Question: STAR ALIGNMENT: FATAL ERROR in reads input: short read sequence line: 0
0
gravatar for ovariohisterectomia
5 weeks ago by
ovariohisterectomia10 wrote:

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
rna-seq star alignment • 151 views
ADD COMMENTlink written 5 weeks ago by ovariohisterectomia10

Did you give a look at the sequence of the read @SRR6657766.4132571? Maybe this would give an hint

ADD REPLYlink written 5 weeks ago by Fabio Marroni2.5k

thank you Fabio, finally the problem was that the file was corrupted....as simple as that... so, i would say

SOLVED

thank you!

ADD REPLYlink written 4 weeks ago by ovariohisterectomia10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1114 users visited in the last hour