STAR ALIGNMENT: FATAL ERROR in reads input: short read sequence line: 0

Question

[ovariohisterectomia]

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

[Fabio Marroni]

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

[ovariohisterectomia]

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

SOLVED

thank you!