Skip to content

Instantly share code, notes, and snippets.

@roryk

roryk/gist:3aade4cc66af6db93496

Created October 27, 2014 21:15
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save roryk/3aade4cc66af6db93496 to your computer and use it in GitHub Desktop.
Save roryk/3aade4cc66af6db93496 to your computer and use it in GitHub Desktop.
Download ZIP
STAR error 2.4.0e with --quantMode
Raw
gistfile1.txt
STAR version=STAR_2.4.0e
STAR compilation time,server,dir=Fri Oct 24 10:43:53 EDT 2014 verona.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.sandbox/source
##### DEFAULT parameters:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
runMode alignReads
runThreadN 1
genomeDir ./GenomeDir/
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
readFilesIn Read1 Read2
readFilesCommand -
readMatesLengthsIn NotEqual
readMapNumber 18446744073709551615
inputBAMfile -
bamRemoveDuplicatesType -
bamRemoveDuplicatesMate2basesN 0
limitGenomeGenerateRAM 31000000000
limitIObufferSize 150000000
limitOutSAMoneReadBytes 100000
limitOutSJcollapsed 1000000
limitOutSJoneRead 1000
limitBAMsortRAM 0
outTmpDir -
outReadsUnmapped None
outQSconversionAdd 0
outSAMtype SAM
outSAMmode Full
outSAMstrandField None
outSAMattributes Standard
outSAMunmapped None
outSAMorder Paired
outSAMprimaryFlag OneBestScore
outSAMreadID Standard
outSAMmapqUnique 255
outSAMattrRGline -
outSAMheaderHD -
outSAMheaderPG -
outSAMheaderCommentFile -
outBAMcompression -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
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
alignSplicedMateMapLmin 0
alignSplicedMateMapLminOverLmate 0.66
alignWindowsPerReadNmax 10000
alignTranscriptsPerWindowNmax 100
alignEndsType Local
chimSegmentMin 0
chimScoreMin 0
chimScoreDropMax 20
chimScoreSeparation 10
chimScoreJunctionNonGTAG -1
chimJunctionOverhangMin 20
sjdbFileChrStartEnd -
sjdbGTFfile -
sjdbGTFchrPrefix -
sjdbGTFfeatureExon exon
sjdbGTFtagExonParentTranscript transcript_id
sjdbOverhang 0
sjdbScore 2
quantMode -
twopass1readsN 0
twopassSJlimit 1000000
##### Command Line:
/usr/local/bin/STAR --genomeDir /v-data/bcbio-nextgen/tests/data/genomes/mm9/star/ --readFilesIn /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq.trimmed.txt.gz /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq.trimmed.txt.gz --runThreadN 1 --outFileNamePrefix startest --outReadsUnmapped Fastx --outFilterMultimapNmax 10 --outStd SAM --quantMode TranscriptomeSAM --outSAMunmapped Within --outSAMattributes NH HI NM MD AS --readFilesCommand zcat --outSAMattrRGline ID:1 PL:illumina PU:1_110907_ERP000591 SM:Test1 --outSAMstrandField intronMotif
##### Initial USER parameters from Command Line:
outFileNamePrefix startest
outStd SAM
###### All USER parameters from Command Line:
genomeDir /v-data/bcbio-nextgen/tests/data/genomes/mm9/star/ ~RE-DEFINED
readFilesIn /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq.trimmed.txt.gz /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq.trimmed.txt.gz ~RE-DEFINED
runThreadN 1 ~RE-DEFINED
outFileNamePrefix startest ~RE-DEFINED
outReadsUnmapped Fastx ~RE-DEFINED
outFilterMultimapNmax 10 ~RE-DEFINED
outStd SAM ~RE-DEFINED
quantMode TranscriptomeSAM ~RE-DEFINED
outSAMunmapped Within ~RE-DEFINED
outSAMattributes NH HI NM MD AS ~RE-DEFINED
readFilesCommand zcat ~RE-DEFINED
outSAMattrRGline ID:1 PL:illumina PU:1_110907_ERP000591 SM:Test1 ~RE-DEFINED
outSAMstrandField intronMotif ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runThreadN 1
genomeDir /v-data/bcbio-nextgen/tests/data/genomes/mm9/star/
readFilesIn /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq.trimmed.txt.gz /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq.trimmed.txt.gz
readFilesCommand zcat
outFileNamePrefix startest
outStd SAM
outReadsUnmapped Fastx
outSAMstrandField intronMotif
outSAMattributes NH HI NM MD AS
outSAMunmapped Within
outSAMattrRGline ID:1 PL:illumina PU:1_110907_ERP000591 SM:Test1
outFilterMultimapNmax 10
quantMode TranscriptomeSAM
-------------------------------
##### Final effective command line:
/usr/local/bin/STAR --runThreadN 1 --genomeDir /v-data/bcbio-nextgen/tests/data/genomes/mm9/star/ --readFilesIn /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq.trimmed.txt.gz /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq.trimmed.txt.gz --readFilesCommand zcat --outFileNamePrefix startest --outStd SAM --outReadsUnmapped Fastx --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS --outSAMunmapped Within --outSAMattrRGline ID:1 PL:illumina PU:1_110907_ERP000591 SM:Test1 --outFilterMultimapNmax 10 --quantMode TranscriptomeSAM
##### Final parameters after user input--------------------------------:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
runMode alignReads
runThreadN 1
genomeDir /v-data/bcbio-nextgen/tests/data/genomes/mm9/star/
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
readFilesIn /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq.trimmed.txt.gz /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq.trimmed.txt.gz
readFilesCommand zcat
readMatesLengthsIn NotEqual
readMapNumber 18446744073709551615
inputBAMfile -
bamRemoveDuplicatesType -
bamRemoveDuplicatesMate2basesN 0
limitGenomeGenerateRAM 31000000000
limitIObufferSize 150000000
limitOutSAMoneReadBytes 100000
limitOutSJcollapsed 1000000
limitOutSJoneRead 1000
limitBAMsortRAM 0
outFileNamePrefix startest
outTmpDir -
outStd SAM
outReadsUnmapped Fastx
outQSconversionAdd 0
outSAMtype SAM
outSAMmode Full
outSAMstrandField intronMotif
outSAMattributes NH HI NM MD AS
outSAMunmapped Within
outSAMorder Paired
outSAMprimaryFlag OneBestScore
outSAMreadID Standard
outSAMmapqUnique 255
outSAMattrRGline ID:1 PL:illumina PU:1_110907_ERP000591 SM:Test1
outSAMheaderHD -
outSAMheaderPG -
outSAMheaderCommentFile -
outBAMcompression -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
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
alignSplicedMateMapLmin 0
alignSplicedMateMapLminOverLmate 0.66
alignWindowsPerReadNmax 10000
alignTranscriptsPerWindowNmax 100
alignEndsType Local
chimSegmentMin 0
chimScoreMin 0
chimScoreDropMax 20
chimScoreSeparation 10
chimScoreJunctionNonGTAG -1
chimJunctionOverhangMin 20
sjdbFileChrStartEnd -
sjdbGTFfile -
sjdbGTFchrPrefix -
sjdbGTFfeatureExon exon
sjdbGTFtagExonParentTranscript transcript_id
sjdbOverhang 0
sjdbScore 2
quantMode TranscriptomeSAM
twopass1readsN 0
twopassSJlimit 1000000
----------------------------------------
Input read files for mate 1, from input string /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq.trimmed.txt.gz
-rw-rw-r-- 1 501 dialout 1321636 Oct 27 20:55 /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq.trimmed.txt.gz
readsCommandsFile:
exec > "startest_STARtmp/tmp.fifo.read1"
echo FILE 0
zcat "/v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq.trimmed.txt.gz"
Input read files for mate 2, from input string /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq.trimmed.txt.gz
-rw-rw-r-- 1 501 dialout 1041034 Oct 27 20:55 /v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq.trimmed.txt.gz
readsCommandsFile:
exec > "startest_STARtmp/tmp.fifo.read2"
echo FILE 0
zcat "/v-data/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq.trimmed.txt.gz"
WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute
WARNING --outSAMstrandField=intronMotif, therefore STAR will output XS attribute
Finished loading and checking parameters
Reading genome generation parameters:
versionGenome 20201 ~RE-DEFINED
genomeFastaFiles /v-data/bcbio-nextgen/tests/data/automated/tool-data/../../genomes/mm9/seq/mm9.fa ~RE-DEFINED
genomeSAindexNbases 14 ~RE-DEFINED
genomeChrBinNbits 18 ~RE-DEFINED
genomeSAsparseD 1 ~RE-DEFINED
sjdbOverhang 99 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
Genome version is compatible with current STAR version
Started loading the genome: Mon Oct 27 21:13:39 2014
Read from SAindex: genomeSAindexNbases=14 nSAi=357913940
Genome file size: 262144 bytes; state: good=1 eof=0 fail=0 bad=0
SA file size: 134467 bytes; state: good=1 eof=0 fail=0 bad=0
nGenome=262144; nSAbyte=134467
GstrandBit=32 SA number of indices=32598
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 262144 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 262144 bytes
SA file size: 134467 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 134467 bytes
Loading SAindex ... done: 1565873616 bytes
Finished loading the genome: Mon Oct 27 21:13:39 2014
Number of real (reference) chromosmes= 1
1 chrM 16299 0
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment