FATAL ERROR in reads input: quality string length is not equal to sequence length #1598
Comments
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Hi @elengss please send me the Log.out file. |
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Here it is. Thank you.
(base) ***@***.*** new]$ cat Log.out
STAR version=2.7.9a
STAR compilation time,server,dir=2022-02-07T16:58:11+0000
rescomp1.hpc.in.bmrc.ox.ac.uk:
/dev/shm/STAR/2.7.9a/GCC-11.2.0/STAR-2.7.9a/source
##### Command Line:
STARlong --runThreadN 1 --genomeDir
/well/ansari/users/yem086/hepb/new/starindex/ --readFilesIn
demultiplex.dT_bc1002RC_PB_3p--dT_PB_5p.hifi_reads.fastq --runMode
alignReads --readNameSeparator space --outFilterMultimapScoreRange 1
--outFilterMismatchNmax 2000 --winAnchorMultimapNmax 200 --scoreGapNoncan
-20 --scoreGapGCAG -4 --scoreGapATAC -8 --scoreDelBase -1 --scoreDelOpen -1
--scoreInsOpen -1 --scoreInsBase -1 --seedSearchLmax 30
--seedSearchStartLmax 50 --seedPerReadNmax 100000 --seedPerWindowNmax 1000
--alignTranscriptsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 10000
--alignEndsType Local
##### Initial USER parameters from Command Line:
###### All USER parameters from Command Line:
runThreadN 1 ~RE-DEFINED
genomeDir
/well/ansari/users/yem086/hepb/new/starindex/ ~RE-DEFINED
readFilesIn
demultiplex.dT_bc1002RC_PB_3p--dT_PB_5p.hifi_reads.fastq ~RE-DEFINED
runMode alignReads ~RE-DEFINED
readNameSeparator space ~RE-DEFINED
outFilterMultimapScoreRange 1 ~RE-DEFINED
outFilterMismatchNmax 2000 ~RE-DEFINED
winAnchorMultimapNmax 200 ~RE-DEFINED
scoreGapNoncan -20 ~RE-DEFINED
scoreGapGCAG -4 ~RE-DEFINED
scoreGapATAC -8 ~RE-DEFINED
scoreDelBase -1 ~RE-DEFINED
scoreDelOpen -1 ~RE-DEFINED
scoreInsOpen -1 ~RE-DEFINED
scoreInsBase -1 ~RE-DEFINED
seedSearchLmax 30 ~RE-DEFINED
seedSearchStartLmax 50 ~RE-DEFINED
seedPerReadNmax 100000 ~RE-DEFINED
seedPerWindowNmax 1000 ~RE-DEFINED
alignTranscriptsPerReadNmax 100000 ~RE-DEFINED
alignTranscriptsPerWindowNmax 10000 ~RE-DEFINED
alignEndsType Local ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runMode alignReads
runThreadN 1
genomeDir
/well/ansari/users/yem086/hepb/new/starindex/
readFilesIn
demultiplex.dT_bc1002RC_PB_3p--dT_PB_5p.hifi_reads.fastq
readNameSeparator space
outFilterMultimapScoreRange 1
outFilterMismatchNmax 2000
winAnchorMultimapNmax 200
scoreGapNoncan -20
scoreGapGCAG -4
scoreGapATAC -8
scoreDelBase -1
scoreDelOpen -1
scoreInsOpen -1
scoreInsBase -1
seedSearchLmax 30
seedSearchStartLmax 50
seedPerReadNmax 100000
seedPerWindowNmax 1000
alignTranscriptsPerReadNmax 100000
alignTranscriptsPerWindowNmax 10000
alignEndsType Local
…-------------------------------
##### Final effective command line:
STARlong --runMode alignReads --runThreadN 1 --genomeDir
/well/ansari/users/yem086/hepb/new/starindex/ --readFilesIn
demultiplex.dT_bc1002RC_PB_3p--dT_PB_5p.hifi_reads.fastq
--readNameSeparator space --outFilterMultimapScoreRange 1
--outFilterMismatchNmax 2000 --winAnchorMultimapNmax 200
--scoreGapNoncan -20 --scoreGapGCAG -4 --scoreGapATAC -8
--scoreDelBase -1 --scoreDelOpen -1 --scoreInsOpen -1 --scoreInsBase
-1 --seedSearchLmax 30 --seedSearchStartLmax 50 --seedPerReadNmax
100000 --seedPerWindowNmax 1000 --alignTranscriptsPerReadNmax 100000
--alignTranscriptsPerWindowNmax 10000 --alignEndsType Local
----------------------------------------
Number of fastq files for each mate = 1
ParametersSolo: --soloCellFilterType CellRanger2.2 filtering parameters:
3000 0.99 10
Finished loading and checking parameters
Reading genome generation parameters:
### STAR --runMode genomeGenerate --runThreadN 1 --genomeDir
/well/ansari/users/yem086/hepb/new/starindex --genomeFastaFiles
/well/ansari/shared/HBV_transcripts_pacbio/refs/D3-pgrna-fl.v2.fasta
--genomeSAindexNbases 4 --sjdbGTFfile
/well/ansari/shared/HBV_transcripts_pacbio/refs/D3.pgrna.v2.gtf
--sjdbOverhang 100
### GstrandBit=32
versionGenome 2.7.4a ~RE-DEFINED
genomeType Full ~RE-DEFINED
genomeFastaFiles
/well/ansari/shared/HBV_transcripts_pacbio/refs/D3-pgrna-fl.v2.fasta
~RE-DEFINED
genomeSAindexNbases 4 ~RE-DEFINED
genomeChrBinNbits 18 ~RE-DEFINED
genomeSAsparseD 1 ~RE-DEFINED
genomeTransformType None ~RE-DEFINED
genomeTransformVCF - ~RE-DEFINED
sjdbOverhang 100 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
sjdbGTFfile
/well/ansari/shared/HBV_transcripts_pacbio/refs/D3.pgrna.v2.gtf
~RE-DEFINED
sjdbGTFchrPrefix - ~RE-DEFINED
sjdbGTFfeatureExon exon ~RE-DEFINED
sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED
sjdbGTFtagExonParentGene gene_id ~RE-DEFINED
sjdbInsertSave Basic ~RE-DEFINED
genomeFileSizes 267571 72471 ~RE-DEFINED
Genome version is compatible with current STAR
Number of real (reference) chromosomes= 1
1 D3-pgrna-fl 3384 0
--sjdbOverhang = 100 taken from the generated genome
Started loading the genome: Sun Jul 10 18:53:26 2022
Genome: size given as a parameter = 267571
SA: size given as a parameter = 72471
SAindex: size given as a parameter = 1
Read from SAindex: pGe.gSAindexNbases=4 nSAi=340
nGenome=267571; nSAbyte=72471
GstrandBit=32 SA number of indices=17568
Shared memory is not used for genomes. Allocated a private copy of the
genome.
Genome file size: 267571 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 267571
bytes
SA file size: 72471 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 72471 bytes
Loading SAindex ... done: 1539 bytes
Finished loading the genome: Sun Jul 10 18:53:26 2022
Processing splice junctions database sjdbN=27, pGe.sjdbOverhang=100
alignIntronMax=alignMatesGapMax=0, the max intron size will be
approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
EXITING because of FATAL ERROR in reads input: quality string length is not
equal to sequence length
@m64176e_220527_114538/20/ccs
TTTTTTTTTTTTTTTTTTTTTTTTTCCTTTCAAAAAAAATTTATTCAATGAATACACAATATAATTCCATTTCGAGTGATTAAAACCTATTTGTTGTTTAGAACCAAACAAAACTACAAGAAAACATTTTCAAAACCTTTTTTTTCAGGCTGAAGAAATCGTTTAATCCATTTTAAAGAAATCTCACATGATGTTCTGTCGGGATTAAAAATATACACGGAAAAAAATAAAACAAAATATATACACAGAAAGAAGCTCGCACAGAGTCAGGCGTGCAGCAACGTCACACACTCATTCCTTTCTGTTTCCTCTGGACACTCAAAATGTGAAAGCAAGTAAGAGGGGGGTGGTTAACCAAACCTTTTGGTCCAAGGAATAAAATTTCTTTAAAAAATTTAAAACGTCAAAACCTGCCAGAATAAGACAATAGAAGAGCGTATCGTCAGGCGCTGGGAATGGCACCACGACAAGGCATTAATGTGGATTCACTTGCACAGCTGCTCTCATAAAAGCTACACGATTCAGAGGTAACCCTAACTATCCGCAATCCCAACCAAAGTCATGTTCATGCCGCTGTCCTAGTCTGGACAATCATCTGTCACTCATCCAACACAGTTATATACAGAATGCGCAGTCCCAGCAACAGTGTA
SOLUTION: fix your fastq file
Jul 10 18:53:26 ...... FATAL ERROR, exiting
On Thu, Jul 7, 2022 at 6:03 PM Alexander Dobin ***@***.***> wrote:
Hi @elengss <https://github.com/elengss>
please send me the Log.out file.
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Hi @elengss could you please extract this read from fastq, e,g, and map it? Thanks! |
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Here it is. Many thanks. Same error.
…On Mon, Jul 18, 2022 at 9:41 PM Alexander Dobin ***@***.***> wrote:
Hi @elengss <https://github.com/elengss>
could you please extract this read from fastq, e,g,
grep -A3 ***@***.***_220527_114538/20/ccs >r1.fq
and map it?
If it still seg-fault, please send this file to me.
Thanks!
Alex
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Hi @elengss the file does not get attached in a reply email, could you please attach it from the github site. Thanks! |
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Hi there, I seem to be getting this issue when running STARlong but I can't identify what is wrong with my fastq file. First 4 lines below. I've read the closed thread but can't find the right answer. Many thanks in advance.
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