Error with rsem-eval-calculate-score #8
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this is the output from the error file reads processed: 89421098reads with at least one alignment: 82447008 (92.20%)reads that failed to align: 6974090 (7.80%)Reported 247724167 paired-end alignments |
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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
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Done!
rsem-build-read-index 32 1 0 Trinity_rsemscore.temp/Trinity_rsemscore_alignable_1.fq Trinity_rsemscore.temp/Trinity_rsemscore_alignable_2.fq
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Build Index Trinity_rsemscore.temp/Trinity_rsemscore_alignable_1.fq is Done!
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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.
The text was updated successfully, but these errors were encountered: