quirogaedaniel
commented
2 months ago this is the output from the error file Setting the index via positional argument will be deprecated in a future release. Please use -x option instead.
reads processed: 89421098
reads with at least one alignment: 82447008 (92.20%)
reads that failed to align: 6974090 (7.80%)
Reported 247724167 paired-end alignments
rsem-eval-run-em: HitContainer.h:67: bool HitContainer
Good afternoon,
We are trying to run the this code:
rsem-eval-calculate-score --paired-end --strand-specific \ --transcript-length-parameters /data/gent/vo/001/gvo00183/vsc46245/Transcriptoma/MQ/post-assembly-quality/detonate/Trinity.txt \ -p 10 /data/gent/vo/001/gvo00183/vsc46245/Transcriptoma/MQ/Clean/uncseqs_1.fq.gz /data/gent/vo/001/gvo00183/vsc46245/Transcriptoma/MQ/Clean/uncseqs_2.fq.gz \ $VSC_DATA_VO/vsc46245/Transcriptoma/MQ/Montaje/Trinity/Trinity.Trinity.fasta Trinity_rsemscore 85
But in the last step of the process we have this error message.
rsem-synthesis-reference-transcripts Trinity_rsemscore.temp/Trinity_rsemscore 0 0 0 /data/gent/vo/001/gvo00183/vsc46245/Transcriptoma/MQ/Montaje/Trinity/Trinity.Trinity.fasta Transcript Information File is generated! Group File is generated! Extracted Sequences File is generated!
rsem-preref Trinity_rsemscore.temp/Trinity_rsemscore.transcripts.fa 1 Trinity_rsemscore.temp/Trinity_rsemscore Refs.makeRefs finished! Refs.saveRefs finished! Trinity_rsemscore.temp/Trinity_rsemscore.idx.fa is generated! Trinity_rsemscore.temp/Trinity_rsemscore.n2g.idx.fa is generated!
bowtie-build -f Trinity_rsemscore.temp/Trinity_rsemscore.n2g.idx.fa Trinity_rsemscore.temp/Trinity_rsemscore Settings: Output files: "Trinity_rsemscore.temp/Trinity_rsemscore..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: Trinity_rsemscore.temp/Trinity_rsemscore.n2g.idx.fa Reading reference sizes Time reading reference sizes: 00:00:01 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: 26039960 Using parameters --bmax 19529970 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 19529970 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:02 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:01 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 Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 QSorting sample offsets, eliminating duplicates time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.488e+07 (target: 19529969) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 7 Reserving size (19529970) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 14690167 for bucket 1 (Using difference cover) Sorting block time: 00:00:15 Returning block of 14690168 for bucket 1 Getting block 2 of 7 Reserving size (19529970) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 16271737 for bucket 2 (Using difference cover) Sorting block time: 00:00:17 Returning block of 16271738 for bucket 2 Getting block 3 of 7 Reserving size (19529970) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 17922227 for bucket 3 (Using difference cover) Sorting block time: 00:00:18 Returning block of 17922228 for bucket 3 Getting block 4 of 7 Reserving size (19529970) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 10911253 for bucket 4 (Using difference cover) Sorting block time: 00:00:11 Returning block of 10911254 for bucket 4 Getting block 5 of 7 Reserving size (19529970) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 70% bucket 5: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 9754624 for bucket 5 (Using difference cover) Sorting block time: 00:00:10 Returning block of 9754625 for bucket 5 Getting block 6 of 7 Reserving size (19529970) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 15619445 for bucket 6 (Using difference cover) Sorting block time: 00:00:17 Returning block of 15619446 for bucket 6 Getting block 7 of 7 Reserving size (19529970) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 18990381 for bucket 7 (Using difference cover) Sorting block time: 00:00:20 Returning block of 18990382 for bucket 7 Exited Ebwt loop fchr[A]: 0 fchr[C]: 30168995 fchr[G]: 51317065 fchr[T]: 70430913 fchr[$]: 104159840 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37356843 bytes to primary EBWT file: Trinity_rsemscore.temp/Trinity_rsemscore.1.ebwt Wrote 13019988 bytes to secondary EBWT file: Trinity_rsemscore.temp/Trinity_rsemscore.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 104159840 bwtLen: 104159841 sz: 26039960 bwtSz: 26039961 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3254996 offsSz: 13019984 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 232500 numSides: 465000 numLines: 465000 ebwtTotLen: 29760000 ebwtTotSz: 29760000 reverse: 0 Total time for call to driver() for forward index: 00:02:08 Reading reference sizes Time reading reference sizes: 00:00:01 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: 26039960 Using parameters --bmax 19529970 --dcv 1024 Doing ahead-of-time memory usage test Passed! Constructing with these parameters: --bmax 19529970 --dcv 1024 Constructing suffix-array element generator Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:00:03 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: 00:00:01 Sanity-checking and returning Building samples Reserving space for 12 sample suffixes Generating random suffixes QSorting 12 sample offsets, eliminating duplicates Multikey QSorting 12 samples (Using difference cover) Multikey QSorting samples time: 00:00:00 QSorting sample offsets, eliminating duplicates time: 00:00:00 Calculating bucket sizes Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 7; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 0; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Splitting and merging Splitting and merging time: 00:00:00 Split 1, merged 1; iterating... Splitting and merging Splitting and merging time: 00:00:00 Avg bucket size: 1.302e+07 (target: 19529969) Converting suffix-array elements to index image Allocating ftab, absorbFtab Entering Ebwt loop Getting block 1 of 8 Reserving size (19529970) for bucket 1 Calculating Z arrays for bucket 1 Entering block accumulator loop for bucket 1: bucket 1: 10% bucket 1: 20% bucket 1: 30% bucket 1: 40% bucket 1: 50% bucket 1: 60% bucket 1: 70% bucket 1: 80% bucket 1: 90% bucket 1: 100% Sorting block of length 15391148 for bucket 1 (Using difference cover) Sorting block time: 00:00:17 Returning block of 15391149 for bucket 1 Getting block 2 of 8 Reserving size (19529970) for bucket 2 Calculating Z arrays for bucket 2 Entering block accumulator loop for bucket 2: bucket 2: 10% bucket 2: 20% bucket 2: 30% bucket 2: 40% bucket 2: 50% bucket 2: 60% bucket 2: 70% bucket 2: 80% bucket 2: 90% bucket 2: 100% Sorting block of length 12646103 for bucket 2 (Using difference cover) Sorting block time: 00:00:13 Returning block of 12646104 for bucket 2 Getting block 3 of 8 Reserving size (19529970) for bucket 3 Calculating Z arrays for bucket 3 Entering block accumulator loop for bucket 3: bucket 3: 10% bucket 3: 20% bucket 3: 30% bucket 3: 40% bucket 3: 50% bucket 3: 60% bucket 3: 70% bucket 3: 80% bucket 3: 90% bucket 3: 100% Sorting block of length 14518306 for bucket 3 (Using difference cover) Sorting block time: 00:00:15 Returning block of 14518307 for bucket 3 Getting block 4 of 8 Reserving size (19529970) for bucket 4 Calculating Z arrays for bucket 4 Entering block accumulator loop for bucket 4: bucket 4: 10% bucket 4: 20% bucket 4: 30% bucket 4: 40% bucket 4: 50% bucket 4: 60% bucket 4: 70% bucket 4: 80% bucket 4: 90% bucket 4: 100% Sorting block of length 8971375 for bucket 4 (Using difference cover) Sorting block time: 00:00:09 Returning block of 8971376 for bucket 4 Getting block 5 of 8 Reserving size (19529970) for bucket 5 Calculating Z arrays for bucket 5 Entering block accumulator loop for bucket 5: bucket 5: 10% bucket 5: 20% bucket 5: 30% bucket 5: 40% bucket 5: 50% bucket 5: 60% bucket 5: 70% bucket 5: 80% bucket 5: 90% bucket 5: 100% Sorting block of length 12997022 for bucket 5 (Using difference cover) Sorting block time: 00:00:14 Returning block of 12997023 for bucket 5 Getting block 6 of 8 Reserving size (19529970) for bucket 6 Calculating Z arrays for bucket 6 Entering block accumulator loop for bucket 6: bucket 6: 10% bucket 6: 20% bucket 6: 30% bucket 6: 40% bucket 6: 50% bucket 6: 60% bucket 6: 70% bucket 6: 80% bucket 6: 90% bucket 6: 100% Sorting block of length 7346814 for bucket 6 (Using difference cover) Sorting block time: 00:00:08 Returning block of 7346815 for bucket 6 Getting block 7 of 8 Reserving size (19529970) for bucket 7 Calculating Z arrays for bucket 7 Entering block accumulator loop for bucket 7: bucket 7: 10% bucket 7: 20% bucket 7: 30% bucket 7: 40% bucket 7: 50% bucket 7: 60% bucket 7: 70% bucket 7: 80% bucket 7: 90% bucket 7: 100% Sorting block of length 14711036 for bucket 7 (Using difference cover) Sorting block time: 00:00:16 Returning block of 14711037 for bucket 7 Getting block 8 of 8 Reserving size (19529970) for bucket 8 Calculating Z arrays for bucket 8 Entering block accumulator loop for bucket 8: bucket 8: 10% bucket 8: 20% bucket 8: 30% bucket 8: 40% bucket 8: 50% bucket 8: 60% bucket 8: 70% bucket 8: 80% bucket 8: 90% bucket 8: 100% Sorting block of length 17578029 for bucket 8 (Using difference cover) Sorting block time: 00:00:19 Returning block of 17578030 for bucket 8 Exited Ebwt loop fchr[A]: 0 fchr[C]: 30168995 fchr[G]: 51317065 fchr[T]: 70430913 fchr[$]: 104159840 Exiting Ebwt::buildToDisk() Returning from initFromVector Wrote 37356843 bytes to primary EBWT file: Trinity_rsemscore.temp/Trinity_rsemscore.rev.1.ebwt Wrote 13019988 bytes to secondary EBWT file: Trinity_rsemscore.temp/Trinity_rsemscore.rev.2.ebwt Re-opening _in1 and _in2 as input streams Returning from Ebwt constructor Headers: len: 104159840 bwtLen: 104159841 sz: 26039960 bwtSz: 26039961 lineRate: 6 linesPerSide: 1 offRate: 5 offMask: 0xffffffe0 isaRate: -1 isaMask: 0xffffffff ftabChars: 10 eftabLen: 20 eftabSz: 80 ftabLen: 1048577 ftabSz: 4194308 offsLen: 3254996 offsSz: 13019984 isaLen: 0 isaSz: 0 lineSz: 64 sideSz: 64 sideBwtSz: 56 sideBwtLen: 224 numSidePairs: 232500 numSides: 465000 numLines: 465000 ebwtTotLen: 29760000 ebwtTotSz: 29760000 reverse: 0 Total time for backward call to driver() for mirror index: 00:02:22
bowtie -q --phred33-quals -n 2 -e 99999999 -l 25 -I 1 -X 1000 --norc -p 10 -a -m 200 -S Trinity_rsemscore.temp/Trinity_rsemscore -1 /data/gent/vo/001/gvo00183/vsc46245/Transcriptoma/MQ/Clean/uncseqs_1.fq.gz -2 /data/gent/vo/001/gvo00183/vsc46245/Transcriptoma/MQ/Clean/uncseqs_2.fq.gz | samtools view -S -b -o Trinity_rsemscore.temp/Trinity_rsemscore.bam -
rsem-parse-alignments Trinity_rsemscore.temp/Trinity_rsemscore Trinity_rsemscore.temp/Trinity_rsemscore Trinity_rsemscore.stat/Trinity_rsemscore b Trinity_rsemscore.temp/Trinity_rsemscore.bam -t 3 -tag XM Parsed 1000000 entries Parsed 2000000 entries Parsed 3000000 entries Parsed 4000000 entries Parsed 5000000 entries Parsed 6000000 entries Parsed 7000000 entries Parsed 8000000 entries Parsed 9000000 entries Parsed 10000000 entries Parsed 11000000 entries Parsed 12000000 entries Parsed 13000000 entries Parsed 14000000 entries Parsed 15000000 entries Parsed 16000000 entries Parsed 17000000 entries Parsed 18000000 entries Parsed 19000000 entries Parsed 20000000 entries Parsed 21000000 entries Parsed 22000000 entries Parsed 23000000 entries Parsed 24000000 entries Parsed 25000000 entries Parsed 26000000 entries Parsed 27000000 entries Parsed 28000000 entries Parsed 29000000 entries Parsed 30000000 entries Parsed 31000000 entries Parsed 32000000 entries Parsed 33000000 entries Parsed 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rsem-build-read-index 32 1 0 Trinity_rsemscore.temp/Trinity_rsemscore_alignable_1.fq Trinity_rsemscore.temp/Trinity_rsemscore_alignable_2.fq FIN 1000000 FIN 2000000 FIN 3000000 FIN 4000000 FIN 5000000 FIN 6000000 FIN 7000000 FIN 8000000 FIN 9000000 FIN 10000000 FIN 11000000 FIN 12000000 FIN 13000000 FIN 14000000 FIN 15000000 FIN 16000000 FIN 17000000 FIN 18000000 FIN 19000000 FIN 20000000 FIN 21000000 FIN 22000000 FIN 23000000 FIN 24000000 FIN 25000000 FIN 26000000 FIN 27000000 FIN 28000000 FIN 29000000 FIN 30000000 FIN 31000000 FIN 32000000 FIN 33000000 FIN 34000000 FIN 35000000 FIN 36000000 FIN 37000000 FIN 38000000 FIN 39000000 FIN 40000000 FIN 41000000 FIN 42000000 FIN 43000000 FIN 44000000 FIN 45000000 FIN 46000000 FIN 47000000 FIN 48000000 FIN 49000000 FIN 50000000 FIN 51000000 FIN 52000000 FIN 53000000 FIN 54000000 FIN 55000000 FIN 56000000 FIN 57000000 FIN 58000000 FIN 59000000 FIN 60000000 FIN 61000000 FIN 62000000 FIN 63000000 FIN 64000000 FIN 65000000 FIN 66000000 FIN 67000000 FIN 68000000 FIN 69000000 FIN 70000000 FIN 71000000 FIN 72000000 FIN 73000000 FIN 74000000 FIN 75000000 FIN 76000000 FIN 77000000 FIN 78000000 FIN 79000000 FIN 80000000 FIN 81000000 FIN 82000000 Build Index Trinity_rsemscore.temp/Trinity_rsemscore_alignable_1.fq is Done! FIN 1000000 FIN 2000000 FIN 3000000 FIN 4000000 FIN 5000000 FIN 6000000 FIN 7000000 FIN 8000000 FIN 9000000 FIN 10000000 FIN 11000000 FIN 12000000 FIN 13000000 FIN 14000000 FIN 15000000 FIN 16000000 FIN 17000000 FIN 18000000 FIN 19000000 FIN 20000000 FIN 21000000 FIN 22000000 FIN 23000000 FIN 24000000 FIN 25000000 FIN 26000000 FIN 27000000 FIN 28000000 FIN 29000000 FIN 30000000 FIN 31000000 FIN 32000000 FIN 33000000 FIN 34000000 FIN 35000000 FIN 36000000 FIN 37000000 FIN 38000000 FIN 39000000 FIN 40000000 FIN 41000000 FIN 42000000 FIN 43000000 FIN 44000000 FIN 45000000 FIN 46000000 FIN 47000000 FIN 48000000 FIN 49000000 FIN 50000000 FIN 51000000 FIN 52000000 FIN 53000000 FIN 54000000 FIN 55000000 FIN 56000000 FIN 57000000 FIN 58000000 FIN 59000000 FIN 60000000 FIN 61000000 FIN 62000000 FIN 63000000 FIN 64000000 FIN 65000000 FIN 66000000 FIN 67000000 FIN 68000000 FIN 69000000 FIN 70000000 FIN 71000000 FIN 72000000 FIN 73000000 FIN 74000000 FIN 75000000 FIN 76000000 FIN 77000000 FIN 78000000 FIN 79000000 FIN 80000000 FIN 81000000 FIN 82000000 Build Index Trinity_rsemscore.temp/Trinity_rsemscore_alignable_2.fq is Done!
rsem-eval-run-em Trinity_rsemscore.temp/Trinity_rsemscore 3 Trinity_rsemscore Trinity_rsemscore.temp/Trinity_rsemscore Trinity_rsemscore.stat/Trinity_rsemscore 1.22356119436796 0.000986510309118638 85 0 -p 10 Refs.loadRefs finished! Thread 0 : N = 1961, NHit = 24779910 Thread 1 : N = 1928, NHit = 24798784 "rsem-eval-run-em Trinity_rsemscore.temp/Trinity_rsemscore 3 Trinity_rsemscore Trinity_rsemscore.temp/Trinity_rsemscore Trinity_rsemscore.stat/Trinity_rsemscore 1.22356119436796 0.000986510309118638 85 0 -p 10" failed! Plase check if you provide correct parameters/options for the pipeline!
Thank´s for the support.