alexdobin
commented
8 years ago Hi Marc,
this look very screwed up. Could you please send me the Log.out file so I can check the parameters, as well as a link to the genome files (fasta, gtf).
Cheers Alex
Closed marcDabad closed 5 years ago
alexdobin
commented
8 years ago Hi Marc,
this look very screwed up. Could you please send me the Log.out file so I can check the parameters, as well as a link to the genome files (fasta, gtf).
Cheers Alex
marcDabad
commented
8 years ago Log.out attached.
FASTA: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/GRCm38.primary_assembly.genome.fa.gz GTF: ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M9/gencode.vM9.annotation.gtf.gz
Marc Dabad
2016-07-01 17:58 GMT+02:00 alexdobin notifications@github.com:
Hi Marc,
this look very screwed up. Could you please send me the Log.out file so I can check the parameters, as well as a link to the genome files (fasta, gtf).
Cheers Alex
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/alexdobin/STAR/issues/167#issuecomment-229983638, or mute the thread https://github.com/notifications/unsubscribe/AEZd5qMeqDBIlRHG84-1RJxmFDP5owovks5qRTkfgaJpZM4JCAJ5 .
alexdobin
commented
8 years ago Hi Marc,
I could not find the attached Log.out file.
If I map with --seedPerReadNmax 100000 --seedPerWindowNmax 1000 --alignTranscriptsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 10000 --outSAMunmapped Within --seedSearchStartLmax 20 --outFilterMismatchNmax 2000 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 it looks all right: 1 0 chr1 132986201 255 81S47M3D49M1D28M1D17M2D99M2D27M1I27M1I25M1D44M3I57M2D18M2D49M3D86M1I63M2D20M2D24M17D632M3D31M1D25M3D51M1D35M8D41M3D66M2D174M1I25M3D109M1D23M2D70M2D53M1D58M4D21M1D30M1D58M1D37M3D22M2D61M2D25M2I52M2D68M2I35M2D81M3D37M2D142M3D48M2D82M1D90M1D47M1D40M1I100M4D116M1I18M3D18M1D32M3D181M4I44M3D49M2D22M2I49M100S * 0 0 ACG... * NH:i:1 HI:i:1 AS:i:2011 nM:i:641
It looks like you are mapping to the same locus but with higher score (AS).
Cheers Alex
marcDabad
commented
8 years ago I'll try with this parameters.
I uploaded log.out file here: https://www.dropbox.com/s/2a86hlun8p5qa7k/sample_1.Log.out?dl=0
Thanks
Marc Dabad
2016-07-07 0:16 GMT+02:00 alexdobin notifications@github.com:
Hi Marc,
I could not find the attached Log.out file.
If I map with --seedPerReadNmax 100000 --seedPerWindowNmax 1000 --alignTranscriptsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 10000 --outSAMunmapped Within --seedSearchStartLmax 20 --outFilterMismatchNmax 2000 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 it looks all right: 1 0 chr1 132986201 255 81S47M3D49M1D28M1D17M2D99M2D27M1I27M1I25M1D44M3I57M2D18M2D49M3D86M1I63M2D20M2D24M17D632M3D31M1D25M3D51M1D35M8D41M3D66M2D174M1I25M3D109M1D23M2D70M2D53M1D58M4D21M1D30M1D58M1D37M3D22M2D61M2D25M2I52M2D68M2I35M2D81M3D37M2D142M3D48M2D82M1D90M1D47M1D40M1I100M4D116M1I18M3D18M1D32M3D181M4I44M3D49M2D22M2I49M100S
- 0 0 ACG... * NH:i:1 HI:i:1 AS:i:2011 nM:i:641
It looks like you are mapping to the same locus but with higher score (AS).
Cheers Alex
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/alexdobin/STAR/issues/167#issuecomment-230923876, or mute the thread https://github.com/notifications/unsubscribe/AEZd5j5Fqob0PzAvTsh9gdTaaVeJXNIlks5qTClDgaJpZM4JCAJ5 .
alexdobin
commented
8 years ago Hi Marc,
I can reproduce the problem when I output BAM file. Will fix it soon, for now you can use the SAM output which seems unaffected.
Cheers Alex
dvanic
commented
7 years ago Hi Alex,
I just wanted to let you know I'm also having the same issues when mapping long reads, and that this causes issues when trying to visualise the data in the UCSC genome browser.
I'm mapping to genome (so not the transcriptome) with gencode M7. The Log.out file is below
I generate a bam file, but it causes bamunpackcigarelement unrecognised opcode in UCSC genome browser trackHubs, with opcodes 9,10,13,14,15 for different genes.
STAR version=STAR_2.5.0a
STAR compilation time,server,dir=Sat Nov 7 13:55:17 EST 2015 modena.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
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 -
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
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
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:
/home/me/bin/STAR/bin/Linux_x86_64/STARlong --readFilesIn /home/me/raw/samplename.fasta.gz --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outFileNamePrefix /home/me/samplename --runThreadN 8 --genomeDir /home/me/Reference/mouse/GRCm38_mm10/STAR --runMode alignReads --outSAMattributes All --readNameSeparator space --outFilterMultimapScoreRange 1 --outFilterMismatchNmax 2000 --alignIntronMax 10000000 --scoreGapNoncan -20 --scoreGapGCAG -4 --scoreGapATAC -8 --scoreDelOpen -1 --scoreDelBase -1 --scoreInsOpen -1 --scoreInsBase -1 --alignEndsType Local --seedSearchStartLmax 50 --seedPerReadNmax 100000 --seedPerWindowNmax 1000 --alignTranscriptsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 10000 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0.10
##### Initial USER parameters from Command Line:
outFileNamePrefix /home/me/samplename
###### All USER parameters from Command Line:
readFilesIn /home/me/raw/samplename.fasta.gz ~RE-DEFINED
outReadsUnmapped Fastx ~RE-DEFINED
outSAMtype BAM SortedByCoordinate ~RE-DEFINED
readFilesCommand zcat ~RE-DEFINED
outFileNamePrefix /home/me/samplename ~RE-DEFINED
runThreadN 8 ~RE-DEFINED
genomeDir /home/me/Reference/mouse/GRCm38_mm10/STAR ~RE-DEFINED
runMode alignReads ~RE-DEFINED
outSAMattributes All ~RE-DEFINED
readNameSeparator space ~RE-DEFINED
outFilterMultimapScoreRange 1 ~RE-DEFINED
outFilterMismatchNmax 2000 ~RE-DEFINED
alignIntronMax 10000000 ~RE-DEFINED
scoreGapNoncan -20 ~RE-DEFINED
scoreGapGCAG -4 ~RE-DEFINED
scoreGapATAC -8 ~RE-DEFINED
scoreDelOpen -1 ~RE-DEFINED
scoreDelBase -1 ~RE-DEFINED
scoreInsOpen -1 ~RE-DEFINED
scoreInsBase -1 ~RE-DEFINED
alignEndsType Local ~RE-DEFINED
seedSearchStartLmax 50 ~RE-DEFINED
seedPerReadNmax 100000 ~RE-DEFINED
seedPerWindowNmax 1000 ~RE-DEFINED
alignTranscriptsPerReadNmax 100000 ~RE-DEFINED
alignTranscriptsPerWindowNmax 10000 ~RE-DEFINED
outFilterScoreMinOverLread 0 ~RE-DEFINED
outFilterMatchNminOverLread 0.1 ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runMode alignReads
runThreadN 8
genomeDir /home/me/Reference/mouse/GRCm38_mm10/STAR
readFilesIn /home/me/raw/samplename.fasta.gz
readFilesCommand zcat
readNameSeparator space
outFileNamePrefix /home/me/samplename
outReadsUnmapped Fastx
outSAMtype BAM SortedByCoordinate
outSAMattributes All
outFilterMultimapScoreRange 1
outFilterScoreMinOverLread 0
outFilterMatchNminOverLread 0.1
outFilterMismatchNmax 2000
scoreGapNoncan -20
scoreGapGCAG -4
scoreGapATAC -8
scoreDelBase -1
scoreDelOpen -1
scoreInsOpen -1
scoreInsBase -1
seedSearchStartLmax 50
seedPerReadNmax 100000
seedPerWindowNmax 1000
alignIntronMax 10000000
alignTranscriptsPerReadNmax 100000
alignTranscriptsPerWindowNmax 10000
alignEndsType Local
-------------------------------
##### Final effective command line:
/home/me/bin/STAR/bin/Linux_x86_64/STARlong --runMode alignReads --runThreadN 8 --genomeDir /home/me/Reference/mouse/GRCm38_mm10/STAR --readFilesIn /home/me/raw/samplename.fasta.gz --readFilesCommand zcat --readNameSeparator space --outFileNamePrefix /home/me/samplename --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outFilterMultimapScoreRange 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0.1 --outFilterMismatchNmax 2000 --scoreGapNoncan -20 --scoreGapGCAG -4 --scoreGapATAC -8 --scoreDelBase -1 --scoreDelOpen -1 --scoreInsOpen -1 --scoreInsBase -1 --seedSearchStartLmax 50 --seedPerReadNmax 100000 --seedPerWindowNmax 1000 --alignIntronMax 10000000 --alignTranscriptsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 10000 --alignEndsType Local
##### Final parameters after user input--------------------------------:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 8
runDirPerm User_RWX
runRNGseed 777
genomeDir /home/me/Reference/mouse/GRCm38_mm10/STAR
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
readFilesIn /home/me/raw/samplename.fasta.gz
readFilesCommand zcat
readMatesLengthsIn NotEqual
readMapNumber 18446744073709551615
readNameSeparator space
inputBAMfile -
bamRemoveDuplicatesType -
bamRemoveDuplicatesMate2basesN 0
limitGenomeGenerateRAM 31000000000
limitIObufferSize 150000000
limitOutSAMoneReadBytes 100000
limitOutSJcollapsed 1000000
limitOutSJoneRead 1000
limitBAMsortRAM 0
limitSjdbInsertNsj 1000000
outFileNamePrefix /home/me/samplename
outTmpDir -
outStd Log
outReadsUnmapped Fastx
outQSconversionAdd 0
outMultimapperOrder Old_2.4
outSAMtype BAM SortedByCoordinate
outSAMmode Full
outSAMstrandField None
outSAMattributes All
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
outFilterMatchNmin 0
outFilterMatchNminOverLread 0.1
outFilterMismatchNmax 2000
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 -20
scoreGapGCAG -4
scoreGapATAC -8
scoreStitchSJshift 1
scoreGenomicLengthLog2scale -0.25
scoreDelBase -1
scoreDelOpen -1
scoreInsOpen -1
scoreInsBase -1
seedSearchLmax 0
seedSearchStartLmax 50
seedSearchStartLmaxOverLread 1
seedPerReadNmax 100000
seedPerWindowNmax 1000
seedNoneLociPerWindow 10
seedMultimapNmax 10000
alignIntronMin 21
alignIntronMax 10000000
alignMatesGapMax 0
alignTranscriptsPerReadNmax 100000
alignSJoverhangMin 5
alignSJDBoverhangMin 3
alignSJstitchMismatchNmax 0 -1 0 0
alignSplicedMateMapLmin 0
alignSplicedMateMapLminOverLmate 0.66
alignWindowsPerReadNmax 10000
alignTranscriptsPerWindowNmax 10000
alignEndsType Local
alignSoftClipAtReferenceEnds Yes
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
----------------------------------------
Input read files for mate 1, from input string /home/me/raw/samplename.fasta.gz
-rwxr-x--- 1 me RDS-SMS-intronret-RW 64463926 Feb 19 17:34 /home/me/raw/samplename.fasta.gz
readsCommandsFile:
exec > "/home/me/samplename_STARtmp/tmp.fifo.read1"
echo FILE 0
zcat "/home/me/raw/samplename.fasta.gz"
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 GRCm38.primary_assembly.genome.fa ~RE-DEFINED
genomeSAindexNbases 14 ~RE-DEFINED
genomeChrBinNbits 18 ~RE-DEFINED
genomeSAsparseD 1 ~RE-DEFINED
sjdbOverhang 100 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
sjdbGTFfile /home/me/data/Reference/mouse/GRCm38/gencode.vM7.primary_assembly.annotation.gtf ~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) chromosmes= 66
1 chr1 195471971 0
2 chr2 182113224 195559424
3 chr3 160039680 377749504
4 chr4 156508116 537919488
5 chr5 151834684 694681600
6 chr6 149736546 846725120
7 chr7 145441459 996671488
8 chr8 129401213 1142161408
9 chr9 124595110 1271660544
10 chr10 130694993 1396441088
11 chr11 122082543 1527250944
12 chr12 120129022 1649410048
13 chr13 120421639 1769734144
14 chr14 124902244 1890320384
15 chr15 104043685 2015363072
16 chr16 98207768 2119434240
17 chr17 94987271 2217738240
18 chr18 90702639 2312896512
19 chr19 61431566 2403860480
20 chrX 171031299 2465464320
21 chrY 91744698 2636644352
22 chrM 16299 2728394752
23 GL456210.1 169725 2728656896
24 GL456211.1 241735 2728919040
25 GL456212.1 153618 2729181184
26 GL456213.1 39340 2729443328
27 GL456216.1 66673 2729705472
28 GL456219.1 175968 2729967616
29 GL456221.1 206961 2730229760
30 GL456233.1 336933 2730491904
31 GL456239.1 40056 2731016192
32 GL456350.1 227966 2731278336
33 GL456354.1 195993 2731540480
34 GL456359.1 22974 2731802624
35 GL456360.1 31704 2732064768
36 GL456366.1 47073 2732326912
37 GL456367.1 42057 2732589056
38 GL456368.1 20208 2732851200
39 GL456370.1 26764 2733113344
40 GL456372.1 28664 2733375488
41 GL456378.1 31602 2733637632
42 GL456379.1 72385 2733899776
43 GL456381.1 25871 2734161920
44 GL456382.1 23158 2734424064
45 GL456383.1 38659 2734686208
46 GL456385.1 35240 2734948352
47 GL456387.1 24685 2735210496
48 GL456389.1 28772 2735472640
49 GL456390.1 24668 2735734784
50 GL456392.1 23629 2735996928
51 GL456393.1 55711 2736259072
52 GL456394.1 24323 2736521216
53 GL456396.1 21240 2736783360
54 JH584292.1 14945 2737045504
55 JH584293.1 207968 2737307648
56 JH584294.1 191905 2737569792
57 JH584295.1 1976 2737831936
58 JH584296.1 199368 2738094080
59 JH584297.1 205776 2738356224
60 JH584298.1 184189 2738618368
61 JH584299.1 953012 2738880512
62 JH584300.1 182347 2739929088
63 JH584301.1 259875 2740191232
64 JH584302.1 155838 2740453376
65 JH584303.1 158099 2740715520
66 JH584304.1 114452 2740977664
--sjdbOverhang = 100 taken from the generated genome
Started loading the genome: Sun Feb 21 01:24:04 2016
checking Genome sizefile size: 2792582042 bytes; state: good=1 eof=0 fail=0 bad=0
checking SA sizefile size: 22306927586 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=2792582042; nSAbyte=22306927586
GstrandBit=32 SA number of indices=5407740020
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 2792582042 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 2792582042 bytes
SA file size: 22306927586 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=1 eof=0 fail=0 bad=0; loaded 22306927586 bytes
Loading SAindex ... done: 1565873619 bytes
Finished loading the genome: Sun Feb 21 01:52:30 2016
Processing splice junctions database sjdbN=255434, sjdbOverhang=100
To accomodate alignIntronMax=10000000 redefined winBinNbits=21
winBinNbits=21 > genomeChrBinNbits=18 redefining:
winBinNbits=18
To accomodate alignIntronMax=10000000 and alignMatesGapMax=0, redefined winFlankNbins=39 and winAnchorDistNbins=78
Opening the file: /home/me/samplename_STARtmp//Unmapped.out.mate1.thread0 ... ok
Opening the file: /home/me/samplename_STARtmp//Unmapped.out.mate1.thread1 ... ok
Opening the file: /home/me/samplename_STARtmp//Unmapped.out.mate1.thread2 ... ok
Opening the file: /home/me/samplename_STARtmp//Unmapped.out.mate1.thread3 ... ok
Opening the file: /home/me/samplename_STARtmp//Unmapped.out.mate1.thread4 ... ok
Opening the file: /home/me/samplename_STARtmp//Unmapped.out.mate1.thread5 ... ok
Opening the file: /home/me/samplename_STARtmp//Unmapped.out.mate1.thread6 ... ok
Opening the file: /home/me/samplename_STARtmp//Unmapped.out.mate1.thread7 ... ok
Created thread # 1
Created thread # 2
Starting to map file # 0
mate 1: /home/me/raw/samplename.fasta.gz
Created thread # 3
Created thread # 4
Created thread # 5
Created thread # 6
Created thread # 7
BAM sorting: 3460 mapped reads
BAM sorting bins genomic start loci:
1 1 25054406
2 1 156388067
3 2 137905424
4 3 156010259
5 4 137295714
6 6 7284079
7 7 23173742
8 7 124863062
9 9 40630043
10 10 42131488
11 10 106780357
12 12 64291144
13 14 5189736
14 15 11066344
15 16 86828789
16 18 29020839
Completed: thread #0
Completed: thread #7
Completed: thread #5
Completed: thread #3
Completed: thread #6
Completed: thread #1
Joined thread # 1
Completed: thread #4
Completed: thread #2
Joined thread # 2
Joined thread # 3
Joined thread # 4
Joined thread # 5
Joined thread # 6
Joined thread # 7
Feb 21 02:29:33 ..... Started sorting BAM
Max memory needed for sorting = 19820551
ALL DONE!
Running STARlong with very long reads, I found two problemes:
May be is a related error.
Example:
read1-example 0 chr1 132986201 255 50623236I51671813S50598660I50598677S50606853S50598660I50676484N51671828=50606852=50676500I50598660=50676484I50606868=50598660I50606852=50598660N74834709S51647812N50598692=70460180=74646851M74646643D74646851M68363587M55788867M50533493^@54817557S74716643N98796308=98771764I51655732=50623267M50623236=50676484I51725060=74646547=74646547M68355395M70452339M55788563I50606852N50623237S50606868I50676484I50676484=50676580=50623237S98771748=54793237S68355187N68425187S68158227=10491189N199570646^@94663968I51672117N56824627P123917090^@59990755I48644898^@488983D66M2D174M1I25M3D109M1D23M2D70M2D53M1D58M4D21M1D30M1D58M1D37M3D22M2D61M2D25M2I52M2D68M2I35M2D81M3D37M2D142M3D48M2D82M1D90M1D47M1D42M1I98M4D58M1I19M1D38M1I18M3D18M1D32M3D181M4I44M3D49M2D22M2I49M100S * 0 0 ACGATTTGCTACTTGCCTGTCGCTCTATCTTCGGCGTCTGCTTGGGTGTTTAACCTAAGCAGTGGTATCAAAGGCAGAGTACACTGATGCCAAACCTTTTTGGAATGAAAACTGTTTAATCACACAAAACACAATAAACCGCATTAAAGCATTACATAGTGCAAACACCCATGTACAGGCTATTAACTTAGTGGCACTGTAAAAATTACATAAGGACACACGAACATTTCCCTCTGGCCTCGTTAGTAAGCTGCCCTTCTTCTCAGTTTATTACCCCTCATTTGCTTCTGCACTGGCAAGTACCAGACTGGGAATGTCATGAATGCCTCTCGACACACAAGTCGAGCAACCTCATGCCACCCACTCAAGTGTATACCAGAATGAATTCCTATACAGCAAGACAGCAAGGAAGTTCCATCAGGGTAGAATGTGCTATCTAGATTTACCATGTGCTTCTCAAAAGCATCTGGGAGACGACTCTTCCTAATCAAGAGCCTAATGTCAAGAAGGACAGGCAGGTGGGCAGGATTAAAGCAGGCAACACAGGTTCCACTGAGCAGGCGGTCAGGAGAACGCACTCATTCCAGAATAGACGCATTCTCAATAAACCTCAGAGCACAGTCGACCAAGACCACTAGCTTCCTCCATCTTCAAGGCAGAGTCCAGCTTTTAAGAGTTGTTCCTCCATAGTCGCCACATCAACTGAGGTGAGAGACGGGTAGCTGTGTGTTGGCTTTACAGGTGAAAAACTGTAGGTTACAACTTCCCCTCCATAGTCGTGGCCTAGGCATAAAAGCGCTGCATCTCCTCCTGTTTTCCGCGATCGGCGTTCTTACTGAAAGGAATGAAAACTATGGGCAGGAAGAGGGGAAGATTAACCTCAAATTCCTTAGTGTTCAAACAAAACCAACACCTCCACAAAGGAGACCCTACAGCTGTGCCCTCCCGGTTCCCTACTCTGTTGGAGCTCGTAGGCAATTCTGTAACCGCAACACTGCTCAGGACAGGCTCAAGGAGGACCCTACATAAGTACACTGTGATTTCTAAACATCCAAGGTGACAGATGGCCTCTCTGGCATAAAAGCAATGTCCAAATGCAGCTAACTCAGAATAGGAGACCATAAAACGGTGAGGGAGGAGGGAGAATGAAGGGAAATGTTTACACACATCAAATACTTGCTGTTTACGAACACAAAGCACCTTTAGTGACAAATTAAATGCTCGTATTGGCCCTCAAGTGTCACAACACAATGTAAAGATCTTCAGTAAGCGTGCCAAGCTCTACAAAACCACTGAAGCAACTACTTGCCCTCTTACTTATCTCTGATCGTGCCCACTTAAGAAAATGGACTTCTACTGTGCTGTGCTCCTAGATGGGACTGAAGGAGGCGCCTATGCAACACATAAGCAACACCATGGATATGAGATCATTTGGTAGACATCAGTTACATGGGCGTGGTAGAAAGGCAGACATCTGTGAGTTTGGGGACAGCCTAATCATACGGCAATTCTAGGTAAACCAAATAGCGAGACTCTGTGTCTCTGAAAACATAACAAAACAAACAAACCCTAAGGCTATCAATAGATCAGAGATAACTTTACAATAAAGTTTAACAATGCTACATTCACCAATAATGGCATTACTTGGATTGCACATTAAGCAAAAGATCTCAAATGTCTACTAAGACAGTCTTTCACAAGAGGGGGAGAGCTGGCAAGCTCCTAAAGAAAACATATAGTGTCTGCAAACCATGAAGAGCTGTCAACAGAAGACCCCAGCTAGGTCTAGGGAGTCACGTTCACCAACCACCTGTCTTGGATACCTCATTAGCAGCTTAGCCTTAGAGGCTCCACAGTTCCTCATAAGCTCAACTGCAACTATCTACCCATACATCTAAGGAACCCCGTGATGCGAGCTCACCGTTCCTAGCTGGCAGTGCAAATTCCACCCATCTGTAACATTGTACACTTTACTTTTGGCAGGACAGCTTCCAGGTTTATCTTTGAAGTGCAGGTTCTAGGAAGCTAGTTCTTTATCTTAAGACATTTTAGCAAAGTAGCATCAATCTATAGTGTGCACATGCATGAATTGTAAGAGGCATCAAAACGAGTATTCTTTAGACTGAATCAACAATTTGGGGTAAAGGAAAATAACAGTCTAATCTAAAGCCATGGAGGTTCAAGAATATCATGGAAACAGAACAAAACAGCGAACAGCTGGTCCAAAAGTGTCTTTCTTTCTAAAGAGGACTAACAATAGTAAAGCCCAGACTGGCGATGATCCCCAATTTCTCAATCAACTTTTCAGCCCCAACATTACATTGAACTGACACAAAGGTTACAAATGATCCTGGCTTTCAGAAATGATTCTTTCAAACCATGCAAAGTATCACACACCTAAATATACATAAATAACCCTGAAATATATATCCACAGTCACAAATGCTTGGCGGTACAATGTAATCTACCGTTCAGCCCTCAATCATAAATCTACTACAACCCCCTGACTCCGAGGGCGGCAGTCACACTATCTGAAGACCCGAGCTCTGAGTCGCTCATCTGACACAGTAGTAAAGAAGCACGTCAACAACCAGGAAGTCCCTGTGGGGAACACAGTAGCCTCGAAGCCCTGGAGACTTTCCTAGTAATCCGACACTCTGCTCTGCATTTTGTCCAAGATAGAGTAACAAAACTTAAATAAAAGCAAAATAAGAAATTTAGTCATTACATGCCTAGAATTCCAGCACTCGAGAGGCAAAAGCAGGAAGGTTACTGCAAAGCTGGAGCCAGCCTGAGATGTAGGGTAAGGCCCAGGCCAGTCATGGTGAAACAGCAGACTCTGCCCAAAGATTAGGAGAAACGTTAGAATGAAGCTGACATACTATCATGTATCCTATTTTGAATGCAGTGCTTGGAATTAAACATCATAATGACCCAATTCCACCCAGCAGGTCCATGTCTAGGAATGACTAAAGTCCAGGGCTAGACATATCATAGCCTATTCTCAAGCAGGGACTGTGAGTGATGGCTTCTAGGATTACCTCTAAGCTACCGTTCTCACTGCCATGGAGATATGGATATACAAGTCTGTTATCAGTCCCCATATGTAGAACGCAAGCAACCCAACAGGAGCTGCAGTATTTTTCAATACAAGCAGAAGACCCATAATAGCAAGGACTTGGCCACTGAGTTTAATAGACATGAAAACCATCAACTGGAGCAATGAAATGACAAGCCATGAGGAAAGTTTCCTCGGCAAAACTGTATGTGGATCGAGAATGCTCCCCTATGCTCATGCTGAGAGTATTTGGTCCCCAGTTGAGGAACTACCTTGAAAGGATTAGGAGATGTGGCTCTGTTTGGGGAGGTCTGTCACATGAAGGCTTGGAGGTTTCAAAGTCCATGCCATCCCCTGGGTTCTCTCTCTTCCTACTTACAGATCAAGATGTAAGCTCTCAACTGTTCTATCATGAACTAAATACCTCTGAAACCATAAACTCAATGCTTTCTTGTACATTCTGCCTTGGTCCTACATGTTTGTCATAGCAATTTTTAGAGTAGCCAGACACAGAAGCTACTACCAGGAAGTGGATCTTTGCTGTGAAAGATAGTGTGACCATGTGAGTTTTTACCCAGGAATGTGTAAGACTTTGGACGAAAGGGTTCAAGGCTGTAAACAGAGCTTAATGGGTCCAGTTGAGGCCTAAGACAGTTAGTACTGAGAGGAGAAGCCTAGATCAAGAGGCTGCAGGGTAGAACAACTATTAACAACTGGCTACCCGTATGCCGCGTTGATACCAAGTGCTTAGGTTAAACACAGAGGACTACAGACGCCGAAAACAGAGCGACAGGCAGTACATATCGTTCTGTTTACGTTT ))))***+1/.-+))++--,/,,,__+++.,+)))-.,-,--,,-,.++)+.,/,-..0--////--,,,,.,,,++-/381..-///./.+,-/13.1-/,,../145/..11/..00111010-------,---.0//./.021-.00023321//0/././//0/.-./012010,,,,,2-+,,+++,,,----.--.-,+,1,-72-100011//,+,+++,,00022154232201-,,,.-/432111.//_,,+/-.21+1,,--+,301.0,,-...,,+++,.0/.,+-++0))))+,--/,++++,+**)+_+++++++--,,.--,+++)),+-+-+1/,/...00-,,+++++++--.,+//+,0/./.-,..+++++,,13110/..,+,00-++++,...+))--++,+.-.-./--,+++,.+-+++,++++,,/.--++++,0+,011//.0../+)))**),,+--//---,,-+-)++)*+**,)))))+,)**))))))+,+-.+,/,,,,,,-+,.---,++)+++,++,,/0011,,++++*+,,+,--..--,,,.,+++-,-,.-,,/--,+,,**)+++-1/-+++,02122/0/2311011---0-+))**,)+)))))****+++-+)())))/.,,,)((())()+//0--,(0**))))))))))))+,.--,)),))/+++,,0001110031-+,00,,++++.-,,-+++,+,--11111-/3/1/014955433363.-1.,,---10.3..131100100271302/30//.-.-,+,+../.+-+,+-++,,-.3/./,,,+,++,,,+--0++--+--,*-,++)**+,+-/,+,//1.-..4.,0441110/-+,+/.0011/.,,,,--...10000/..---..20.....03000//./.-,-.0,+++,,,,+,+++++++++,-.....-,,---,-,-,++++-+++++,0,,++*,,,,-,,./.,--.00.-,.0/-,-,+++,,,,,,-..,--0,/---./00,/1-+_+++-./11003//0/1110/.--/++10+,00,+++_+,+++++..+++-./,,,,,,0100./.,,++,++++,./01000//-+++,,,---0--.+,/--,+.++,.-///.---132/11//.-/0-./0,+++-+,.0..,-+,.22/.-,,,,+-,,,/.-,-+/.+,1/-/./.-/-),10111111321/./+++.,-./0-.-.2---01112,++,-.123222331111332223322011/..//...,,+1.-,.1023555/322--,-,++,+-/0212/.-0,.--,-..363244/.----.,,/-,++**,,.2+.,-,-,,-..00.41...,,-+,,,-///,-+,,+-..++-+,+.1.,+,.,+,/--,+++++++++.))))**++**)/+,++).5/+2-.++++12..,-++++),+,.//00...+,,++.-----.,,-,-.22-.01/-,-,,,++++,,,,1230//6/0//-----.2/--.11112,+,+++,./.06101442122233332.-,,--////..0+,+,++.-,-.0/22222.00010/0./,,,-.-++...-0/1/--11.-.-...221200.----,,,,//.//./0/23121200..//,,-0////21.--.1126356571111235754332359542222//./2/542215112111//.-...011234-0,++*-////.00/1/...+-,,++**,++++**,--17110070-,,+++++++++,.,,-/0+2,311/1./0000//01//.-,,-++++,,-021013332333330210/3/,,,,10..,,,+,,++.++++--/000/-.-+++.**-./-,,+,,-0///102/+**+,0.++.+./--,.,-/..2+_+-,,-,210+/42.,.,,,,+_+,+/.2..110/,,+++,++,-/01220+-,,./-.33-,051-,,,+,-.,--.01111,072/+,+++,+++,22/./0-+,,.-/,,.-.-)++,.,-,,+-+))+))*,,--0.60121/++++,-0,**)++-2---0..+)))))++,,++,-0/2-,.,.23/.++-+))**/.+))-_+1+-.**++,/-,,,,,-----10/22------32582//,,++,,-1-+,,--/../...0112231-/-.01/01200/13333231/.--24,0+.++-.--./22200030/+++**+,,0300/-))))+++,,,+.,,,++_+)+,,+-+)),+++++,,,,)))))++,,,,,,,,10/0/01-+,+))),,/0013242,+031,000421......+++**+--.)*)))****++-0.,+++,,-..0..-.0/00..--/,++,42-++++,,,-/10//..-./24/-.//3.-.32000034/-3--22/.1.-..3100/0/0/-.++++.-140/---,+,,+++++-32/00..//0-/0101/..-1,-+++++-+-++-.---122222.50,,/,+0--./.,-+,,,,-+,--.1----,++,,++-+,++-2+++-,,,--/220-,.++++,++-+-,+++++++++++++,,-----/4-++**,,+)))+****,,,,,+,/.,+)+,.../-.,,/+,+++,--+,++****+++,,+,,,,-,,,+++++,+++--..,++*))+..././----/--,+,+,++,--++,++,..-.21113122210002/0000000..12.----.0.-+++,124121.--,,.12011.-00-.--****)),++++//+-0.**++,---,,--,-,,,/220.-485-01/.-...-..//0,,,---,,,++,+,,+++,,-,+,,+)+,))))))))))).0.../.+,,+,,.....-,++++++,-++)))-,3--/5,+++.--++++++-,++++++1,,,,++))+)))**,)))*****)+,+,,--+,++.--+++++**,-+.//0,,,-,-0120/-...,+00//0,,/.220/,++,)+),)))--,-+,.,,.1.---,,,--+))))))())++,+++)****+))))+++*-//.///000/11222353310/-,++,,,,.00,,-.--/020./00027432/0..--/210/..--.-20-///////00000///./.2//122120//0-010/0011//-/,,++,,,1220/,,,++,,-./0..,,-.-012510/..-,-,+**))+---+),551)))+-/+))-+**)))-,+/,,.++,,,//0012+**)._+,0---.,,,+++./.---,,+,+,--//2211/..,+,,+,,++1/0///.--,++++++++,-/2/.++22-.111////.--.---,++,++++)++,0/0/.,.,+,,,,,+.++-+-,.+----.-((()())))())--))()())+++)(_+,))))+/.-++++_))(-.) NH:i:1 HI:i:0 NM:i:594 MD:Z:2A1A3A4A1A0C0A0A2A25^AAC3A0T1A2C1G0C0A0T1A32^G28^G17^GA99^AC1C25T51^A44A2T0G0C0T2T0C2A0G0C0A0T0C0T6A22G7^GA18^AG2A0C22T22^CCG1A1T1A1T1C1A0G0A1T0A1A0G0G0A0T0T0C2A0A0T56T0C0A0G38A0C0T0G0A1G0T3A9^TG20^GA24A0G0A0G0T1G0G0A0C0A0C0A0A2T0G0C0T1G0C2^AGGCGGCCT26^TTTT0A1G1G0G0T0C1T0T0C1T0A0C0T0G0A0A1G0G1A1G21^G58A0G2A0G16A1C1^TCCC1A1C0T32A50C68^AT0A0G1A0G0A0C1A0T0A12A0G50A18^G2A45C0T2T0C1T0C0A0G0T0A0A1G0C0G0T1T0G1C1A0G0C0T0C0T0A31G0C1T0A0T0C0T0C0T0G0A1T0C0T0G2C0A0C1T1A0G56^AAG31^T3T1G0T0A17^GTG47A0A2^A51A3A0C2A0A0A0C2A0A0A0A0C0C1T1^AGGCTATCAAGGT0A13T2A0C0A1T0A43^GA0T1G0C0A0C0A0T1A0C1T14A0T0G0T0C0T0A0C23A0G0A0G0C0T0G1C0A0G0C0T1C0T125^GCT1C0A2G0T0T0C0C0T68C0T0A0T0G1C0A0G0T0G0C0A17^A23^CA40A0A0G27^TA0G0C0A2G47^A4A0T31C0A3A1G3A0T1A0C0A0G0T0C1^CAGT21^C30^A42A0C1A0G0T0A1C1T1G0G2^A5G0A30^AAG22^AC34T0A25^CA25T0G0A1T6C0C0A38^CG0T1C26T2T0A0A0A0T0G0G0G1G0A0G2C0G1C0A0G0T0C0A0C0A0C45^AC44A1A0G33^CCT2G0C0T2G0C0A1T25^AC0T1A2T0A71C12A0G49^AAG1C0T2G0C0C2A37^TA82^A90^T47^T2G1G0A0G1C0T0G1A2G0C0A1C71G0C2C1A2A0G0T0G1A0A0T1A0T0C0A0A0C0T0G1G1G0C0A1T0G0A0A0T0G1C0A0A0G0C0C0A0T1^GCTA1G2A0G12C0T0G2G0G0T0G0T2A0T45^G10T1G43^AGG18^A32^GCC102G0G0G0A0T0G0T17A0G0A0G0T0A0G0C1A45C0C0T0G0A1C0A0T0G0T0G6T0T0G0G22^TAA43G0A4^AA71 AS:i:2561 nM:i:446 RG:Z:example_sample