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6.3 years ago
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.
