Entering edit mode
4.9 years ago
ovariohisterectomia
▴
40
Hi all. Hope you may help me...
Im trying to do an alignment with STAR, but it prints me an error
First i performed a Trimming with trimGalore
trim_galore --quality 25 --length 50 --max_n 0 --trim-n --output_dir /media/isma/6CAE9DAF1D4BB3FE/BOVINOS/ncbi/public/sra/salidas_trimming --fastqc -- SRR6657766_1.fastq SRR6657766_2.fastq
After that i tried to perform the alignment with STAR , as this:
STAR --genomeDir /media/isma/6CAE9DAF1D4BB3FE/BOVINOS/STAR/STAR-master/bin/Linux_x86_64_static/Genome_data/star --runThreadN 15 --outSAMtype BAM Unsorted --outFileNamePrefix /media/isma/6CAE9DAF1D4BB3FE/BOVINOS/STAR/STAR-master/bin/Linux_x86_64_static/Genome_data/star/766 --readFilesIn 766_1.fq 766_2.fq
And appears this output
Jan 19 18:43:22 ..... started STAR run
Jan 19 18:43:22 ..... loading genome
Jan 19 18:44:02 ..... started mapping
EXITING because of FATAL ERROR in reads input: short read sequence line: 0
Read Name=@SRR6657766.4132571
Read Sequence====
DEF_readNameLengthMax=50000
DEF_readSeqLengthMax=650
I have seen other solutions like work in a conda environment, but it doesnt work too. I Have spend many time here, and i do not know what happens.
This is the LOG OUT File , thank you all
STAR version=2.7.1a
STAR compilation time,server,dir=<not set in Debian>
##### DEFAULT parameters:
versionGenome 2.7.1a
parametersFiles -
sysShell -
runMode alignReads
runThreadN 1
runDirPerm User_RWX
runRNGseed 777
genomeDir ./GenomeDir/
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeChainFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
genomeSuffixLengthMax 18446744073709551615
genomeFileSizes 0
genomeConsensusFile -
readFilesType Fastx
readFilesIn Read1 Read2
readFilesPrefix -
readFilesCommand -
readMatesLengthsIn NotEqual
readMapNumber 18446744073709551615
readNameSeparator /
inputBAMfile -
bamRemoveDuplicatesType -
bamRemoveDuplicatesMate2basesN 0
limitGenomeGenerateRAM 31000000000
limitIObufferSize 150000000
limitOutSAMoneReadBytes 100000
limitOutSJcollapsed 1000000
limitOutSJoneRead 1000
limitBAMsortRAM 0
limitSjdbInsertNsj 1000000
limitNreadsSoft 18446744073709551615
outTmpDir -
outTmpKeep None
outStd Log
outReadsUnmapped None
outQSconversionAdd 0
outMultimapperOrder Old_2.4
outSAMtype SAM
outSAMmode Full
outSAMstrandField None
outSAMattributes Standard
outSAMunmapped None
outSAMorder Paired
outSAMprimaryFlag OneBestScore
outSAMreadID Standard
outSAMmapqUnique 255
outSAMflagOR 0
outSAMflagAND 65535
outSAMattrRGline -
outSAMheaderHD -
outSAMheaderPG -
outSAMheaderCommentFile -
outBAMcompression 1
outBAMsortingThreadN 0
outBAMsortingBinsN 50
outSAMfilter None
outSAMmultNmax 18446744073709551615
outSAMattrIHstart 1
outSAMtlen 1
outSJfilterReads All
outSJfilterCountUniqueMin 3 1 1 1
outSJfilterCountTotalMin 3 1 1 1
outSJfilterOverhangMin 30 12 12 12
outSJfilterDistToOtherSJmin 10 0 5 10
outSJfilterIntronMaxVsReadN 50000 100000 200000
outWigType None
outWigStrand Stranded
outWigReferencesPrefix -
outWigNorm RPM
outFilterType Normal
outFilterMultimapNmax 10
outFilterMultimapScoreRange 1
outFilterScoreMin 0
outFilterScoreMinOverLread 0.66
outFilterMatchNmin 0
outFilterMatchNminOverLread 0.66
outFilterMismatchNmax 10
outFilterMismatchNoverLmax 0.3
outFilterMismatchNoverReadLmax 1
outFilterIntronMotifs None
outFilterIntronStrands RemoveInconsistentStrands
clip5pNbases 0
clip3pNbases 0
clip3pAfterAdapterNbases 0
clip3pAdapterSeq -
clip3pAdapterMMp 0.1
winBinNbits 16
winAnchorDistNbins 9
winFlankNbins 4
winAnchorMultimapNmax 50
winReadCoverageRelativeMin 0.5
winReadCoverageBasesMin 0
scoreGap 0
scoreGapNoncan -8
scoreGapGCAG -4
scoreGapATAC -8
scoreStitchSJshift 1
scoreGenomicLengthLog2scale -0.25
scoreDelBase -2
scoreDelOpen -2
scoreInsOpen -2
scoreInsBase -2
seedSearchLmax 0
seedSearchStartLmax 50
seedSearchStartLmaxOverLread 1
seedPerReadNmax 1000
seedPerWindowNmax 50
seedNoneLociPerWindow 10
seedMultimapNmax 10000
seedSplitMin 12
alignIntronMin 21
alignIntronMax 0
alignMatesGapMax 0
alignTranscriptsPerReadNmax 10000
alignSJoverhangMin 5
alignSJDBoverhangMin 3
alignSJstitchMismatchNmax 0 -1 0 0
alignSplicedMateMapLmin 0
alignSplicedMateMapLminOverLmate 0.66
alignWindowsPerReadNmax 10000
alignTranscriptsPerWindowNmax 100
alignEndsType Local
alignSoftClipAtReferenceEnds Yes
alignEndsProtrude 0 ConcordantPair
alignInsertionFlush None
peOverlapNbasesMin 0
peOverlapMMp 0.01
chimSegmentMin 0
chimScoreMin 0
chimScoreDropMax 20
chimScoreSeparation 10
chimScoreJunctionNonGTAG -1
chimMainSegmentMultNmax 10
chimJunctionOverhangMin 20
chimOutType Junctions
chimFilter banGenomicN
chimSegmentReadGapMax 0
chimMultimapNmax 0
chimMultimapScoreRange 1
chimNonchimScoreDropMin 20
chimOutJunctionFormat 0
sjdbFileChrStartEnd -
sjdbGTFfile -
sjdbGTFchrPrefix -
sjdbGTFfeatureExon exon
sjdbGTFtagExonParentTranscript transcript_id
sjdbGTFtagExonParentGene gene_id
sjdbGTFtagExonParentGeneName gene_name
sjdbGTFtagExonParentGeneType gene_type gene_biotype
sjdbOverhang 100
sjdbScore 2
sjdbInsertSave Basic
varVCFfile -
waspOutputMode None
quantMode -
quantTranscriptomeBAMcompression 1
Did you give a look at the sequence of the read
@SRR6657766.4132571? Maybe this would give an hintthank you Fabio, finally the problem was that the file was corrupted....as simple as that... so, i would say
SOLVED
thank you!