Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder
changeset 13:e905fcc6fd15 draft
planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 4c88ff739e2fb47369e5256151eb55cc5cb47c9d
| author | sanbi-uwc |
|---|---|
| date | Tue, 16 Feb 2016 02:11:37 -0500 |
| parents | a42dbab7917c |
| children | 70316134a316 |
| files | Log.out data_manager/rnastar_index_builder.py |
| diffstat | 2 files changed, 4095 insertions(+), 2 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Log.out Tue Feb 16 02:11:37 2016 -0500 @@ -0,0 +1,4093 @@ +STAR version=STAR_2.4.2a +STAR compilation time,server,dir=Mon Jul 6 23:12:07 UTC 2015 :/build/rna-star-sPv25W/rna-star-2.4.2a+dfsg/source +##### 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 +outFileNamePrefix ./ +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: +STAR --runMode genomeGenerate --genomeDir /home/zipho/workspace/sanbi/dev/galaxy/database/job_working_directory/000/65/dataset_65_files --genomeFastaFiles /home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa --runThreadN 1 +##### Initial USER parameters from Command Line: +###### All USER parameters from Command Line: +runMode genomeGenerate ~RE-DEFINED +genomeDir /home/zipho/workspace/sanbi/dev/galaxy/database/job_working_directory/000/65/dataset_65_files ~RE-DEFINED +genomeFastaFiles /home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa ~RE-DEFINED +runThreadN 1 ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runMode genomeGenerate +runThreadN 1 +genomeDir /home/zipho/workspace/sanbi/dev/galaxy/database/job_working_directory/000/65/dataset_65_files +genomeFastaFiles /home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa + +------------------------------- +##### Final effective command line: +STAR --runMode genomeGenerate --runThreadN 1 --genomeDir /home/zipho/workspace/sanbi/dev/galaxy/database/job_working_directory/000/65/dataset_65_files --genomeFastaFiles /home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa + +##### Final parameters after user input--------------------------------: +versionSTAR 20201 +versionGenome 20101 20200 +parametersFiles - +sysShell - +runMode genomeGenerate +runThreadN 1 +runDirPerm User_RWX +genomeDir /home/zipho/workspace/sanbi/dev/galaxy/database/job_working_directory/000/65/dataset_65_files +genomeLoad NoSharedMemory +genomeFastaFiles /home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa +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 +outFileNamePrefix ./ +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 +---------------------------------------- + +Finished loading and checking parameters +Feb 15 15:25:33 ... Starting to generate Genome files +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 0 "scaffold_1" chrStart: 0 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 1 "scaffold_2" chrStart: 3145728 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 2 "scaffold_3" chrStart: 4980736 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 3 "scaffold_4" chrStart: 5242880 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 4 "scaffold_5" chrStart: 7602176 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 5 "scaffold_6" chrStart: 8126464 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 6 "scaffold_7" chrStart: 8388608 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 7 "scaffold_8" chrStart: 10223616 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 8 "scaffold_9" chrStart: 11796480 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 9 "scaffold_10" chrStart: 12058624 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 10 "scaffold_11" chrStart: 18874368 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 11 "scaffold_12" chrStart: 19660800 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 12 "scaffold_13" chrStart: 19922944 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 13 "scaffold_14" chrStart: 20971520 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 14 "scaffold_15" chrStart: 21757952 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 15 "scaffold_16" chrStart: 22806528 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 16 "scaffold_17" chrStart: 24641536 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 17 "scaffold_18" chrStart: 25427968 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 18 "scaffold_19" chrStart: 39845888 +/home/zipho/workspace/sanbi/dev/dev_data/seabass.masked.fa : chr # 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--- a/data_manager/rnastar_index_builder.py Mon Feb 15 06:55:55 2016 -0500 +++ b/data_manager/rnastar_index_builder.py Tue Feb 16 02:11:37 2016 -0500 @@ -36,12 +36,12 @@ else: nslots = 1 - cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadsN {}'.format( + cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadN {}'.format( output_directory, fasta_filename, nslots) cmdline = shlex.split(cmdline_str) - # cmdline = ('touch', '{}/foo'.format(output_directory)) + #cmdline = ('touch', '{}/foo'.format(output_directory)) try: check_call(cmdline) except CalledProcessError: