_1:318-834 [****** ] 26% > Processing Locus no_0_3116640_0:474-1885 [****** ] 27% > Processing Locus no_0_3128142_0:26-824 [******* ] 28% > Processing Locus no_0_3128142_0:1736-2923 [******* ] 29% > Processing Locus oy_0_3001818_0:56-155 [******* ] 30% > Processing Locus po_0_3324652_0:0-126 [******* ] 31% > Processing Locus po_0_3382155_0:1-141 [******** ] 32% > Processing Locus rsch_4_4032032_0:0-89 [******** ] 34% > Processing Locus rsch_4_4055167_0:0-107 [******** ] 35% > Processing Locus rsch_4_4275442_0:68-602 [********* ] 36% > Processing Locus sf_2_2459023_0:2-110 [********* ] 37% > Processing Locus sf_2_2524453_0:1-163 [********* ] 38% > Processing Locus wil_2_2925323_0:53-185 [********* ] 39% > Processing Locus wil_2_3054893_0:26-574 [********** ] 40% > Processing Locus wil_2_3079625_0:16-628 [********** ] 41% > Processing Locus wil_2_3088151_0:5-533 [********** ] 42% > Processing Locus wil_2_3088151_0:653-1547 [********** ] 43% > Processing Locus ws_0_3181530_0:2-182 [*********** ] 44% > Processing Locus ws_0_3339092_0:2-657 [*********** ] 45% > Processing Locus ws_0_3344070_0:14-915 [*********** ] 46% > Processing Locus ws_0_3349444_1:574-750 [*********** ] 47% > Processing Locus ws_0_3371988_0:0-160 [************ ] 48% > Processing Locus ws_0_3373604_0:1594-2760 [************ ] 49% > Processing Locus ws_0_3380934_0:4-211 [************ ] 50% > Processing Locus ws_0_3381390_0:0-586 [************ ] 51% > Processing Locus ws_0_3381390_0:693-1636 [************* ] 52% > Processing Locus ws_0_3382500_0:145-3781 [************* ] 53% > Processing Locus ws_0_3382728_0:47-643 [************* ] 54% > Processing Locus ws_0_3382728_0:954-3077 [************* ] 55% > Processing Locus zu_0_3118546_0:4-143 [************** ] 56% > Processed 56 loci. [*************************] 100% [Mon Apr 4 14:14:18 2011] Retrieving sequences for splices [Mon Apr 4 14:14:18 2011] Indexing splices [Mon Apr 4 14:14:18 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:14:20 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:14:22 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:14:22 2011] Retrieving sequences for splices [Mon Apr 4 14:14:22 2011] Indexing splices [Mon Apr 4 14:14:22 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:14:24 2011] Joining segment hits [Mon Apr 4 14:14:25 2011] Mapping reads against segment_juncs with Bowtie [Mon Apr 4 14:14:25 2011] Reporting output tracks [Mon Apr 4 14:14:27 2011] Mapping reads against segment_juncs with Bowtie ----------------------------------------------- Run complete [00:01:03 elapsed] [Mon Apr 4 14:14:29 2011] Joining segment hits [Mon Apr 4 14:14:30 2011] Reporting output tracks cufflinks -p 4 -o ./Wu_0 -r it2.fa ./Wu_0/accepted_hits.bam [14:14:30] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1868430_0:33-149 [ ] 0% > Processing Locus can_0_3076940_0:3-142 [ ] 0% > Processing Locus can_0_3093852_0:0-126 [ ] 0% > Processing Locus can_0_3189753_0:1-200 [ ] 1% > Processing Locus can_0_3217045_0:8-700 [ ] 1% > Processing Locus can_0_3270131_0:179-1538 [ ] 2% > Processing Locus can_0_3270131_0:1754-2187 [ ] 2% > Processing Locus ct_1_3082021_0:3-126 [ ] 2% > Processing Locus ct_1_3132277_0:2-177 [ ] 2% > Processing Locus ct_1_3241157_0:16-764 [ ] 3% > Processing Locus ct_1_3247037_0:31-109 [ ] 3% > Processing Locus ct_1_3247037_0:280-504 [ ] 3% > Processing Locus ct_1_3302721_0:1261-1339 [* ] 4% > Processing Locus edi_0_2859720_0:5-525 [* ] 4% > Processing Locus edi_0_2889434_0:4-857 [* ] 5% > Processing Locus hi_0_2755116_0:6-84 [* ] 5% > Processing Locus hi_0_2778596_0:1-168 [* ] 5% > Processing Locus hi_0_2916184_0:14-535 [* ] 6% > Processing Locus hi_0_2961678_0:95-1508 [* ] 6% > Processing Locus kn_0_3594465_0:4-159 [* ] 7% > Processing Locus kn_0_3613403_0:0-175 [* ] 7% > Processing Locus kn_0_3617271_0:17-180 [* ] 7% > Processing Locus kn_0_3626969_0:8-189 [** ] 8% > Processing Locus ler_0_3998410_0:1-163 [** ] 8% > Processing Locus ler_0_4018856_0:4-170 [** ] 9% > Processing Locus ler_0_4165287_0:394-472 [** ] 9% > Processing Locus ler_0_4225073_0:42-696 [** ] 10% > Processing Locus mt_0_4193196_0:0-166 [** ] 10% > Processing Locus mt_0_4217716_0:5-183 [** ] 10% > Processing Locus mt_0_4229662_0:1-197 [** ] 11% > Processing Locus mt_0_4231054_0:2-198 [** ] 11% > Processing Locus mt_0_4528444_1:491-1246 [*** ] 12% > Processing Locus no_0_2885444_0:9-110 [*** ] 12% > Processing Locus no_0_2905273_0:0-121 [*** ] 13% > Processing Locus no_0_2951521_0:0-151 [*** ] 13% > Processing Locus no_0_2956652_0:4-177 [*** ] 13% > Processing Locus no_0_2959683_0:8-182 [*** ] 14% > Processing Locus no_0_3128142_0:1763-1857 [*** ] 14% > Processing Locus no_0_3128142_0:1957-2259 [*** ] 14% > Processing Locus no_0_3128142_0:2499-2961 [*** ] 14% > Processing Locus oy_0_2965192_0:49-135 [*** ] 15% > Processing Locus oy_0_3001818_0:65-154 [*** ] 15% > Processing Locus oy_0_3098144_0:15-336 [*** ] 15% > Processing Locus oy_0_3148368_0:628-706 [**** ] 16% > Processing Locus oy_0_3148368_0:957-1035 [**** ] 16% > Processing Locus po_0_3340213_0:5-139 [**** ] 16% > Processing Locus po_0_3372769_0:0-165 [**** ] 17% > Processing Locus rsch_4_4032032_0:0-89 [**** ] 17% > Processing Locus rsch_4_4034850_0:0-102 [**** ] 18% > Processing Locus rsch_4_4055167_0:0-107 [**** ] 18% > Processing Locus rsch_4_4091241_0:5-124 [**** ] 18% > Processing Locus rsch_4_4118145_0:5-164 [**** ] 19% > Processing Locus rsch_4_4219071_0:12-426 [**** ] 19% > Processing Locus sf_2_2459023_0:3-110 [***** ] 20% > Processing Locus sf_2_2486157_0:1-128 [***** ] 20% > Processing Locus sf_2_2524453_0:1-165 [***** ] 21% > Processing Locus sf_2_2532172_0:9-180 [***** ] 21% > Processing Locus sf_2_2662232_0:28-116 [***** ] 21% > Processing Locus sf_2_2680171_0:2-296 [***** ] 22% > Processing Locus sf_2_2687774_0:208-286 [***** ] 22% > Processing Locus sf_2_2687774_0:599-1429 [***** ] 22% > Processing Locus sf_2_2687786_0:84-2175 [***** ] 23% > Processing Locus tsu_0_3036945_0:52-130 [***** ] 23% > Processing Locus tsu_0_3229935_0:17-1281 [***** ] 23% > Processing Locus wil_2_2834553_0:0-88 [****** ] 24% > Processing Locus wil_2_2915899_0:46-171 [****** ] 24% > Processing Locus wil_2_2925323_0:10-193 [****** ] 25% > Processing Locus wil_2_3050523_0:17-272 [****** ] 25% > Processing Locus wil_2_3052273_0:103-988 [****** ] 26% > Processing Locus wil_2_3054893_0:22-565 [****** ] 26% > Processing Locus wil_2_3079625_0:529-607 [****** ] 26% > Processing Locus wil_2_3092619_0:795-873 [****** ] 27% > Processing Locus wil_2_3092619_0:1124-1202 [****** ] 27% > Processing Locus ws_0_3182508_0:5-163 [****** ] 27% > Processing Locus ws_0_3326342_0:12-416 [******* ] 28% > Processing Locus ws_0_3340488_0:199-1138 [******* ] 28% > Processing Locus ws_0_3347582_0:171-856 [******* ] 28% > Processing Locus ws_0_3347582_0:980-1360 [******* ] 28% > Processing Locus ws_0_3371988_0:0-222 [******* ] 29% > Processing Locus ws_0_3371988_0:1918-2245 [******* ] 29% > Processing Locus ws_0_3372048_0:17-996 [******* ] 29% > Processing Locus ws_0_3372048_0:1104-1281 [******* ] 29% > Processing Locus ws_0_3380934_0:5-211 [******* ] 30% > Processing Locus ws_0_3381390_0:8-1622 [******* ] 30% > Processing Locus wu_0_2654219_0:2-149 [******* ] 31% > Processing Locus wu_0_2655481_0:2-148 [******* ] 31% > Processing Locus wu_0_2678387_0:2-170 [******* ] 31% > Processing Locus wu_0_2679395_0:1-133 [******** ] 32% > Processing Locus wu_0_2687576_0:15-171 [******** ] 32% > Processing Locus wu_0_2824308_0:20-842 [******** ] 33% > Processing Locus zu_0_3022629_0:0-112 [******** ] 33% > Processing Locus zu_0_3082201_0:1-148 [******** ] 34% > Processing Locus zu_0_3092045_0:2-158 [******** ] 34% > Processing Locus zu_0_3118546_0:4-168 [******** ] 34% > Processing Locus zu_0_3190435_0:8-300 [******** ] 35% > Processing Locus zu_0_3238769_0:294-372 [******** ] 35% > Processing Locus zu_0_3243571_0:58-179 [********* ] 36% > Processing Locus zu_0_3243571_0:327-797 [********* ] 36% > Processed 98 loci. [*************************] 100% > Map Properties: > Total Map Mass: 5480.62 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:14:30] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1868430_0:33-149 [ ] 0% > Processing Locus can_0_3076940_0:3-142 [ ] 1% > Processing Locus can_0_3093852_0:0-126 [ ] 2% > Processing Locus can_0_3189753_0:1-200 [ ] 3% > Processing Locus can_0_3217045_0:8-700 [* ] 4% > Processing Locus can_0_3270131_0:179-1538 [* ] 5% > Processing Locus can_0_3270131_0:1754-2187 [* ] 6% > Processing Locus ct_1_3082021_0:3-126 [* ] 7% > Processing Locus ct_1_3132277_0:2-177 [** ] 8% > Processing Locus ct_1_3241157_0:16-764 [** ] 9% > Processing Locus ct_1_3247037_0:31-109 [** ] 10% > Processing Locus ct_1_3247037_0:280-504 [** ] 11% > Processing Locus ct_1_3302721_0:1261-1339 [*** ] 12% > Processing Locus edi_0_2859720_0:5-525 [*** ] 13% > Processing Locus edi_0_2889434_0:4-857 [*** ] 14% > Processing Locus hi_0_2755116_0:6-84 [*** ] 15% > Processing Locus hi_0_2778596_0:1-168 [**** ] 16% > Processing Locus hi_0_2916184_0:14-535 [**** ] 17% > Processing Locus hi_0_2961678_0:95-1508 [**** ] 18% > Processing Locus kn_0_3594465_0:4-159 [**** ] 19% > Processing Locus kn_0_3613403_0:0-175 [***** ] 20% > Processing Locus kn_0_3617271_0:17-180 [***** ] 21% > Processing Locus kn_0_3626969_0:8-189 [***** ] 22% > Processing Locus ler_0_3998410_0:1-163 [***** ] 23% > Processing Locus ler_0_4018856_0:4-170 [****** ] 24% > Processing Locus ler_0_4165287_0:394-472 [****** ] 25% > Processing Locus ler_0_4225073_0:42-696 [****** ] 26% > Processing Locus mt_0_4193196_0:0-166 [****** ] 27% > Processing Locus mt_0_4217716_0:5-183 [******* ] 28% > Processing Locus mt_0_4229662_0:1-197 [******* ] 29% > Processing Locus mt_0_4231054_0:2-198 [******* ] 30% > Processing Locus mt_0_4528444_1:491-1246 [******* ] 31% > Processing Locus no_0_2885444_0:9-110 [******** ] 32% > Processing Locus no_0_2905273_0:0-121 [******** ] 33% > Processing Locus no_0_2951521_0:0-151 [******** ] 34% > Processing Locus no_0_2956652_0:4-177 [******** ] 35% > Processing Locus no_0_2959683_0:8-182 [********* ] 36% > Processing Locus no_0_3128142_0:1763-1857 [********* ] 37% > Processing Locus no_0_3128142_0:1957-2259 [********* ] 38% > Processing Locus no_0_3128142_0:2499-2961 [********* ] 39% > Processing Locus oy_0_2965192_0:49-135 [********** ] 40% > Processing Locus oy_0_3001818_0:65-154 [********** ] 41% > Processing Locus oy_0_3098144_0:15-336 [********** ] 42% > Processing Locus oy_0_3148368_0:628-706 [********** ] 43% > Processing Locus oy_0_3148368_0:957-1035 [*********** ] 44% > Processing Locus po_0_3340213_0:5-139 [*********** ] 45% > Processing Locus po_0_3372769_0:0-165 [*********** ] 46% > Processing Locus rsch_4_4032032_0:0-89 [*********** ] 47% > Processing Locus rsch_4_4034850_0:0-102 [************ ] 48% > Processing Locus rsch_4_4055167_0:0-107 [************ ] 50% > Processing Locus rsch_4_4091241_0:5-124 [************ ] 51% > Processing Locus rsch_4_4118145_0:5-164 [************* ] 52% > Processing Locus rsch_4_4219071_0:12-426 [************* ] 53% > Processing Locus sf_2_2459023_0:3-110 [************* ] 54% > Processing Locus sf_2_2486157_0:1-128 [************* ] 55% > Processing Locus sf_2_2524453_0:1-165 [************** ] 56% > Processing Locus sf_2_2532172_0:9-180 [************** ] 57% > Processing Locus sf_2_2662232_0:28-116 [************** ] 58% > Processing Locus sf_2_2680171_0:2-296 [************** ] 59% > Processing Locus sf_2_2687774_0:208-286 [*************** ] 60% > Processing Locus sf_2_2687774_0:599-1429 [*************** ] 61% > Processing Locus sf_2_2687786_0:84-2175 [*************** ] 62% > Processing Locus tsu_0_3036945_0:52-130 [*************** ] 63% > Processing Locus tsu_0_3229935_0:17-1281 [**************** ] 64% > Processing Locus wil_2_2834553_0:0-88 [**************** ] 65% > Processing Locus wil_2_2915899_0:46-171 [**************** ] 66% > Processing Locus wil_2_2925323_0:10-193 [**************** ] 67% > Processing Locus wil_2_3050523_0:17-272 [***************** ] 68% > Processing Locus wil_2_3052273_0:103-988 [***************** ] 69% > Processing Locus wil_2_3054893_0:22-565 [***************** ] 70% > Processing Locus wil_2_3079625_0:529-607 [***************** ] 71% > Processing Locus wil_2_3092619_0:795-873 [****************** ] 72% > Processing Locus wil_2_3092619_0:1124-1202 [****************** ] 73% > Processing Locus ws_0_3182508_0:5-163 [****************** ] 74% > Processing Locus ws_0_3326342_0:12-416 [****************** ] 75% > Processing Locus ws_0_3340488_0:199-1138 [******************* ] 76% > Processing Locus ws_0_3347582_0:171-856 [******************* ] 77% > Processing Locus ws_0_3347582_0:980-1360 [******************* ] 78% > Processing Locus ws_0_3371988_0:0-222 [******************* ] 79% > Processing Locus ws_0_3371988_0:1918-2245 [******************** ] 80% > Processing Locus ws_0_3372048_0:17-996 [******************** ] 81% > Processing Locus ws_0_3372048_0:1104-1281 [******************** ] 82% > Processing Locus ws_0_3380934_0:5-211 [******************** ] 83% > Processing Locus ws_0_3381390_0:8-1622 [********************* ] 84% > Processing Locus wu_0_2654219_0:2-149 [********************* ] 85% > Processing Locus wu_0_2655481_0:2-148 [********************* ] 86% > Processing Locus wu_0_2678387_0:2-170 [********************* ] 87% > Processing Locus wu_0_2679395_0:1-133 [********************** ] 88% > Processing Locus wu_0_2687576_0:15-171 [********************** ] 89% > Processing Locus wu_0_2824308_0:20-842 [********************** ] 90% > Processing Locus zu_0_3022629_0:0-112 [********************** ] 91% > Processing Locus zu_0_3082201_0:1-148 [*********************** ] 92% > Processing Locus zu_0_3092045_0:2-158 [*********************** ] 93% > Processing Locus zu_0_3118546_0:4-168 [*********************** ] 94% > Processing Locus zu_0_3190435_0:8-300 [*********************** ] 95% > Processing Locus zu_0_3238769_0:294-372 [************************ ] 96% > Processing Locus zu_0_3243571_0:58-179 [************************ ] 97% > Processing Locus zu_0_3243571_0:327-797 [************************ ] 98% > Processed 98 loci. [*************************] 100% [14:14:30] Loading reference annotation and sequence [14:14:30] Learning bias parameters. > Processing Locus bur_0_1868430_0:33-149 [ ] 0% > Processing Locus can_0_3076940_0:3-142 [ ] 1% > Processing Locus can_0_3189753_0:1-200 [ ] 2% > Processing Locus can_0_3217045_0:8-700 [ ] 3% > Processing Locus can_0_3270131_0:179-1538 [* ] 4% > Processing Locus ct_1_3082021_0:3-126 [* ] 5% > Processing Locus ct_1_3132277_0:2-177 [* ] 6% > Processing Locus ct_1_3241157_0:16-764 [* ] 7% > Processing Locus edi_0_2859720_0:5-525 [** ] 8% > Processing Locus edi_0_2889434_0:4-857 [** ] 9% > Processing Locus hi_0_2778596_0:1-168 [** ] 10% > Processing Locus hi_0_2916184_0:14-535 [** ] 11% > Processing Locus hi_0_2961678_0:95-1508 [*** ] 12% > Processing Locus kn_0_3594465_0:4-159 [*** ] 13% > Processing Locus kn_0_3613403_0:0-175 [*** ] 14% > Processing Locus kn_0_3617271_0:17-180 [*** ] 15% > Processing Locus kn_0_3626969_0:8-189 [**** ] 16% > Processing Locus ler_0_3998410_0:1-163 [**** ] 17% > Processing Locus ler_0_4018856_0:4-170 [**** ] 18% > Processing Locus ler_0_4225073_0:42-696 [**** ] 19% > Processing Locus mt_0_4193196_0:0-166 [***** ] 20% > Processing Locus mt_0_4217716_0:5-183 [***** ] 21% > Processing Locus mt_0_4229662_0:1-197 [***** ] 22% > Processing Locus mt_0_4231054_0:2-198 [***** ] 23% > Processing Locus mt_0_4528444_1:491-1246 [****** ] 24% > Processing Locus no_0_2885444_0:9-110 [****** ] 25% > Processing Locus no_0_2905273_0:0-121 [****** ] 26% > Processing Locus no_0_2956652_0:4-177 [****** ] 27% > Processing Locus no_0_2959683_0:8-182 [******* ] 28% > Processing Locus no_0_3128142_0:1957-2259 [******* ] 29% > Processing Locus oy_0_3001818_0:65-154 [******* ] 30% > Processing Locus oy_0_3098144_0:15-336 [******* ] 31% > Processing Locus po_0_3372769_0:0-165 [******** ] 32% > Processing Locus rsch_4_4032032_0:0-89 [******** ] 33% > Processing Locus rsch_4_4034850_0:0-102 [******** ] 34% > Processing Locus rsch_4_4055167_0:0-107 [******** ] 35% > Processing Locus rsch_4_4091241_0:5-124 [********* ] 36% > Processing Locus rsch_4_4118145_0:5-164 [********* ] 37% > Processing Locus rsch_4_4219071_0:12-426 [********* ] 38% > Processing Locus sf_2_2459023_0:3-110 [********* ] 39% > Processing Locus sf_2_2486157_0:1-128 [********** ] 40% > Processing Locus sf_2_2524453_0:1-165 [********** ] 41% > Processing Locus sf_2_2532172_0:9-180 [********** ] 42% > Processing Locus sf_2_2662232_0:28-116 [********** ] 43% > Processing Locus sf_2_2680171_0:2-296 [*********** ] 44% > Processing Locus sf_2_2687774_0:599-1429 [*********** ] 45% > Processing Locus sf_2_2687786_0:84-2175 [*********** ] 46% > Processing Locus wil_2_2925323_0:10-193 [*********** ] 47% > Processing Locus wil_2_3050523_0:17-272 [************ ] 48% > Processing Locus wil_2_3052273_0:103-988 [************ ] 50% > Processing Locus wil_2_3054893_0:22-565 [************ ] 51% > Processing Locus ws_0_3182508_0:5-163 [************* ] 52% > Processing Locus ws_0_3340488_0:199-1138 [************* ] 53% > Processing Locus ws_0_3347582_0:171-856 [************* ] 54% > Processing Locus ws_0_3347582_0:980-1360 [************* ] 55% > Processing Locus ws_0_3371988_0:0-222 [************** ] 56% > Processing Locus ws_0_3380934_0:5-211 [************** ] 57% > Processing Locus ws_0_3381390_0:8-1622 [************** ] 58% > Processing Locus wu_0_2654219_0:2-149 [************** ] 59% > Processing Locus wu_0_2655481_0:2-148 [*************** ] 60% > Processing Locus wu_0_2678387_0:2-170 [*************** ] 61% > Processing Locus wu_0_2679395_0:1-133 [*************** ] 62% > Processing Locus wu_0_2687576_0:15-171 [*************** ] 63% > Processing Locus wu_0_2824308_0:20-842 [**************** ] 64% > Processing Locus zu_0_3022629_0:0-112 [**************** ] 65% > Processing Locus zu_0_3082201_0:1-148 [**************** ] 66% > Processing Locus zu_0_3092045_0:2-158 [**************** ] 67% > Processing Locus zu_0_3118546_0:4-168 [***************** ] 68% > Processing Locus zu_0_3190435_0:8-300 [***************** ] 69% > Processing Locus zu_0_3243571_0:327-797 [***************** ] 70% > Processed 70 loci. [*************************] 100% [14:14:30] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1868430_0:33-149 [ ] 0% > Processing Locus can_0_3076940_0:3-142 [ ] 1% > Processing Locus can_0_3189753_0:1-200 [ ] 2% > Processing Locus can_0_3217045_0:8-700 [ ] 3% > Processing Locus can_0_3270131_0:179-1538 [* ] 4% > Processing Locus ct_1_3082021_0:3-126 [* ] 5% > Processing Locus ct_1_3132277_0:2-177 [* ] 6% > Processing Locus ct_1_3241157_0:16-764 [* ] 7% > Processing Locus edi_0_2859720_0:5-525 [** ] 8% > Processing Locus edi_0_2889434_0:4-857 [** ] 9% > Processing Locus hi_0_2778596_0:1-168 [** ] 10% > Processing Locus hi_0_2916184_0:14-535 [** ] 11% > Processing Locus hi_0_2961678_0:95-1508 [*** ] 12% > Processing Locus kn_0_3594465_0:4-159 [*** ] 13% > Processing Locus kn_0_3613403_0:0-175 [*** ] 14% > Processing Locus kn_0_3617271_0:17-180 [*** ] 15% > Processing Locus kn_0_3626969_0:8-189 [**** ] 16% > Processing Locus ler_0_3998410_0:1-163 [**** ] 17% > Processing Locus ler_0_4018856_0:4-170 [**** ] 18% > Processing Locus ler_0_4225073_0:42-696 [**** ] 19% > Processing Locus mt_0_4193196_0:0-166 [***** ] 20% > Processing Locus mt_0_4217716_0:5-183 [***** ] 21% > Processing Locus mt_0_4229662_0:1-197 [***** ] 22% > Processing Locus mt_0_4231054_0:2-198 [***** ] 23% > Processing Locus mt_0_4528444_1:491-1246 [****** ] 24% > Processing Locus no_0_2885444_0:9-110 [****** ] 25% > Processing Locus no_0_2905273_0:0-121 [****** ] 26% > Processing Locus no_0_2956652_0:4-177 [****** ] 27% > Processing Locus no_0_2959683_0:8-182 [******* ] 28% > Processing Locus no_0_3128142_0:1957-2259 [******* ] 29% > Processing Locus oy_0_3001818_0:65-154 [******* ] 30% > Processing Locus oy_0_3098144_0:15-336 [******* ] 31% > Processing Locus po_0_3372769_0:0-165 [******** ] 32% > Processing Locus rsch_4_4032032_0:0-89 [******** ] 33% > Processing Locus rsch_4_4034850_0:0-102 [******** ] 34% > Processing Locus rsch_4_4055167_0:0-107 [******** ] 35% > Processing Locus rsch_4_4091241_0:5-124 [********* ] 36% > Processing Locus rsch_4_4118145_0:5-164 [********* ] 37% > Processing Locus rsch_4_4219071_0:12-426 [********* ] 38% > Processing Locus sf_2_2459023_0:3-110 [********* ] 39% > Processing Locus sf_2_2486157_0:1-128 [********** ] 40% > Processing Locus sf_2_2524453_0:1-165 [********** ] 41% > Processing Locus sf_2_2532172_0:9-180 [********** ] 42% > Processing Locus sf_2_2662232_0:28-116 [********** ] 43% > Processing Locus sf_2_2680171_0:2-296 [*********** ] 44% > Processing Locus sf_2_2687774_0:599-1429 [*********** ] 45% > Processing Locus sf_2_2687786_0:84-2175 [*********** ] 46% > Processing Locus wil_2_2925323_0:10-193 [*********** ] 47% > Processing Locus wil_2_3050523_0:17-272 [************ ] 48% > Processing Locus wil_2_3052273_0:103-988 [************ ] 50% > Processing Locus wil_2_3054893_0:22-565 [************ ] 51% > Processing Locus ws_0_3182508_0:5-163 [************* ] 52% > Processing Locus ws_0_3340488_0:199-1138 [************* ] 53% > Processing Locus ws_0_3347582_0:171-856 [************* ] 54% > Processing Locus ws_0_3347582_0:980-1360 [************* ] 55% > Processing Locus ws_0_3371988_0:0-222 [************** ] 56% > Processing Locus ws_0_3380934_0:5-211 [************** ] 57% > Processing Locus ws_0_3381390_0:8-1622 [************** ] 58% > Processing Locus wu_0_2654219_0:2-149 [************** ] 59% > Processing Locus wu_0_2655481_0:2-148 [*************** ] 60% > Processing Locus wu_0_2678387_0:2-170 [*************** ] 61% > Processing Locus wu_0_2679395_0:1-133 [*************** ] 62% > Processing Locus wu_0_2687576_0:15-171 [*************** ] 63% > Processing Locus wu_0_2824308_0:20-842 [**************** ] 64% > Processing Locus zu_0_3022629_0:0-112 [**************** ] 65% > Processing Locus zu_0_3082201_0:1-148 [**************** ] 66% > Processing Locus zu_0_3092045_0:2-158 [**************** ] 67% > Processing Locus zu_0_3118546_0:4-168 [***************** ] 68% > Processing Locus zu_0_3190435_0:8-300 [***************** ] 69% > Processing Locus zu_0_3243571_0:327-797 [***************** ] 70% > Processed 70 loci. [*************************] 100% ----------------------------------------------- Run complete [00:01:10 elapsed] cufflinks -p 4 -o ./Zu_0 -r it2.fa ./Zu_0/accepted_hits.bam [14:14:36] Inspecting reads and determining fragment length distribution. > Processing Locus bur_0_1873494_0:17-187 [ ] 0% > Processing Locus bur_0_1969548_0:6-676 [ ] 0% > Processing Locus bur_0_2020452_0:2-1282 [ ] 0% > Processing Locus bur_0_2020452_0:1492-1570 [ ] 0% > Processing Locus bur_0_2020452_0:1827-2234 [ ] 0% > Processing Locus can_0_3017860_0:2-80 [ ] 1% > Processing Locus can_0_3076940_0:0-142 [ ] 1% > Processing Locus can_0_3093852_0:2-119 [ ] 2% > Processing Locus can_0_3223655_0:46-124 [ ] 2% > Processing Locus can_0_3231205_0:13-879 [ ] 2% > Processing Locus can_0_3258779_0:103-233 [ ] 3% > Processing Locus can_0_3258779_0:359-626 [ ] 3% > Processing Locus can_0_3270131_0:16-377 [ ] 3% > Processing Locus can_0_3270131_0:662-915 [ ] 3% > Processing Locus can_0_3270131_0:1068-1761 [ ] 3% > Processing Locus can_0_3270131_0:1939-2118 [ ] 3% > Processing Locus ct_1_3082021_0:2-128 [* ] 4% > Processing Locus ct_1_3133995_0:80-195 [* ] 4% > Processing Locus edi_0_2859720_0:137-518 [* ] 5% > Processing Locus edi_0_2932438_0:2-288 [* ] 5% > Processing Locus hi_0_2939638_0:55-642 [* ] 5% > Processing Locus kn_0_3594465_0:14-152 [* ] 6% > Processing Locus kn_0_3613403_0:0-130 [* ] 6% > Processing Locus kn_0_3617271_0:16-171 [* ] 7% > Processing Locus kn_0_3626969_0:41-164 [* ] 7% > Processing Locus ler_0_3998410_0:1-164 [* ] 7% > Processing Locus ler_0_4018856_0:0-176 [** ] 8% > Processing Locus ler_0_4153595_0:230-661 [** ] 8% > Processing Locus mt_0_4193196_0:0-164 [** ] 9% > Processing Locus mt_0_4217716_0:2-181 [** ] 9% > Processing Locus mt_0_4229662_0:1-196 [** ] 10% > Processing Locus mt_0_4230874_0:43-185 [** ] 10% > Processing Locus mt_0_4231054_0:0-197 [** ] 10% > Processing Locus no_0_2885444_0:10-111 [** ] 11% > Processing Locus no_0_2905273_0:7-118 [** ] 11% > Processing Locus no_0_2951521_0:0-144 [*** ] 12% > Processing Locus no_0_2956652_0:2-174 [*** ] 12% > Processing Locus no_0_2959683_0:7-179 [*** ] 13% > Processing Locus no_0_3116640_0:429-1875 [*** ] 13% > Processing Locus no_0_3128142_0:5-899 [*** ] 13% > Processing Locus no_0_3128142_0:1112-1333 [*** ] 13% > Processing Locus no_0_3128142_0:1717-2954 [*** ] 13% > Processing Locus oy_0_3121110_0:51-543 [*** ] 14% > Processing Locus oy_0_3162092_0:1575-1653 [*** ] 14% > Processing Locus po_0_3293868_0:39-117 [*** ] 15% > Processing Locus po_0_3299272_0:12-119 [*** ] 15% > Processing Locus po_0_3324652_0:2-132 [*** ] 15% > Processing Locus po_0_3332479_0:0-136 [**** ] 16% > Processing Locus po_0_3372769_0:47-125 [**** ] 16% > Processing Locus po_0_3393401_0:44-122 [**** ] 17% > Processing Locus po_0_3573778_0:336-1280 [**** ] 17% > Processing Locus po_0_3606391_0:1119-1275 [**** ] 18% > Processing Locus po_0_3606391_0:1398-1788 [**** ] 18% > Processing Locus po_0_3606391_0:1976-2879 [**** ] 18% > Processing Locus po_0_3606391_1:25-120 [**** ] 18% > Processing Locus po_0_3606391_1:658-987 [**** ] 18% > Processing Locus rsch_4_4032032_0:0-89 [**** ] 18% > Processing Locus rsch_4_4034850_0:0-99 [**** ] 19% > Processing Locus rsch_4_4091241_0:6-128 [**** ] 19% > Processing Locus rsch_4_4118145_0:5-160 [***** ] 20% > Processing Locus rsch_4_4214541_0:1-234 [***** ] 20% > Processing Locus rsch_4_4219071_0:12-364 [***** ] 21% > Processing Locus rsch_4_4255532_0:1-278 [***** ] 21% > Processing Locus rsch_4_4266550_0:5-1149 [***** ] 21% > Processing Locus rsch_4_4292194_1:8-1135 [***** ] 22% > Processing Locus rsch_4_4297142_0:164-242 [***** ] 22% > Processing Locus sf_2_2459023_0:7-109 [***** ] 23% > Processing Locus sf_2_2504999_0:5-140 [***** ] 23% > Processing Locus sf_2_2653966_0:2-691 [***** ] 23% > Processing Locus sf_2_2680171_0:0-1163 [****** ] 24% > Processing Locus sf_2_2687786_0:0-981 [****** ] 24% > Processing Locus sf_2_2687786_0:1085-2189 [****** ] 24% > Processing Locus sf_2_2701328_0:1-724 [****** ] 25% > Processing Locus tsu_0_3135135_0:3-166 [****** ] 25% > Processing Locus tsu_0_3175121_0:5-416 [****** ] 26% > Processing Locus tsu_0_3175121_0:570-703 [****** ] 26% > Processing Locus tsu_0_3215671_0:149-275 [****** ] 26% > Processing Locus tsu_0_3215671_0:760-838 [****** ] 26% > Processing Locus tsu_0_3215737_0:13-1098 [****** ] 26% > Processing Locus tsu_0_3242833_1:25-914 [****** ] 27% > Processing Locus wil_2_2892485_0:38-138 [****** ] 27% > Processing Locus wil_2_3050523_0:1-218 [******* ] 28% > Processing Locus wil_2_3090237_0:250-494 [******* ] 28% > Processing Locus wil_2_3092619_0:1091-1169 [******* ] 28% > Processing Locus ws_0_3182508_0:1-182 [******* ] 29% > Processing Locus ws_0_3190679_0:25-171 [******* ] 29% > Processing Locus ws_0_3190963_0:13-180 [******* ] 30% > Processing Locus ws_0_3326342_0:12-364 [******* ] 30% > Processing Locus ws_0_3339092_0:361-439 [******* ] 31% > Processing Locus ws_0_3347582_0:69-1370 [******* ] 31% > Processing Locus ws_0_3380934_0:3-211 [******* ] 31% > Processing Locus wu_0_2654219_0:68-147 [******** ] 32% > Processing Locus wu_0_2678387_0:10-182 [******** ] 32% > Processing Locus zu_0_3022629_0:0-112 [******** ] 33% > Processing Locus zu_0_3075813_0:14-134 [******** ] 33% > Processing Locus zu_0_3082201_0:1-148 [******** ] 34% > Processing Locus zu_0_3092045_0:8-157 [******** ] 34% > Processing Locus zu_0_3118546_0:4-153 [******** ] 34% > Processing Locus zu_0_3119698_0:79-177 [******** ] 35% > Processing Locus zu_0_3190435_0:8-295 [******** ] 35% > Processing Locus zu_0_3242889_0:3-251 [********* ] 36% > Processing Locus zu_0_3243571_0:49-127 [********* ] 36% > Processing Locus zu_0_3243571_0:231-801 [********* ] 36% > Processing Locus zu_0_3255503_0:1072-1357 [********* ] 36% > Processing Locus zu_0_3259399_1:88-320 [********* ] 37% > Processing Locus zu_0_3260131_0:156-400 [********* ] 37% > Processing Locus zu_0_3277661_0:263-908 [********* ] 38% > Processing Locus zu_0_3278243_0:11-93 [********* ] 38% > Processing Locus zu_0_3280213_0:148-2101 [********* ] 39% > Processed 109 loci. [*************************] 100% > Map Properties: > Total Map Mass: 6568.50 > Read Type: 78bp single-end > Fragment Length Distribution: Gaussian (default) > Estimated Mean: 210.19 > Estimated Std Dev: 70.09 [14:14:36] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1873494_0:17-187 [ ] 0% > Processing Locus bur_0_1969548_0:6-676 [ ] 0% > Processing Locus bur_0_2020452_0:2-1282 [ ] 1% > Processing Locus bur_0_2020452_0:1492-1570 [ ] 2% > Processing Locus bur_0_2020452_0:1827-2234 [ ] 3% > Processing Locus can_0_3017860_0:2-80 [* ] 4% > Processing Locus can_0_3076940_0:0-142 [* ] 5% > Processing Locus can_0_3093852_0:2-119 [* ] 6% > Processing Locus can_0_3223655_0:46-124 [* ] 7% > Processing Locus can_0_3231205_0:13-879 [** ] 8% > Processing Locus can_0_3258779_0:103-233 [** ] 9% > Processing Locus can_0_3258779_0:359-626 [** ] 10% > Processing Locus can_0_3270131_0:16-377 [** ] 11% > Processing Locus can_0_3270131_0:662-915 [** ] 11% > Processing Locus can_0_3270131_0:1068-1761 [*** ] 12% > Processing Locus can_0_3270131_0:1939-2118 [*** ] 13% > Processing Locus ct_1_3082021_0:2-128 [*** ] 14% > Processing Locus ct_1_3133995_0:80-195 [*** ] 15% > Processing Locus edi_0_2859720_0:137-518 [**** ] 16% > Processing Locus edi_0_2932438_0:2-288 [**** ] 17% > Processing Locus hi_0_2939638_0:55-642 [**** ] 18% > Processing Locus kn_0_3594465_0:14-152 [**** ] 19% > Processing Locus kn_0_3613403_0:0-130 [***** ] 20% > Processing Locus kn_0_3617271_0:16-171 [***** ] 21% > Processing Locus kn_0_3626969_0:41-164 [***** ] 22% > Processing Locus ler_0_3998410_0:1-164 [***** ] 22% > Processing Locus ler_0_4018856_0:0-176 [***** ] 23% > Processing Locus ler_0_4153595_0:230-661 [****** ] 24% > Processing Locus mt_0_4193196_0:0-164 [****** ] 25% > Processing Locus mt_0_4217716_0:2-181 [****** ] 26% > Processing Locus mt_0_4229662_0:1-196 [****** ] 27% > Processing Locus mt_0_4230874_0:43-185 [******* ] 28% > Processing Locus mt_0_4231054_0:0-197 [******* ] 29% > Processing Locus no_0_2885444_0:10-111 [******* ] 30% > Processing Locus no_0_2905273_0:7-118 [******* ] 31% > Processing Locus no_0_2951521_0:0-144 [******** ] 32% > Processing Locus no_0_2956652_0:2-174 [******** ] 33% > Processing Locus no_0_2959683_0:7-179 [******** ] 33% > Processing Locus no_0_3116640_0:429-1875 [******** ] 34% > Processing Locus no_0_3128142_0:5-899 [******** ] 35% > Processing Locus no_0_3128142_0:1112-1333 [********* ] 36% > Processing Locus no_0_3128142_0:1717-2954 [********* ] 37% > Processing Locus oy_0_3121110_0:51-543 [********* ] 38% > Processing Locus oy_0_3162092_0:1575-1653 [********* ] 39% > Processing Locus po_0_3293868_0:39-117 [********** ] 40% > Processing Locus po_0_3299272_0:12-119 [********** ] 41% > Processing Locus po_0_3324652_0:2-132 [********** ] 42% > Processing Locus po_0_3332479_0:0-136 [********** ] 43% > Processing Locus po_0_3372769_0:47-125 [*********** ] 44% > Processing Locus po_0_3393401_0:44-122 [*********** ] 44% > Processing Locus po_0_3573778_0:336-1280 [*********** ] 45% > Processing Locus po_0_3606391_0:1119-1275 [*********** ] 46% > Processing Locus po_0_3606391_0:1398-1788 [*********** ] 47% > Processing Locus po_0_3606391_0:1976-2879 [************ ] 48% > Processing Locus po_0_3606391_1:25-120 [************ ] 49% > Processing Locus po_0_3606391_1:658-987 [************ ] 50% > Processing Locus rsch_4_4032032_0:0-89 [************ ] 51% > Processing Locus rsch_4_4034850_0:0-99 [************* ] 52% > Processing Locus rsch_4_4091241_0:6-128 [************* ] 53% > Processing Locus rsch_4_4118145_0:5-160 [************* ] 54% > Processing Locus rsch_4_4214541_0:1-234 [************* ] 55% > Processing Locus rsch_4_4219071_0:12-364 [************* ] 55% > Processing Locus rsch_4_4255532_0:1-278 [************** ] 56% > Processing Locus rsch_4_4266550_0:5-1149 [************** ] 57% > Processing Locus rsch_4_4292194_1:8-1135 [************** ] 58% > Processing Locus rsch_4_4297142_0:164-242 [************** ] 59% > Processing Locus sf_2_2459023_0:7-109 [*************** ] 60% > Processing Locus sf_2_2504999_0:5-140 [*************** ] 61% > Processing Locus sf_2_2653966_0:2-691 [*************** ] 62% > Processing Locus sf_2_2680171_0:0-1163 [*************** ] 63% > Processing Locus sf_2_2687786_0:0-981 [**************** ] 64% > Processing Locus sf_2_2687786_0:1085-2189 [**************** ] 65% > Processing Locus sf_2_2701328_0:1-724 [**************** ] 66% > Processing Locus tsu_0_3135135_0:3-166 [**************** ] 66% > Processing Locus tsu_0_3175121_0:5-416 [**************** ] 67% > Processing Locus tsu_0_3175121_0:570-703 [***************** ] 68% > Processing Locus tsu_0_3215671_0:149-275 [***************** ] 69% > Processing Locus tsu_0_3215671_0:760-838 [***************** ] 70% > Processing Locus tsu_0_3215737_0:13-1098 [***************** ] 71% > Processing Locus tsu_0_3242833_1:25-914 [****************** ] 72% > Processing Locus wil_2_2892485_0:38-138 [****************** ] 73% > Processing Locus wil_2_3050523_0:1-218 [****************** ] 74% > Processing Locus wil_2_3090237_0:250-494 [****************** ] 75% > Processing Locus wil_2_3092619_0:1091-1169 [******************* ] 76% > Processing Locus ws_0_3182508_0:1-182 [******************* ] 77% > Processing Locus ws_0_3190679_0:25-171 [******************* ] 77% > Processing Locus ws_0_3190963_0:13-180 [******************* ] 78% > Processing Locus ws_0_3326342_0:12-364 [******************* ] 79% > Processing Locus ws_0_3339092_0:361-439 [******************** ] 80% > Processing Locus ws_0_3347582_0:69-1370 [******************** ] 81% > Processing Locus ws_0_3380934_0:3-211 [******************** ] 82% > Processing Locus wu_0_2654219_0:68-147 [******************** ] 83% > Processing Locus wu_0_2678387_0:10-182 [********************* ] 84% > Processing Locus zu_0_3022629_0:0-112 [********************* ] 85% > Processing Locus zu_0_3075813_0:14-134 [********************* ] 86% > Processing Locus zu_0_3082201_0:1-148 [********************* ] 87% > Processing Locus zu_0_3092045_0:8-157 [********************** ] 88% > Processing Locus zu_0_3118546_0:4-153 [********************** ] 88% > Processing Locus zu_0_3119698_0:79-177 [********************** ] 89% > Processing Locus zu_0_3190435_0:8-295 [********************** ] 90% > Processing Locus zu_0_3242889_0:3-251 [********************** ] 91% > Processing Locus zu_0_3243571_0:49-127 [*********************** ] 92% > Processing Locus zu_0_3243571_0:231-801 [*********************** ] 93% > Processing Locus zu_0_3255503_0:1072-1357 [*********************** ] 94% > Processing Locus zu_0_3259399_1:88-320 [*********************** ] 95% > Processing Locus zu_0_3260131_0:156-400 [************************ ] 96% > Processing Locus zu_0_3277661_0:263-908 [************************ ] 97% > Processing Locus zu_0_3278243_0:11-93 [************************ ] 98% > Processing Locus zu_0_3280213_0:148-2101 [************************ ] 99% > Processed 109 loci. [*************************] 100% [14:14:36] Loading reference annotation and sequence [14:14:36] Learning bias parameters. > Processing Locus bur_0_1873494_0:17-187 [ ] 0% > Processing Locus bur_0_1969548_0:6-676 [ ] 0% > Processing Locus bur_0_2020452_0:2-1282 [ ] 1% > Processing Locus can_0_3076940_0:0-142 [ ] 2% > Processing Locus can_0_3231205_0:13-879 [ ] 3% > Processing Locus can_0_3270131_0:1068-1761 [* ] 4% > Processing Locus ct_1_3082021_0:2-128 [* ] 5% > Processing Locus ct_1_3133995_0:80-195 [* ] 6% > Processing Locus edi_0_2859720_0:137-518 [* ] 7% > Processing Locus edi_0_2932438_0:2-288 [** ] 8% > Processing Locus hi_0_2939638_0:55-642 [** ] 9% > Processing Locus kn_0_3594465_0:14-152 [** ] 10% > Processing Locus kn_0_3613403_0:0-130 [** ] 11% > Processing Locus kn_0_3617271_0:16-171 [** ] 11% > Processing Locus ler_0_3998410_0:1-164 [*** ] 12% > Processing Locus ler_0_4018856_0:0-176 [*** ] 13% > Processing Locus ler_0_4153595_0:230-661 [*** ] 14% > Processing Locus mt_0_4193196_0:0-164 [*** ] 15% > Processing Locus mt_0_4217716_0:2-181 [**** ] 16% > Processing Locus mt_0_4229662_0:1-196 [**** ] 17% > Processing Locus mt_0_4230874_0:43-185 [**** ] 18% > Processing Locus mt_0_4231054_0:0-197 [**** ] 19% > Processing Locus no_0_2885444_0:10-111 [***** ] 20% > Processing Locus no_0_2905273_0:7-118 [***** ] 21% > Processing Locus no_0_2951521_0:0-144 [***** ] 22% > Processing Locus no_0_2956652_0:2-174 [***** ] 22% > Processing Locus no_0_3116640_0:429-1875 [***** ] 23% > Processing Locus no_0_3128142_0:5-899 [****** ] 24% > Processing Locus no_0_3128142_0:1717-2954 [****** ] 25% > Processing Locus oy_0_3121110_0:51-543 [****** ] 26% > Processing Locus po_0_3299272_0:12-119 [****** ] 27% > Processing Locus po_0_3324652_0:2-132 [******* ] 28% > Processing Locus po_0_3332479_0:0-136 [******* ] 29% > Processing Locus po_0_3573778_0:336-1280 [******* ] 30% > Processing Locus po_0_3606391_1:658-987 [******* ] 31% > Processing Locus rsch_4_4032032_0:0-89 [******** ] 32% > Processing Locus rsch_4_4034850_0:0-99 [******** ] 33% > Processing Locus rsch_4_4118145_0:5-160 [******** ] 33% > Processing Locus rsch_4_4214541_0:1-234 [******** ] 34% > Processing Locus rsch_4_4255532_0:1-278 [******** ] 35% > Processing Locus rsch_4_4266550_0:5-1149 [********* ] 36% > Processing Locus rsch_4_4292194_1:8-1135 [********* ] 37% > Processing Locus sf_2_2459023_0:7-109 [********* ] 38% > Processing Locus sf_2_2504999_0:5-140 [********* ] 39% > Processing Locus sf_2_2653966_0:2-691 [********** ] 40% > Processing Locus sf_2_2680171_0:0-1163 [********** ] 41% > Processing Locus sf_2_2687786_0:0-981 [********** ] 42% > Processing Locus sf_2_2687786_0:1085-2189 [********** ] 43% > Processing Locus sf_2_2701328_0:1-724 [*********** ] 44% > Processing Locus tsu_0_3175121_0:5-416 [*********** ] 44% > Processing Locus tsu_0_3175121_0:570-703 [*********** ] 45% > Processing Locus tsu_0_3215737_0:13-1098 [*********** ] 46% > Processing Locus tsu_0_3242833_1:25-914 [*********** ] 47% > Processing Locus ws_0_3182508_0:1-182 [************ ] 48% > Processing Locus ws_0_3190963_0:13-180 [************ ] 49% > Processing Locus ws_0_3347582_0:69-1370 [************ ] 50% > Processing Locus ws_0_3380934_0:3-211 [************ ] 51% > Processing Locus wu_0_2678387_0:10-182 [************* ] 52% > Processing Locus zu_0_3022629_0:0-112 [************* ] 53% > Processing Locus zu_0_3082201_0:1-148 [************* ] 54% > Processing Locus zu_0_3118546_0:4-153 [************* ] 55% > Processing Locus zu_0_3190435_0:8-295 [************* ] 55% > Processing Locus zu_0_3242889_0:3-251 [************** ] 56% > Processing Locus zu_0_3243571_0:231-801 [************** ] 57% > Processing Locus zu_0_3255503_0:1072-1357 [************** ] 58% > Processing Locus zu_0_3259399_1:88-320 [************** ] 59% > Processing Locus zu_0_3277661_0:263-908 [*************** ] 60% > Processing Locus zu_0_3280213_0:148-2101 [*************** ] 61% > Processed 68 loci. [*************************] 100% [14:14:36] Assembling transcripts and estimating abundances. > Processing Locus bur_0_1873494_0:17-187 [ ] 0% > Processing Locus bur_0_1969548_0:6-676 [ ] 0% > Processing Locus bur_0_2020452_0:2-1282 [ ] 1% > Processing Locus can_0_3076940_0:0-142 [ ] 2% > Processing Locus can_0_3231205_0:13-879 [ ] 3% > Processing Locus can_0_3270131_0:1068-1761 [* ] 4% > Processing Locus ct_1_3082021_0:2-128 [* ] 5% > Processing Locus ct_1_3133995_0:80-195 [* ] 6% > Processing Locus edi_0_2859720_0:137-518 [* ] 7% > Processing Locus edi_0_2932438_0:2-288 [** ] 8% > Processing Locus hi_0_2939638_0:55-642 [** ] 9% > Processing Locus kn_0_3594465_0:14-152 [** ] 10% > Processing Locus kn_0_3613403_0:0-130 [** ] 11% > Processing Locus kn_0_3617271_0:16-171 [** ] 11% > Processing Locus ler_0_3998410_0:1-164 [*** ] 12% > Processing Locus ler_0_4018856_0:0-176 [*** ] 13% > Processing Locus ler_0_4153595_0:230-661 [*** ] 14% > Processing Locus mt_0_4193196_0:0-164 [*** ] 15% > Processing Locus mt_0_4217716_0:2-181 [**** ] 16% > Processing Locus mt_0_4229662_0:1-196 [**** ] 17% > Processing Locus mt_0_4230874_0:43-185 [**** ] 18% > Processing Locus mt_0_4231054_0:0-197 [**** ] 19% > Processing Locus no_0_2885444_0:10-111 [***** ] 20% > Processing Locus no_0_2905273_0:7-118 [***** ] 21% > Processing Locus no_0_2951521_0:0-144 [***** ] 22% > Processing Locus no_0_2956652_0:2-174 [***** ] 22% > Processing Locus no_0_3116640_0:429-1875 [***** ] 23% > Processing Locus no_0_3128142_0:5-899 [****** ] 24% > Processing Locus no_0_3128142_0:1717-2954 [****** ] 25% > Processing Locus oy_0_3121110_0:51-543 [****** ] 26% > Processing Locus po_0_3299272_0:12-119 [****** ] 27% > Processing Locus po_0_3324652_0:2-132 [******* ] 28% > Processing Locus po_0_3332479_0:0-136 [******* ] 29% > Processing Locus po_0_3573778_0:336-1280 [******* ] 30% > Processing Locus po_0_3606391_1:658-987 [******* ] 31% > Processing Locus rsch_4_4032032_0:0-89 [******** ] 32% > Processing Locus rsch_4_4034850_0:0-99 [******** ] 33% > Processing Locus rsch_4_4118145_0:5-160 [******** ] 33% > Processing Locus rsch_4_4214541_0:1-234 [******** ] 34% > Processing Locus rsch_4_4255532_0:1-278 [******** ] 35% > Processing Locus rsch_4_4266550_0:5-1149 [********* ] 36% > Processing Locus rsch_4_4292194_1:8-1135 [********* ] 37% > Processing Locus sf_2_2459023_0:7-109 [********* ] 38% > Processing Locus sf_2_2504999_0:5-140 [********* ] 39% > Processing Locus sf_2_2653966_0:2-691 [********** ] 40% > Processing Locus sf_2_2680171_0:0-1163 [********** ] 41% > Processing Locus sf_2_2687786_0:0-981 [********** ] 42% > Processing Locus sf_2_2687786_0:1085-2189 [********** ] 43% > Processing Locus sf_2_2701328_0:1-724 [*********** ] 44% > Processing Locus tsu_0_3175121_0:5-416 [*********** ] 44% > Processing Locus tsu_0_3175121_0:570-703 [*********** ] 45% > Processing Locus tsu_0_3215737_0:13-1098 [*********** ] 46% > Processing Locus tsu_0_3242833_1:25-914 [*********** ] 47% > Processing Locus ws_0_3182508_0:1-182 [************ ] 48% > Processing Locus ws_0_3190963_0:13-180 [************ ] 49% > Processing Locus ws_0_3347582_0:69-1370 [************ ] 50% > Processing Locus ws_0_3380934_0:3-211 [************ ] 51% > Processing Locus wu_0_2678387_0:10-182 [************* ] 52% > Processing Locus zu_0_3022629_0:0-112 [************* ] 53% > Processing Locus zu_0_3082201_0:1-148 [************* ] 54% > Processing Locus zu_0_3118546_0:4-153 [************* ] 55% > Processing Locus zu_0_3190435_0:8-295 [************* ] 55% > Processing Locus zu_0_3242889_0:3-251 [************** ] 56% > Processing Locus zu_0_3243571_0:231-801 [************** ] 57% > Processing Locus zu_0_3255503_0:1072-1357 [************** ] 58% > Processing Locus zu_0_3259399_1:88-320 [************** ] 59% > Processing Locus zu_0_3277661_0:263-908 [*************** ] 60% > Processing Locus zu_0_3280213_0:148-2101 [*************** ] 61% > Processed 68 loci. [*************************] 100% /Net/fs1/home/xianggan/svncode/novGene//sta_bams.pl -o 0 Bur_0.Toit2.merge.bam Can_0.Toit2.merge.bam Col_0.Toit2.merge.bam Ct_1.Toit2.merge.bam Edi_0.Toit2.merge.bam Hi_0.Toit2.merge.bam Kn_0.Toit2.merge.bam Ler_0.Toit2.merge.bam Mt_0.Toit2.merge.bam No_0.Toit2.merge.bam Oy_0.Toit2.merge.bam Po_0.Toit2.merge.bam Rsch_4.Toit2.merge.bam Sf_2.Toit2.merge.bam Tsu_0.Toit2.merge.bam Wil_2.Toit2.merge.bam Ws_0.Toit2.merge.bam Wu_0.Toit2.merge.bam Zu_0.Toit2.merge.bam