nohup: ignoring input reference: novel221.contig.fa samtools faidx novel221.contig.fa Settings: Output files: "novel221.contig.*.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: novel221.contig.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: 50124 Using parameters --bmax 37593 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 37593 --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 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 Avg bucket size: 28641.6 (target: 37592) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (37593) 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 23289 (Using difference cover) Sorting block time: 00:00:00 Returning block of 23290 Getting block 2 of 7 Reserving size (37593) 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 34547 (Using difference cover) Sorting block time: 00:00:00 Returning block of 34548 Getting block 3 of 7 Reserving size (37593) 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 28896 (Using difference cover) Sorting block time: 00:00:00 Returning block of 28897 Getting block 4 of 7 Reserving size (37593) 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 36734 (Using difference cover) Sorting block time: 00:00:00 Returning block of 36735 Getting block 5 of 7 Reserving size (37593) 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 4846 (Using difference cover) Sorting block time: 00:00:00 Returning block of 4847 Getting block 6 of 7 Reserving size (37593) 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 36528 (Using difference cover) Sorting block time: 00:00:00 Returning block of 36529 Getting block 7 of 7 Reserving size (37593) 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 35651 (Using difference cover) Sorting block time: 00:00:00 Returning block of 35652 Exited Ebwt loop fchr[A]: 0 fchr[C]: 59613 fchr[G]: 101187 fchr[T]: 140853 fchr[$]: 200497 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4258547 bytes to primary EBWT file: novel221.contig.1.ebwt Wrote 25068 bytes to secondary EBWT file: novel221.contig.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 200497 bwtLen: 200498 sz: 50125 bwtSz: 50125 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6266 offsSz: 25064 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 448 numSides: 896 numLines: 896 ebwtTotLen: 57344 ebwtTotSz: 57344 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: 50124 Using parameters --bmax 37593 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 37593 --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 Avg bucket size: 28641.6 (target: 37592) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (37593) 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 26944 (Using difference cover) Sorting block time: 00:00:00 Returning block of 26945 Getting block 2 of 7 Reserving size (37593) 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 34954 (Using difference cover) Sorting block time: 00:00:00 Returning block of 34955 Getting block 3 of 7 Reserving size (37593) 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 35911 (Using difference cover) Sorting block time: 00:00:00 Returning block of 35912 Getting block 4 of 7 Reserving size (37593) 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 18197 (Using difference cover) Sorting block time: 00:00:00 Returning block of 18198 Getting block 5 of 7 Reserving size (37593) 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 27565 (Using difference cover) Sorting block time: 00:00:00 Returning block of 27566 Getting block 6 of 7 Reserving size (37593) 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 35689 (Using difference cover) Sorting block time: 00:00:00 Returning block of 35690 Getting block 7 of 7 Reserving size (37593) 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 21231 (Using difference cover) Sorting block time: 00:00:00 Returning block of 21232 Exited Ebwt loop fchr[A]: 0 fchr[C]: 59613 fchr[G]: 101187 fchr[T]: 140853 fchr[$]: 200497 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 4258547 bytes to primary EBWT file: novel221.contig.rev.1.ebwt Wrote 25068 bytes to secondary EBWT file: novel221.contig.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 200497 bwtLen: 200498 sz: 50125 bwtSz: 50125 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 6266 offsSz: 25064 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 448 numSides: 896 numLines: 896 ebwtTotLen: 57344 ebwtTotSz: 57344 reverse: 0 Total time for backward call to driver() for mirror index: 00:00:00 tophat --num-threads 4 --library-type fr-firststrand --mate-inner-dist 38 --mate-std-dev 40 --max-multihits 10 --coverage-search --microexon-search -o Can_0/ -G novel221.gtf novel221.contig Can_0//Run33_lane1_Can_0_seedling.fastq.unmap_1.flt_1.fq [Wed May 25 15:49:26 2011] Beginning TopHat run (v1.2.0) ----------------------------------------------- [Wed May 25 15:49:26 2011] Preparing output location Can_0// [Wed May 25 15:49:26 2011] Checking for Bowtie index files [Wed May 25 15:49:26 2011] Checking for reference FASTA file [Wed May 25 15:49:26 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Wed May 25 15:49:26 2011] Checking for Samtools Samtools Version: 0.1.7 [Wed May 25 15:49:27 2011] Checking reads min read length: 82bp, max read length: 82bp format: fastq quality scale: phred33 (default) [Wed May 25 15:50:58 2011] Reading known junctions from GTF file [Wed May 25 15:51:20 2011] Mapping reads against novel221.contig with Bowtie [Wed May 25 15:51:58 2011] Joining segment hits [Wed May 25 15:53:33 2011] Mapping reads against novel221.contig with Bowtie(1/3) [Wed May 25 15:54:03 2011] Mapping reads against novel221.contig with Bowtie(2/3) [Wed May 25 15:54:35 2011] Mapping reads against novel221.contig with Bowtie(3/3) [Wed May 25 15:55:05 2011] Searching for junctions via segment mapping [Wed May 25 15:58:31 2011] Retrieving sequences for splices [Wed May 25 15:58:31 2011] Indexing splices [Wed May 25 15:58:32 2011] Mapping reads against segment_juncs with Bowtie [Wed May 25 15:58:51 2011] Mapping reads against segment_juncs with Bowtie [Wed May 25 15:59:10 2011] Mapping reads against segment_juncs with Bowtie [Wed May 25 15:59:31 2011] Joining segment hits [Wed May 25 15:59:43 2011] Reporting output tracks ----------------------------------------------- Run complete [00:10:31 elapsed] [main_samview] fail to open file for reading. open: No such file or directory [bam_index_build2] fail to open the BAM file. open: No such file or directory [main_samview] fail to open file for reading. cufflinks -p 4 -G novel221.gtf -o Can_0/ -r novel221.contig.fa Can_0//accepted_hits.bam