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Created February 4, 2015 16:15
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gistfile1.txt
STAR version=STAR_2.4.0i
STAR compilation time,server,dir=Wed Jan 14 18:19:54 EST 2015 modena.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/Releases/STAR_2.4.0i/source
##### DEFAULT parameters:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
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
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
sjdbFileChrStartEnd -
sjdbGTFfile -
sjdbGTFchrPrefix -
sjdbGTFfeatureExon exon
sjdbGTFtagExonParentTranscript transcript_id
sjdbGTFtagExonParentGene gene_id
sjdbOverhang 0
sjdbScore 2
quantMode -
quantTranscriptomeBAMcompression 1
twopass1readsN 0
twopassSJlimit 1000000
##### Command Line:
/n/home05/kirchner/.linuxbrew/bin/STAR --genomeDir /n/regal/hsph_bioinfo/bcbio_nextgen/genomes/AAlbimanus/AalbS1/star/ --readFilesIn /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_1.trimmed.fastq.gz /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_2.trimmed.fastq.gz --runThreadN 16 --outFileNamePrefix /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus --outReadsUnmapped Fastx --outFilterMultimapNmax 10 --outStd SAM --outSAMunmapped Within --outSAMattributes NH HI NM MD AS --readFilesCommand zcat --outSAMattrRGline ID:32 PL:illumina PU:32_2015-01-14_albimanus SM:AT3_ALBI_Sp_V --outSAMstrandField intronMotif
##### Initial USER parameters from Command Line:
outFileNamePrefix /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus
outStd SAM
###### All USER parameters from Command Line:
genomeDir /n/regal/hsph_bioinfo/bcbio_nextgen/genomes/AAlbimanus/AalbS1/star/ ~RE-DEFINED
readFilesIn /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_1.trimmed.fastq.gz /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_2.trimmed.fastq.gz ~RE-DEFINED
runThreadN 16 ~RE-DEFINED
outFileNamePrefix /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus ~RE-DEFINED
outReadsUnmapped Fastx ~RE-DEFINED
outFilterMultimapNmax 10 ~RE-DEFINED
outStd SAM ~RE-DEFINED
outSAMunmapped Within ~RE-DEFINED
outSAMattributes NH HI NM MD AS ~RE-DEFINED
readFilesCommand zcat ~RE-DEFINED
outSAMattrRGline ID:32 PL:illumina PU:32_2015-01-14_albimanus SM:AT3_ALBI_Sp_V ~RE-DEFINED
outSAMstrandField intronMotif ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runThreadN 16
genomeDir /n/regal/hsph_bioinfo/bcbio_nextgen/genomes/AAlbimanus/AalbS1/star/
readFilesIn /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_1.trimmed.fastq.gz /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_2.trimmed.fastq.gz
readFilesCommand zcat
outFileNamePrefix /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus
outStd SAM
outReadsUnmapped Fastx
outSAMstrandField intronMotif
outSAMattributes NH HI NM MD AS
outSAMunmapped Within
outSAMattrRGline ID:32 PL:illumina PU:32_2015-01-14_albimanus SM:AT3_ALBI_Sp_V
outFilterMultimapNmax 10
-------------------------------
##### Final effective command line:
/n/home05/kirchner/.linuxbrew/bin/STAR --runThreadN 16 --genomeDir /n/regal/hsph_bioinfo/bcbio_nextgen/genomes/AAlbimanus/AalbS1/star/ --readFilesIn /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_1.trimmed.fastq.gz /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_2.trimmed.fastq.gz --readFilesCommand zcat --outFileNamePrefix /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus --outStd SAM --outReadsUnmapped Fastx --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS --outSAMunmapped Within --outSAMattrRGline ID:32 PL:illumina PU:32_2015-01-14_albimanus SM:AT3_ALBI_Sp_V --outFilterMultimapNmax 10
##### Final parameters after user input--------------------------------:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 16
genomeDir /n/regal/hsph_bioinfo/bcbio_nextgen/genomes/AAlbimanus/AalbS1/star/
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
readFilesIn /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_1.trimmed.fastq.gz /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_2.trimmed.fastq.gz
readFilesCommand zcat
readMatesLengthsIn NotEqual
readMapNumber 18446744073709551615
inputBAMfile -
bamRemoveDuplicatesType -
bamRemoveDuplicatesMate2basesN 0
limitGenomeGenerateRAM 31000000000
limitIObufferSize 150000000
limitOutSAMoneReadBytes 100000
limitOutSJcollapsed 1000000
limitOutSJoneRead 1000
limitBAMsortRAM 0
outFileNamePrefix /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus
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
outSAMflagOR 0
outSAMflagAND 65535
outSAMattrRGline ID:32 PL:illumina PU:32_2015-01-14_albimanus SM:AT3_ALBI_Sp_V
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
sjdbFileChrStartEnd -
sjdbGTFfile -
sjdbGTFchrPrefix -
sjdbGTFfeatureExon exon
sjdbGTFtagExonParentTranscript transcript_id
sjdbGTFtagExonParentGene gene_id
sjdbOverhang 0
sjdbScore 2
quantMode -
quantTranscriptomeBAMcompression 1
twopass1readsN 0
twopassSJlimit 1000000
----------------------------------------
Input read files for mate 1, from input string /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_1.trimmed.fastq.gz
-rw-rw-r-- 1 kirchner hsph_bioinfo 8950485419 Jan 24 21:16 /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_1.trimmed.fastq.gz
readsCommandsFile:
exec > "/n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp/tmp.fifo.read1"
echo FILE 0
zcat "/n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_1.trimmed.fastq.gz"
Input read files for mate 2, from input string /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_2.trimmed.fastq.gz
-rw-rw-r-- 1 kirchner hsph_bioinfo 9148916007 Jan 24 21:16 /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_2.trimmed.fastq.gz
readsCommandsFile:
exec > "/n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp/tmp.fifo.read2"
echo FILE 0
zcat "/n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_2.trimmed.fastq.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 /n/regal/hsph_bioinfo/bcbio_nextgen/genomes/AAlbimanus/AalbS1/seq/AalbS1.fa ~RE-DEFINED
genomeSAindexNbases 14 ~RE-DEFINED
genomeChrBinNbits 18 ~RE-DEFINED
genomeSAsparseD 1 ~RE-DEFINED
sjdbOverhang 99 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
sjdbGTFfile /n/regal/hsph_bioinfo/bcbio_nextgen/genomes/AAlbimanus/AalbS1/seq/../rnaseq/ref-transcripts.gtf ~RE-DEFINED
sjdbGTFchrPrefix - ~RE-DEFINED
sjdbGTFfeatureExon exon ~RE-DEFINED
sjdbGTFtagExonParentTranscripttranscript_id ~RE-DEFINED
Genome version is compatible with current STAR version
Started loading the genome: Tue Feb 3 10:04:10 2015
Read from SAindex: genomeSAindexNbases=14 nSAi=357913940
Genome file size: 226164043 bytes; state: good=1 eof=0 fail=0 bad=0
SA file size: 1417574046 bytes; state: good=1 eof=0 fail=0 bad=0
nGenome=226164043; nSAbyte=1417574046
GstrandBit=32 SA number of indices=343654314
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 226164043 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 226164043 bytes
SA file size: 1417574046 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 1417574046 bytes
Loading SAindex ... done: 1565873616 bytes
Finished loading the genome: Tue Feb 3 10:04:31 2015
Number of real (reference) chromosmes= 204
1 KB672412 221820 0
2 KB672356 1485 262144
3 KB672314 2592 524288
4 KB672343 1796 786432
5 KB672438 12164 1048576
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204 KB672289 3284 217579520
Processing splice junctions database sjdbN=41821, sjdbOverhang=99
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread0 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread0 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread1 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread1 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread2 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread2 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread3 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread3 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread4 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread4 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread5 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread5 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread6 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread6 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread7 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread7 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread8 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread8 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread9 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread9 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread10 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread10 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread11 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread11 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread12 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread12 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread13 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread13 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread14 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread14 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate1.thread15 ... ok
Opening the file: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/align/AT3_ALBI_Sp_V/32_2015-01-14_albimanus_STARtmp//Unmapped.out.mate2.thread15 ... ok
Created thread # 1
Created thread # 2
Starting to map file # 0
mate 1: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_1.trimmed.fastq.gz
mate 2: /n/regal/hsph_bioinfo/kirchner/mosquito/albimanus/albimanus/work/trimmed/AT3_ALBI_Sp_V_2.trimmed.fastq.gz
Created thread # 3
Created thread # 4
Created thread # 5
Created thread # 6
Created thread # 7
Created thread # 8
Created thread # 9
Created thread # 10
Created thread # 11
Created thread # 12
Created thread # 13
Created thread # 14
Created thread # 15
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