segmentation fault for bacterial genome
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sanchez cavani
Nov 18, 2016, 11:30:00 AM11/18/16
to rna-star
I'm using STAR 2.4.2a and 2.5.2b to map reads onto bacterial genomes. However there was segmentation error. I tried --genomeSAindexNbases 8 but got the same problem.
Alexander Dobin
Nov 18, 2016, 4:45:16 PM11/18/16
to rna-star
Hi Sanchez,
please send me the Log.out file of the failed run.
Cheers
Alex
sanchez cavani
Nov 19, 2016, 1:27:15 AM11/19/16
to rna-...@googlegroups.com
mn##### DEFAULT parameters:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 1
runDirPerm User_RWX
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
limitSjdbInsertNsj 1000000
outTmpDir -
outStd Log
outReadsUnmapped None
outQSconversionAdd 0
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
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
alignSoftClipAtReferenceEnds Yes
chimSegmentMin 0
chimScoreMin 0
chimScoreDropMax 20
chimScoreSeparation 10
chimScoreJunctionNonGTAG -1
chimJunctionOverhangMin 20
chimOutType SeparateSAMold
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
##### Command Line:
~/software/NGS/STAR-STAR_2.4.2a/STAR --genomeDir ../../../../../STAR_indexes/test/ --readFilesIn 1.fq --outFileNamePrefix output --runThreadN 3 --outSAMtype BAM SortedByCoordinate --genomeSAindexNbases 2
##### Initial USER parameters from Command Line:
outFileNamePrefix output
###### All USER parameters from Command Line:
genomeDir ../../../../../STAR_indexes/test/ ~RE-DEFINED
readFilesIn 1.fq ~RE-DEFINED
outFileNamePrefix output ~RE-DEFINED
runThreadN 3 ~RE-DEFINED
outSAMtype BAM SortedByCoordinate ~RE-DEFINED
genomeSAindexNbases 2 ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runThreadN 3
genomeDir ../../../../../STAR_indexes/test/
genomeSAindexNbases 2
readFilesIn 1.fq
outFileNamePrefix output
outSAMtype BAM SortedByCoordinate
-------------------------------
##### Final effective command line:
~/software/NGS/STAR-STAR_2.4.2a/STAR --runThreadN 3 --genomeDir ../../../../../STAR_indexes/test/ --genomeSAindexNbases 2 --readFilesIn 1.fq --outFileNamePrefix output --outSAMtype BAM SortedByCoordinate
##### Final parameters after user input--------------------------------:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 3
runDirPerm User_RWX
genomeDir ../../../../../STAR_indexes/test/
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeSAindexNbases 2
genomeChrBinNbits 18
genomeSAsparseD 1
readFilesIn 1.fq
readFilesCommand -
readMatesLengthsIn NotEqual
readMapNumber 18446744073709551615
inputBAMfile -
bamRemoveDuplicatesType -
bamRemoveDuplicatesMate2basesN 0
limitGenomeGenerateRAM 31000000000
limitIObufferSize 150000000
limitOutSAMoneReadBytes 100000
limitOutSJcollapsed 1000000
limitOutSJoneRead 1000
limitBAMsortRAM 0
limitSjdbInsertNsj 1000000
outFileNamePrefix output
outTmpDir -
outStd Log
outReadsUnmapped None
outQSconversionAdd 0
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
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
alignSoftClipAtReferenceEnds Yes
chimSegmentMin 0
chimScoreMin 0
chimScoreDropMax 20
chimScoreSeparation 10
chimScoreJunctionNonGTAG -1
chimJunctionOverhangMin 20
chimOutType SeparateSAMold
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
----------------------------------------
WARNING: --limitBAMsortRAM=0, will use genome sizeas RAM linit foro BAM sorting
Finished loading and checking parameters
Reading genome generation parameters:
versionGenome 20201 ~RE-DEFINED
genomeFastaFiles ../sequences/Mace.genome.fa ~RE-DEFINED
genomeSAindexNbases 14 ~RE-DEFINED
genomeChrBinNbits 18 ~RE-DEFINED
genomeSAsparseD 1 ~RE-DEFINED
sjdbOverhang 0 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
sjdbGTFfile - ~RE-DEFINED
sjdbGTFchrPrefix - ~RE-DEFINED
sjdbGTFfeatureExon exon ~RE-DEFINED
sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED
sjdbGTFtagExonParentGene gene_id ~RE-DEFINED
sjdbInsertSave Basic ~RE-DEFINED
Genome version is compatible with current STAR version
Started loading the genome: Fri Nov 18 22:26:30 2016
checking Genome sizefile size: 5767168 bytes; state: good=1 eof=0 fail=0 bad=0
checking SA sizefile size: 47449810 bytes; state: good=1 eof=0 fail=0 bad=0
checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0
Read from SAindex: genomeSAindexNbases=14 nSAi=357913940
nGenome=5767168; nSAbyte=47449810
GstrandBit=32 SA number of indices=11502984
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 5767168 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 5767168 bytes
SA file size: 47449812 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=0 eof=1 fail=1 bad=0; loaded 47449810 bytes
Loading SAindex ... done: 1565873619 bytes
Finished loading the genome: Fri Nov 18 22:26:32 2016
Number of real (reference) chromosmes= 1
1 NC_003552 5751492 0
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Created thread # 1
Created thread # 2
在 2016年11月18日星期五 UTC-8下午1:45:16，Alexander Dobin写道：
sanchez cavani
Nov 19, 2016, 11:56:06 AM11/19/16
to rna-...@googlegroups.com
Alexander Dobin
Nov 21, 2016, 11:11:05 AM11/21/16
to rna-star
Hi Sanchez,
there seems to be a problem with genome generation/loading.
Could you please generate genome with 2.5.2b and map with 2.5.2b, and send me the Log.out file.
Also, you can try to further reduce --genomeSAindexNbases (7,6,...).
Cheers
Alex
sanchez cavani
Nov 21, 2016, 10:30:29 PM11/21/16
to rna-star
It doesn't work. The log is shown as follows.
STAR version=STAR_2.5.2b
STAR compilation time,server,dir=Wed Nov 16 18:13:35 EST 2016 florence.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.sandbox/source
##### DEFAULT parameters:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 1
runDirPerm User_RWX
runRNGseed 777
genomeDir ./GenomeDir/
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
genomeSuffixLengthMax 18446744073709551615
readFilesIn Read1 Read2
readFilesCommand -
readMatesLengthsIn NotEqual
readMapNumber 18446744073709551615
readNameSeparator /
inputBAMfile -
bamRemoveDuplicatesType -
bamRemoveDuplicatesMate2basesN 0
limitGenomeGenerateRAM 31000000000
limitIObufferSize 150000000
limitOutSAMoneReadBytes 100000
limitOutSJcollapsed 1000000
limitOutSJoneRead 1000
limitBAMsortRAM 0
limitSjdbInsertNsj 1000000
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
outSAMfilter None
outSAMmultNmax 18446744073709551615
outSAMattrIHstart 1
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
chimMainSegmentMultNmax 10
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
##### Command Line:
~/software/NGS/STAR-STAR_2.5.2/bin/Linux_x86_64_static/STAR --genomeDir index --readFilesIn 1.fq --outFileNamePrefix output --runThreadN 3 --outSAMtype BAM SortedByCoordinate --genomeSAindexNbases 2
##### Initial USER parameters from Command Line:
outFileNamePrefix output
###### All USER parameters from Command Line:
genomeDir index ~RE-DEFINED
readFilesIn 1.fq ~RE-DEFINED
outFileNamePrefix output ~RE-DEFINED
runThreadN 3 ~RE-DEFINED
outSAMtype BAM SortedByCoordinate ~RE-DEFINED
genomeSAindexNbases 2 ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runThreadN 3
genomeDir index
genomeSAindexNbases 2
readFilesIn 1.fq
outFileNamePrefix output
outSAMtype BAM SortedByCoordinate
-------------------------------
##### Final effective command line:
~/software/NGS/STAR-STAR_2.5.2/bin/Linux_x86_64_static/STAR --runThreadN 3 --genomeDir index --genomeSAindexNbases 2 --readFilesIn 1.fq --outFileNamePrefix output --outSAMtype BAM SortedByCoordinate
##### Final parameters after user input--------------------------------:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 3
runDirPerm User_RWX
runRNGseed 777
genomeDir index
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeSAindexNbases 2
genomeChrBinNbits 18
genomeSAsparseD 1
genomeSuffixLengthMax 18446744073709551615
readFilesIn 1.fq
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 output
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
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
chimMainSegmentMultNmax 10
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
----------------------------------------
WARNING: --limitBAMsortRAM=0, will use genome size as RAM limit for BAM sorting
Finished loading and checking parameters
Reading genome generation parameters:
versionGenome 20201 ~RE-DEFINED
genomeFastaFiles ../../../sequences/Mace.genome.fa ~RE-DEFINED
genomeSAindexNbases 14 ~RE-DEFINED
genomeChrBinNbits 18 ~RE-DEFINED
genomeSAsparseD 1 ~RE-DEFINED
sjdbOverhang 0 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
sjdbGTFfile - ~RE-DEFINED
sjdbGTFchrPrefix - ~RE-DEFINED
sjdbGTFfeatureExon exon ~RE-DEFINED
sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED
sjdbGTFtagExonParentGene gene_id ~RE-DEFINED
sjdbInsertSave Basic ~RE-DEFINED
Genome version is compatible with current STAR version
Number of real (reference) chromosomes= 1
1 NC_003552 5751492 0
Started loading the genome: Mon Nov 21 19:27:50 2016
checking Genome sizefile size: 5767168 bytes; state: good=1 eof=0 fail=0 bad=0
checking SA sizefile size: 47449812 bytes; state: good=1 eof=0 fail=0 bad=0
checking /SAindex sizefile size: 1565873619 bytes; state: good=1 eof=0 fail=0 bad=0
Read from SAindex: genomeSAindexNbases=14 nSAi=357913940
nGenome=5767168; nSAbyte=47449812
GstrandBit=32 SA number of indices=11502984
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 5767168 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 5767168 bytes
SA file size: 47449812 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 47449812 bytes
Loading SAindex ... done: 1565873619 bytes
Finished loading the genome: Mon Nov 21 19:27:51 2016
sanchez cavani
Nov 21, 2016, 10:31:40 PM11/21/16
to rna-star
The log file of generation of index is shown as below.
outFileNamePrefix ./
~/software/NGS/STAR-STAR_2.5.2/bin/Linux_x86_64_static/STAR --runMode genomeGenerate --genomeDir index --genomeFastaFiles ../../../sequences/Mace.genome.fa --runThreadN 2
##### Initial USER parameters from Command Line:
###### All USER parameters from Command Line:
runMode genomeGenerate ~RE-DEFINED
genomeDir index ~RE-DEFINED
genomeFastaFiles ../../../sequences/Mace.genome.fa ~RE-DEFINED
runThreadN 2 ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runMode genomeGenerate
runThreadN 2
genomeDir index
genomeFastaFiles ../../../sequences/Mace.genome.fa
-------------------------------
##### Final effective command line:
~/software/NGS/STAR-STAR_2.5.2/bin/Linux_x86_64_static/STAR --runMode genomeGenerate --runThreadN 2 --genomeDir index --genomeFastaFiles ../../../sequences/Mace.genome.fa
##### Final parameters after user input--------------------------------:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode genomeGenerate
runThreadN 2
runDirPerm User_RWX
runRNGseed 777
genomeDir index
genomeLoad NoSharedMemory
genomeFastaFiles ../../../sequences/Mace.genome.fa
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
genomeSuffixLengthMax 18446744073709551615
readFilesIn Read1 Read2
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 ./
----------------------------------------
Finished loading and checking parameters
Nov 21 19:25:46 ... starting to generate Genome files
../../../sequences/Mace.genome.fa : chr # 0 "NC_003552" chrStart: 0
Number of SA indices: 11502984
Nov 21 19:25:46 ... starting to sort Suffix Array. This may take a long time...
Number of chunks: 1; chunks size limit: 92023872 bytes
Nov 21 19:25:46 ... sorting Suffix Array chunks and saving them to disk...
Writing 92023872 bytes into index/SA_0 ; empty space on disk = 315612782592 bytes ... done
Nov 21 19:25:51 ... loading chunks from disk, packing SA...
Nov 21 19:25:52 ... finished generating suffix array
Nov 21 19:25:52 ... generating Suffix Array index
Nov 21 19:25:56 ... completed Suffix Array index
Nov 21 19:25:56 ... writing Genome to disk ...
Writing 5767168 bytes into index/Genome ; empty space on disk = 315612364800 bytes ... done
SA size in bytes: 47449812
Nov 21 19:25:56 ... writing Suffix Array to disk ...
Writing 47449812 bytes into index/SA ; empty space on disk = 315606577152 bytes ... done
Nov 21 19:25:56 ... writing SAindex to disk
Writing 8 bytes into index/SAindex ; empty space on disk = 315558981632 bytes ... done
Writing 120 bytes into index/SAindex ; empty space on disk = 315558981632 bytes ... done
Writing 1565873491 bytes into index/SAindex ; empty space on disk = 315558981632 bytes ... done
Nov 21 19:25:58 ..... finished successfully
DONE: Genome generation, EXITING
Alexander Dobin
Nov 22, 2016, 9:41:07 AM11/22/16
to rna-star
Hi Sanchez,
--genomeSAindexNbases 8 (or lower) has to be used at the genome generation step, not at the mapping stage.
Hopefully this will solve the problem.
Cheers
Alex
On Saturday, November 19, 2016 at 11:56:06 AM UTC-5, sanchez cavani wrote:
mn##### DEFAULT parameters:versionSTAR 20201versionGenome 20101 20200parametersFiles -sysShell -runMode alignReadsrunThreadN 1
runDirPerm User_RWX--genomeSAindexNbases
sanchez cavani
Nov 22, 2016, 1:55:54 PM11/22/16
to rna-star
Hi Alex,
Thank you a lot it solves the problem pretty well!
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