Question: STAR aligner exits with no output
0
gravatar for damayanthikherath
17 months ago by
damayanthikherath0 wrote:

I am trying to align the reads from Brooks et al [1] using the STAR aligner. With the reads from the sample GSM461179, the STAR aligner does not generate any output. Once the command is run for aligning reads, it exits on the terminal with no output and the generated BAM file is 0 bytes.

Below is the log.out file for this run.

STAR version=STAR_2.5.2a
STAR compilation time,server,dir=Tue May 10 17:35:33 EDT 2016 florence.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.sandbox/source
##### DEFAULT parameters:
>> Truncated<<
##### Command Line:
./STAR --runThreadN 4 --runMode alignReads --genomeDir /media/damayanthi/sudu3/DTU-simulation/genome-data-sta --readFilesIn /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031718.fastq /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031719.fastq /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031720.fastq /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031721.fastq /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031722.fastq /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031723.fastq --outFileNamePrefix /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/alignments/treated-1/treated_1 --outSAMtype BAM SortedByCoordinate
##### Initial USER parameters from Command Line:
outFileNamePrefix                 /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/alignments/treated-1/treated_1
###### All USER parameters from Command Line:
runThreadN                    4     ~RE-DEFINED
runMode                       alignReads     ~RE-DEFINED
genomeDir                     /media/damayanthi/sudu3/DTU-simulation/genome-data-sta     ~RE-DEFINED
readFilesIn                   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031718.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031719.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031720.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031721.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031722.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031723.fastq        ~RE-DEFINED
outFileNamePrefix             /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/alignments/treated-1/treated_1     ~RE-DEFINED
outSAMtype                    BAM   SortedByCoordinate        ~RE-DEFINED
##### Finished reading parameters from all sources

##### Final user re-defined parameters-----------------:
runMode                           alignReads
runThreadN                        4
genomeDir                         /media/damayanthi/sudu3/DTU-simulation/genome-data-sta
readFilesIn                       /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031718.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031719.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031720.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031721.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031722.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031723.fastq   
outFileNamePrefix                 /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/alignments/treated-1/treated_1
outSAMtype                        BAM   SortedByCoordinate   

-------------------------------
##### Final effective command line:
./STAR   --runMode alignReads   --runThreadN 4   --genomeDir /media/damayanthi/sudu3/DTU-simulation/genome-data-sta   --readFilesIn /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031718.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031719.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031720.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031721.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031722.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031723.fastq      --outFileNamePrefix /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/alignments/treated-1/treated_1   --outSAMtype BAM   SortedByCoordinate   

##### Final parameters after user input--------------------------------:
versionSTAR                       20201
versionGenome                     20101   20200   
parametersFiles                   -   
sysShell                          -
runMode                           alignReads
runThreadN                        4
runDirPerm                        User_RWX
runRNGseed                        777
genomeDir                         /media/damayanthi/sudu3/DTU-simulation/genome-data-sta
genomeLoad                        NoSharedMemory
genomeFastaFiles                  -   
genomeSAindexNbases               14
genomeChrBinNbits                 18
genomeSAsparseD                   1
genomeSuffixLengthMax             18446744073709551615
readFilesIn                       /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031718.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031719.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031720.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031721.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031722.fastq   /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/fq-files/treated-1/SRR031723.fastq   
readFilesCommand                  -   
readMatesLengthsIn                NotEqual
readMapNumber                     18446744073709551615
readNameSeparator                 /   
inputBAMfile                      -
bamRemoveDuplicatesType           -
bamRemoveDuplicatesMate2basesN    0
limitGenomeGenerateRAM            31000000000
limitIObufferSize                 150000000
limitOutSAMoneReadBytes           100000
limitOutSJcollapsed               1000000
limitOutSJoneRead                 1000
limitBAMsortRAM                   0
limitSjdbInsertNsj                1000000
outFileNamePrefix                 /media/damayanthi/sudu3/RQ2/brooks-et-al-data-analysis/data/alignments/treated-1/treated_1
outTmpDir                         -
outTmpKeep                        None
outStd                            Log
outReadsUnmapped                  None
outQSconversionAdd                0
outMultimapperOrder               Old_2.4
outSAMtype                        BAM   SortedByCoordinate   
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
outSAMfilter                      None   
outSAMmultNmax                    18446744073709551615
outSAMattrIHstart                 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
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
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   
chimSegmentMin                    0
chimScoreMin                      0
chimScoreDropMax                  20
chimScoreSeparation               10
chimScoreJunctionNonGTAG          -1
chimJunctionOverhangMin           20
chimOutType                       SeparateSAMold
chimFilter                        banGenomicN   
chimSegmentReadGapMax             0
sjdbFileChrStartEnd               -   
sjdbGTFfile                       -
sjdbGTFchrPrefix                  -
sjdbGTFfeatureExon                exon
sjdbGTFtagExonParentTranscript    transcript_id
sjdbGTFtagExonParentGene          gene_id
sjdbOverhang                      100
sjdbScore                         2
sjdbInsertSave                    Basic
quantMode                         -   
quantTranscriptomeBAMcompression    1
quantTranscriptomeBan             IndelSoftclipSingleend
twopass1readsN                    18446744073709551615
twopassMode                       None

I would be quite grateful on any insight on what happens here.

[1] Brooks, Angela N., et al. "Conservation of an RNA regulatory map between Drosophila and mammals." Genome research 21.2 (2011): 193-202.

star rna-seq aligner • 897 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by damayanthikherath0
0
gravatar for damayanthikherath
17 months ago by
damayanthikherath0 wrote:

I have resolved the issue by separating the FASTAQ file names with comma instead of space.

ADD COMMENTlink written 17 months ago by damayanthikherath0
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