Sorting Suffix Array chunks

luisafmc commented 2 years ago

Hi, I'm just trying to create a index for mapping my RNA reads in mouse (GRCm38), but every time that I tried it says: Jan 14 15:28:11 ... sorting Suffix Array chunks and saving them to disk... terminate called recursively

This is my command singularity exec ~/Programs/singularity-ubuntu18/singularity-rnaseq_0004.sif STAR --runThreadN 8 --runMode genomeGenerate --genomeDir ~/RNA_Analysis/02_Mapping/STAR/RNA_mouse_index --genomeFastaFiles ~/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna --sjdbGTFfile ~/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.gtf.gz --sjdbOverhang 99

I running the program through Singularity and with 10G and 4 cores. Do I need to use a in-build index? How can I used it?

Thank you for your help!

luisafmc commented 2 years ago

This is my Log file STAR version=STAR_2.5.4b STAR compilation time,server,dir=

DEFAULT parameters:

versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode alignReads runThreadN 1 runDirPerm User_RWX runRNGseed 777 genomeDir ./GenomeDir/ genomeLoad NoSharedMemory genomeFastaFiles - genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 genomeConsensusFile - readFilesType Fastx readFilesIn Read1 Read2 readFilesPrefix - 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 outFilterIntronStrands RemoveInconsistentStrands 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 seedSplitMin 12 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:

/usr/bin/STAR --runThreadN 6 --runMode genomeGenerate --genomeDir /home/luisafmc/RN A_Analysis/02_Mapping/STAR/RNA_mouse_index --genomeFastaFiles /home/luisafmc/Data/M _musculus/GCF_000001635.26_GRCm38.p6_genomic.fna --sjdbGTFfile /home/luisafmc/Data/ M_musculus/GCF_000001635.26_GRCm38.p6_genomic.gtf.gz --sjdbOverhang 99

Initial USER parameters from Command Line:

All USER parameters from Command Line:

runThreadN 6 ~RE-DEFINED runMode genomeGenerate ~RE-DEFINED genomeDir /home/luisafmc/RNA_Analysis/02_Mapping/STAR/RNA_mouse _index ~RE-DEFINED genomeFastaFiles /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm3 8.p6_genomic.fna ~RE-DEFINED sjdbGTFfile /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm3 8.p6_genomic.gtf.gz ~RE-DEFINED sjdbOverhang 99 ~RE-DEFINED

Finished reading parameters from all sources

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

runMode genomeGenerate runThreadN 6 genomeDir /home/luisafmc/RNA_Analysis/02_Mapping/STAR/RNA_m ouse_index genomeFastaFiles /home/luisafmc/Data/M_musculus/GCF_000001635.26_G RCm38.p6_genomic.fna sjdbGTFfile /home/luisafmc/Data/M_musculus/GCF_000001635.26_G RCm38.p6_genomic.gtf.gz sjdbOverhang 99

Final effective command line:

/usr/bin/STAR --runMode genomeGenerate --runThreadN 6 --genomeDir /home/luisa fmc/RNA_Analysis/02_Mapping/STAR/RNA_mouse_index --genomeFastaFiles /home/luisafm c/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna --sjdbGTFfile /home/l uisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.gtf.gz --sjdbOverhang 99

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

versionSTAR 20201 versionGenome 20101 20200 parametersFiles - sysShell - runMode genomeGenerate runThreadN 6 runDirPerm User_RWX runRNGseed 777 genomeDir /home/luisafmc/RNA_Analysis/02_Mapping/STAR/RNA_m ouse_index genomeLoad NoSharedMemory genomeFastaFiles /home/luisafmc/Data/M_musculus/GCF_000001635.26_G RCm38.p6_genomic.fna genomeChainFiles - genomeSAindexNbases 14 genomeChrBinNbits 18 genomeSAsparseD 1 genomeSuffixLengthMax 18446744073709551615 genomeFileSizes 0 genomeConsensusFile - readFilesType Fastx readFilesIn Read1 Read2 readFilesPrefix - 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 outFilterIntronStrands RemoveInconsistentStrands 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 seedSplitMin 12 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 /home/luisafmc/Data/M_musculus/GCF_000001635.26_G RCm38.p6_genomic.gtf.gz sjdbGTFchrPrefix - sjdbGTFfeatureExon exon sjdbGTFtagExonParentTranscript transcript_id sjdbGTFtagExonParentGene gene_id sjdbOverhang 99 sjdbScore 2 sjdbInsertSave Basic quantMode - quantTranscriptomeBAMcompression 1 quantTranscriptomeBan IndelSoftclipSingleend twopass1readsN 18446744073709551615 twopassMode None

Finished loading and checking parameters Jan 14 13:21:13 ... starting to generate Genome files /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 0 "N C_000067.6" chrStart: 0 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 1 "N T_166280.1" chrStart: 195559424 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 2 "N T_166281.1" chrStart: 195821568 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 3 "N T_166282.1" chrStart: 196083712 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 4 "N T_166283.1" chrStart: 196345856 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 5 "N T_162750.1" chrStart: 196608000 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 6 "N C_000068.7" chrStart: 196870144 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 7 "N C_000069.6" chrStart: 379060224 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 8 "N C_000070.6" chrStart: 539230208 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 9 "N T_166291.1" chrStart: 695992320 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 10 " NT_187052.1" chrStart: 696254464 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 11 " NT_166434.1" chrStart: 696516608 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 12 " NT_187053.1" chrStart: 696778752 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 13 " NT_187054.1" chrStart: 697040896 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 14 " NT_187055.1" chrStart: 697303040 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 15 " NC_000071.6" chrStart: 697565184 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 16 " NT_187056.1" chrStart: 849608704 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 17 " NT_187057.1" chrStart: 849870848 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 18 " NT_187058.1" chrStart: 850132992 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 19 " NT_166438.1" chrStart: 850395136 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 20 " NT_187059.1" chrStart: 850657280 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 21 " NC_000072.6" chrStart: 851705856 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 22 " NC_000073.6" chrStart: 1001652224 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 23 " NT_166307.1" chrStart: 1147142144 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 24 " NC_000074.6" chrStart: 1147404288 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 25 " NC_000075.6" chrStart: 1276903424 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 26 " NC_000076.6" chrStart: 1401683968 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 27 " NC_000077.6" chrStart: 1532493824 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 28 " NC_000078.6" chrStart: 1654652928 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 29 " NC_000079.6" chrStart: 1774977024 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 30 " NC_000080.6" chrStart: 1895563264 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 31 " NC_000081.6" chrStart: 2020605952 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 32 " NC_000082.6" chrStart: 2124677120 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 33 " NC_000083.6" chrStart: 2222981120 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 34 " NC_000084.6" chrStart: 2318139392 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 35 " NC_000085.6" chrStart: 2409103360 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 36 " NC_000086.7" chrStart: 2470707200 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 37 " NT_165789.2" chrStart: 2641887232 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 38 " NC_000087.7" chrStart: 2642411520 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 39 " NT_187060.1" chrStart: 2734161920 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 40 " NT_187061.1" chrStart: 2734424064 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 41 " NT_187062.1" chrStart: 2734686208 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 42 " NT_187063.1" chrStart: 2734948352 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 43 " NT_166338.1" chrStart: 2735210496 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 44 " NT_166451.1" chrStart: 2735472640 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 45 " NT_166462.1" chrStart: 2735734784 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 46 " NT_166465.1" chrStart: 2735996928 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 47 " NT_166466.1" chrStart: 2736259072 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 48 " NT_166467.1" chrStart: 2736521216 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 49 " NT_166469.1" chrStart: 2736783360 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 50 " NT_166474.1" chrStart: 2737045504 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 51 " NT_166476.1" chrStart: 2737307648 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 52 " NT_166477.1" chrStart: 2737569792 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 53 " NT_166478.1" chrStart: 2737831936 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 54 " NT_166443.1" chrStart: 2738094080 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 55 " NT_166444.1" chrStart: 2738356224 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 56 " NT_166480.1" chrStart: 2738618368 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 57 " NT_166456.1" chrStart: 2738880512 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 58 " NT_166471.1" chrStart: 2739142656 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 59 " NT_166473.1" chrStart: 2739404800 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 60 " NT_166454.1" chrStart: 2739666944 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 61 " NT_166463.1" chrStart: 2739929088 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 62 " NT_166450.1" chrStart: 2740191232 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 63 " NT_166452.1" chrStart: 2740453376 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 64 " NT_187064.1" chrStart: 2740715520 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 65 " NW_016097314.1" chrStart: 2740977664 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 66 " NW_006763128.1" chrStart: 2741764096 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 67 " NW_016097312.1" chrStart: 2742288384 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 68 " NW_016097313.1" chrStart: 2742550528 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 69 " NW_016097315.1" chrStart: 2743074816 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 70 " NW_016097316.1" chrStart: 2743336960 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 71 " NW_012132900.1" chrStart: 2743599104 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 72 " NW_019168505.1" chrStart: 2743861248 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 73 " NW_019168504.1" chrStart: 2744385536 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 74 " NW_019168503.1" chrStart: 2744647680 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 75 " NW_012132901.1" chrStart: 2744909824 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 76 " NW_012132902.1" chrStart: 2745171968 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 77 " NW_019168509.1" chrStart: 2745696256 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 78 " NW_019168506.1" chrStart: 2746220544 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 79 " NW_012132903.1" chrStart: 2747006976 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 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179 "NT_039739.2" chrStart: 2794979328 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 180 "NT_099024.1" chrStart: 2795503616 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 181 "NT_187017.1" chrStart: 2795765760 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 182 "NT_039195.1" chrStart: 2796027904 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 183 "NT_039296.1" chrStart: 2796290048 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 184 "NT_039372.2" chrStart: 2796552192 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 185 "NT_039367.1" chrStart: 2797076480 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 186 "NT_039525.1" chrStart: 2797338624 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 187 "NT_096797.1" chrStart: 2797600768 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 188 "NT_039630.5" chrStart: 2797862912 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 189 "NT_039662.3" chrStart: 2798125056 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 190 "NT_039593.1" chrStart: 2800222208 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 191 "NT_166394.1" chrStart: 2800484352 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 192 "NT_166397.1" chrStart: 2800746496 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 193 "NT_166400.1" chrStart: 2801008640 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 194 "NT_095534.1" chrStart: 2801270784 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 195 "NT_096355.1" chrStart: 2801532928 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 196 "NT_187028.1" chrStart: 2801795072 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 197 "NT_187029.1" chrStart: 2802057216 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 198 "NT_187030.1" chrStart: 2802319360 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 199 "NT_166396.1" chrStart: 2802581504 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 200 "NT_166398.1" chrStart: 2802843648 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 201 "NT_166399.1" chrStart: 2803105792 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 202 "NT_187019.1" chrStart: 2803367936 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 203 "NT_187020.1" chrStart: 2804416512 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 204 "NT_187021.1" chrStart: 2808348672 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 205 "NT_039252.1" chrStart: 2808872960 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 206 "NT_039247.2" chrStart: 2809397248 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 207 "NT_039257.4" chrStart: 2809659392 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 208 "NT_187022.1" chrStart: 2809921536 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 209 "NT_166287.2" chrStart: 2811232256 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 210 "NT_114257.4" chrStart: 2811756544 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 211 "NT_187023.1" chrStart: 2812542976 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 212 "NT_187024.1" chrStart: 2815688704 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 213 "NT_166299.2" chrStart: 2815950848 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 214 "NT_187025.1" chrStart: 2819358720 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 215 "NT_187026.1" chrStart: 2821193728 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 216 "NT_166317.2" chrStart: 2822766592 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 217 "NT_187027.1" chrStart: 2824339456 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 218 "NT_080256.1" chrStart: 2828795904 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 219 "NT_187002.1" chrStart: 2829058048 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 220 "NT_166305.2" chrStart: 2830893056 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 221 "NT_187003.1" chrStart: 2836922368 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 222 "NT_187005.1" chrStart: 2840068096 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 223 "NT_187004.1" chrStart: 2842165248 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 224 "NT_166433.1" chrStart: 2847145984 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 225 "NT_165784.1" chrStart: 2847408128 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 226 "NT_039292.1" chrStart: 2847670272 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 227 "NT_109318.2" chrStart: 2847932416 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 228 "NT_078651.1" chrStart: 2848194560 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 229 "NT_097336.1" chrStart: 2848456704 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 230 "NT_187018.1" chrStart: 2848718848 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 231 "NT_187000.1" chrStart: 2848980992 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 232 "NT_186999.1" chrStart: 2849505280 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 233 "NT_166295.1" chrStart: 2849767424 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 234 "NT_166293.1" chrStart: 2850029568 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 235 "NT_166294.1" chrStart: 2850553856 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 236 "NT_166322.1" chrStart: 2850816000 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 237 "NT_187001.1" chrStart: 2851078144 /home/luisafmc/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna : chr # 238 "NC_005089.1" chrStart: 2851340288 Number of SA indices: 5479077390 Jan 14 13:21:58 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 19; chunks size limit: 2529677504 bytes Jan 14 13:22:14 ... sorting Suffix Array chunks and saving them to disk...

alexdobin commented 2 years ago

Hi @luisafmc

10GB of RAM won't be enough for the mouse genome, you need at least 16GB, and ideally 32GB.

Cheers Alex

luisafmc commented 2 years ago

Hi @alexdobin,

I have changed the RAM to 32GB but it still having the same output: Jan 17 10:42:15 ..... started STAR run Jan 17 10:42:15 ... starting to generate Genome files Jan 17 10:43:13 ... starting to sort Suffix Array. This may take a long time... Jan 17 10:43:27 ... sorting Suffix Array chunks and saving them to disk...

Do yo have any other idea?

luisafmc commented 2 years ago

This is the tail view of the Log.out

Number of SA indices: 5479077390 Jan 18 11:41:12 ... starting to sort Suffix Array. This may take a long time... Number of chunks: 30; chunks size limit: 1577806504 bytes Jan 18 11:41:28 ... sorting Suffix Array chunks and saving them to disk...

This is my code now singularity exec ~/Programs/singularity-ubuntu18/singularity-rnaseq_0004.sif STAR --runThreadN 10 --runMode genomeGenerate --genomeDir ~/RNA_Analysis/02_Mapping/STAR/RNA_mouse_index2 --genomeFastaFiles ~/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.fna --sjdbGTFfile ~/Data/M_musculus/GCF_000001635.26_GRCm38.p6_genomic.gtf.gz --sjdbOverhang 99 --limitGenomeGenerateRAM 32000000000 --genomeSuffixLengthMax 1000

alexdobin commented 2 years ago

Hi @luisafmc,

the GTF file has to be unzipped. Also, I would use slightly smaller --limitGenomeGenerateRAM 30000000000 Also, I recommend using GTF and FASTA release by GENCODE: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M28/GRCm39.primary_assembly.genome.fa.gz https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M28/gencode.vM28.primary_assembly.annotation.gtf.gz

If these suggestions do not help, please send me entire Log.out file. Cheers Alex

luisafmc commented 2 years ago

Hi Alex,

It seems to work! Because I see a couple of new files. However, due to a problem with the space in my disk, it looks like the program did not run completely.

[image: imagen.png]

I will delete some files and try it again with these parameters.

There is my log file

El vie, 21 ene 2022 a la(s) 04:31, Alexander Dobin @.***) escribió:

Hi @luisafmc https://github.com/luisafmc,

the GTF file has to be unzipped. Also, I would use slightly smaller --limitGenomeGenerateRAM 30000000000 Also, I recommend using GTF and FASTA release by GENCODE:

https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M28/GRCm39.primary_assembly.genome.fa.gz

https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M28/gencode.vM28.primary_assembly.annotation.gtf.gz

If these suggestions do not help, please send me entire Log.out file. Cheers Alex

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