STAR stops when...sorting Suffix Array chunks and saving them to disk...

anagd00 commented 8 years ago

Hello, I am having problmes trying to generate the index of mouse GRCm38 from Ensembl. STAR stops when.. sorting Suffix Array chunks and saving them to disk... is running without any error so my Genome file for the next step is not generated.

I am running STAR using cygwin from windows and I have 64Gb RAM. I heard that maybe the problem ends up with STAR's pre-compiled build. I am not an expert in informatics and RNA-seq analysis is also new for me, so I don't understand well how I have to compile STAR executable but what I did is set the working directory in cd STAR/source and runing STAR from here. Also I set the path to STAR executable in PATH enviroment variable in windows setting system. You guys did you have similar problems?

Im very stuck in this step for several days and I dont know what to do. Any help is welcoming. Could I use a already index generated from STAR in case I cannot do my own indexes?

I have a Intel Xeon CPU 3.5Ghz Number of Cores 4, Number of logical Procss 8 The mouse genome and genes.gtf files I downloaded them from iGenome website and I am using the WholeGenome.fa file from Ensembl. Is this genome too big and I have RAM limitiation? Should I generate my index chromosome per chromosome? How long could be last the index generation?

This is my command:

./STAR --runMode genomeGenerate --genomeDir /cygdrive/c//index --genomeFastaFiles /cygdrive/c/Genome/reference/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa --runThreadN 6 --sjdbGTFfile /cygdrive/c/Genome/GTF_files/referenceGTF/genes.gtf --sjdbOverhang 75 --genomeSAsparseD parameter 1

alexdobin commented 8 years ago

Hi @anagd00

please send me the Log.out file of this run - it should be located in the directory you run STAR from.

Cheers Alex

anagd00 commented 8 years ago

STAR version=STAR_2.5.2b STAR compilation time,server,dir=jue, 13 de oct de 2016 23:34:26 P2-0037-NI82CL:/cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/Programas/STAR/STAR-2.5.2b/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 outFileNamePrefix ./ 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 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

Command Line:

./STAR --runMode genomeGenerate --genomeDir /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/index --genomeFastaFiles /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa --runThreadN 4 --sjdbGTFfile /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/Genome/GTF_files/Mus_musculus.GRCm38.86.gtf genomeSAsparseD 2 --genomeSAindexNbases 13 --sjdbOverhang 74

Initial USER parameters from Command Line:

All USER parameters from Command Line:

runMode genomeGenerate ~RE-DEFINED genomeDir /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/index ~RE-DEFINED genomeFastaFiles /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa ~RE-DEFINED runThreadN 4 ~RE-DEFINED sjdbGTFfile /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/Genome/GTF_files/Mus_musculus.GRCm38.86.gtf ~RE-DEFINED genomeSAindexNbases 13 ~RE-DEFINED sjdbOverhang 74 ~RE-DEFINED

Finished reading parameters from all sources

Final user re-defined parameters-----------------:

runMode genomeGenerate runThreadN 4 genomeDir /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/index genomeFastaFiles /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa
genomeSAindexNbases 13 sjdbGTFfile /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/Genome/GTF_files/Mus_musculus.GRCm38.86.gtf sjdbOverhang 74

Final effective command line:

./STAR --runMode genomeGenerate --runThreadN 4 --genomeDir /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/index --genomeFastaFiles /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa --genomeSAindexNbases 13 --sjdbGTFfile /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/Genome/GTF_files/Mus_musculus.GRCm38.86.gtf --sjdbOverhang 74

Final parameters after user input--------------------------------:

versionSTAR 20201 versionGenome 20101 20200
parametersFiles -
sysShell - runMode genomeGenerate runThreadN 4 runDirPerm User_RWX runRNGseed 777 genomeDir /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/index genomeLoad NoSharedMemory genomeFastaFiles /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa
genomeSAindexNbases 13 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 ./ 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 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 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/Genome/GTF_files/Mus_musculus.GRCm38.86.gtf sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 74 sjdbScore 2 sjdbInsertSave Basic quantMode -
quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615

twopassMode None

Finished loading and checking parameters Oct 25 17:44:29 ... starting to generate Genome files /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 0 "1" chrStart: 0 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 1 "10" chrStart: 195559424 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 2 "11" chrStart: 326369280 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 3 "12" chrStart: 448528384 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 4 "13" chrStart: 568852480 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 5 "14" chrStart: 689438720 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 6 "15" chrStart: 814481408 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 7 "16" chrStart: 918552576 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 8 "17" chrStart: 1016856576 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 9 "18" chrStart: 1112014848 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 10 "19" chrStart: 1202978816 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 11 "2" chrStart: 1264582656 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 12 "3" chrStart: 1446772736 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 13 "4" chrStart: 1606942720 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 14 "5" chrStart: 1763704832 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 15 "6" chrStart: 1915748352 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 16 "7" chrStart: 2065694720 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 17 "8" chrStart: 2211184640 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 18 "9" chrStart: 2340683776 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 19 "MT" chrStart: 2465464320 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 20 "X" chrStart: 2465726464 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 21 "Y" chrStart: 2636906496 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 22 "JH584299.1" chrStart: 2728656896 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 23 "GL456233.1" chrStart: 2729705472 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 24 "JH584301.1" chrStart: 2730229760 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 25 "GL456211.1" chrStart: 2730491904 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 26 "GL456350.1" chrStart: 2730754048 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 27 "JH584293.1" chrStart: 2731016192 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 28 "GL456221.1" chrStart: 2731278336 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 29 "JH584297.1" chrStart: 2731540480 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 30 "JH584296.1" chrStart: 2731802624 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 31 "GL456354.1" chrStart: 2732064768 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 32 "JH584294.1" chrStart: 2732326912 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 33 "JH584298.1" chrStart: 2732589056 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 34 "JH584300.1" chrStart: 2732851200 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 35 "GL456219.1" chrStart: 2733113344 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 36 "GL456210.1" chrStart: 2733375488 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 37 "JH584303.1" chrStart: 2733637632 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 38 "JH584302.1" chrStart: 2733899776 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 39 "GL456212.1" chrStart: 2734161920 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 40 "JH584304.1" chrStart: 2734424064 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 41 "GL456379.1" chrStart: 2734686208 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 42 "GL456216.1" chrStart: 2734948352 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 43 "GL456393.1" chrStart: 2735210496 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 44 "GL456366.1" chrStart: 2735472640 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 45 "GL456367.1" chrStart: 2735734784 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 46 "GL456239.1" chrStart: 2735996928 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 47 "GL456213.1" chrStart: 2736259072 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 48 "GL456383.1" chrStart: 2736521216 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 49 "GL456385.1" chrStart: 2736783360 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 50 "GL456360.1" chrStart: 2737045504 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 51 "GL456378.1" chrStart: 2737307648 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 52 "GL456389.1" chrStart: 2737569792 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 53 "GL456372.1" chrStart: 2737831936 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 54 "GL456370.1" chrStart: 2738094080 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 55 "GL456381.1" chrStart: 2738356224 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 56 "GL456387.1" chrStart: 2738618368 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 57 "GL456390.1" chrStart: 2738880512 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 58 "GL456394.1" chrStart: 2739142656 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 59 "GL456392.1" chrStart: 2739404800 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 60 "GL456382.1" chrStart: 2739666944 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 61 "GL456359.1" chrStart: 2739929088 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 62 "GL456396.1" chrStart: 2740191232 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 63 "GL456368.1" chrStart: 2740453376 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 64 "JH584292.1" chrStart: 2740715520 /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/CM1_FACS/20160818_Carpeta_de_trabajo_H3YJLBGXY/dna/Mus_musculus.GRCm38.dna.chromosome.1.fa : chr # 65 "JH584295.1" chrStart: 2740977664 Number of SA indices: 5305567000 Oct 25 17:45:56 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 12; chunks size limit: 3827625056 bytes Oct 25 17:46:10 ... sorting Suffix Array chunks and saving them to disk...

This is the log out

alexdobin commented 8 years ago

Hi @anagd00

there is nothing suspicious in the Log.out file. Your genome should fit in under 32GB of RAM. Please send me the links to the fasta and gtf files, and I will try running it on my system. If it works will post the index for you to download.

You can try to run the pre-compiled executable. Basically specify the full path to it: /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/Programas/STAR/STAR-2.5.2b/Linux_x86_64/STAR --runMode genomeGenerate --genomeDir /cygdrive/c//index --genomeFastaFiles /cygdrive/c/Genome/reference/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa --runThreadN 6 --sjdbGTFfile /cygdrive/c/Genome/GTF_files/referenceGTF/genes.gtf --sjdbOverhang 75

or the static executable: /cygdrive/c/Ana_GÃ³mez_SecuenciaciÃ³n/Programas/STAR/STAR-2.5.2b/Linux_x86_64_static/STAR

Cheers Alex

TorHou commented 7 years ago

I'm not sure if my issue is related, but it might be. When I try to create the index for Drosophila melanogaster with

./STAR --runMode genomeGenerate --genomeDir dm --genomeFastaFiles ../../../dm6.fa --runThreadN 1 and I choose runThreadN too small, the process will get stuck at Jun 12 15:07:33 ... sorting Suffix Array chunks and saving them to disk... I have to set runThreadN to at least 3 so that it finishes. If i set runThreadN to 3 the process finishes in less that 4 minutes. The process I started with --runThreadN 1 has not finished after 5 days. Note that dm6.fa is 140 Megabytes big. I tried it with some viruses (up to 10 Megabytes file size) where I did not encounter that problem.

Current version I'm using: b51a6591b0942b129e1921bb6e5270dfb95a2116

alexdobin commented 7 years ago

Hi Torsten,

sorry for belayed reply. It's better to start a new issue than continue with the old one. Please send me the Log.out file for the failed run.

Cheers Alex

TorHou commented 7 years ago

Thanks for the reply. I added the log files to the new issue #287

alexdobin / STAR