single cell RNA seq mapping issue to pig genome by cellranger2.20 which wrapped STAR
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Yong Liu
Oct 29, 2018, 11:46:18 AM10/29/18
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Hi Alex,
I have issues when I run the cellranger 2.20 from 10x to count the fastq file to the pig reference genome.
Best,
Yong
Here is the log out files
STAR version= STAR_2.5.1b
STAR compilation time,server,dir=Fri Sep 1 18:26:03 PDT 2017 :/mnt/home/jenkins/workspace/module-STAR-5dda596---latest/sake/modules/STAR/5dda596/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 -
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:
STAR --genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA --readFilesIn /dev/fd/63
##### Initial USER parameters from Command Line:
outStd SAM
###### All USER parameters from Command Line:
genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star ~RE-DEFINED
outSAMmultNmax 18446744073709551615 ~RE-DEFINED
runThreadN 4 ~RE-DEFINED
readNameSeparator space ~RE-DEFINED
outSAMunmapped Within ~RE-DEFINED
outSAMtype SAM ~RE-DEFINED
outStd SAM ~RE-DEFINED
outSAMorder PairedKeepInputOrder ~RE-DEFINED
outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA ~RE-DEFINED
readFilesIn /dev/fd/63 ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runThreadN 4
genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star
readFilesIn /dev/fd/63
readNameSeparator space
outStd SAM
outSAMtype SAM
outSAMunmapped Within
outSAMorder PairedKeepInputOrder
outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA
outSAMmultNmax 18446744073709551615
-------------------------------
##### Final effective command line:
STAR --runThreadN 4 --genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star --readFilesIn /dev/fd/63 --readNameSeparator space --outStd SAM --outSAMtype SAM --outSAMunmapped Within --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA --outSAMmultNmax 18446744073709551615
##### Final parameters after user input--------------------------------:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 4
runDirPerm User_RWX
runRNGseed 777
genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
genomeSuffixLengthMax 18446744073709551615
readFilesIn /dev/fd/63
readFilesCommand -
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 ./
outTmpDir -
outStd SAM
outReadsUnmapped None
outQSconversionAdd 0
outMultimapperOrder Old_2.4
outSAMtype SAM
outSAMmode Full
outSAMstrandField None
outSAMattributes Standard
outSAMunmapped Within
outSAMorder PairedKeepInputOrder
outSAMprimaryFlag OneBestScore
outSAMreadID Standard
outSAMmapqUnique 255
outSAMflagOR 0
outSAMflagAND 65535
outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA
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
----------------------------------------
WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute
Finished loading and checking parameters
Reading genome generation parameters:
versionGenome 20201 ~RE-DEFINED
genomeFastaFiles /home/yong/Downloads/Sscrofa11.1/fasta/genome.fa ~RE-DEFINED
genomeSAindexNbases 14 ~RE-DEFINED
genomeChrBinNbits 18 ~RE-DEFINED
genomeSAsparseD 3 ~RE-DEFINED
sjdbOverhang 100 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
sjdbGTFfile /home/yong/Downloads/Sscrofa11.1/genes/genes.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= 613
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251 AEMK02000229.1 61233 2525757440
252 AEMK02000636.1 61061 2526019584
253 AEMK02000676.1 60710 2526281728
254 AEMK02000247.1 60458 2526543872
255 AEMK02000135.1 60359 2526806016
256 AEMK02000382.1 60335 2527068160
257 AEMK02000561.1 59899 2527330304
258 AEMK02000659.1 59742 2527592448
259 AEMK02000445.1 59679 2527854592
260 AEMK02000571.1 59490 2528116736
261 AEMK02000627.1 59096 2528378880
262 AEMK02000595.1 59052 2528641024
263 AEMK02000280.1 58992 2528903168
264 AEMK02000592.1 58548 2529165312
265 AEMK02000169.1 58416 2529427456
266 AEMK02000339.1 58201 2529689600
267 AEMK02000275.1 58047 2529951744
268 AEMK02000631.1 57870 2530213888
269 AEMK02000363.1 57548 2530476032
270 AEMK02000509.1 57178 2530738176
271 AEMK02000647.1 56960 2531000320
272 AEMK02000179.1 56626 2531262464
273 FPKY02000003.1 56573 2531524608
274 AEMK02000439.1 56510 2531786752
275 AEMK02000403.1 56236 2532048896
276 AEMK02000183.1 55954 2532311040
277 AEMK02000542.1 55808 2532573184
278 AEMK02000304.1 55662 2532835328
279 AEMK02000309.1 55519 2533097472
280 AEMK02000130.1 55490 2533359616
281 AEMK02000315.1 55444 2533621760
282 AEMK02000282.1 55403 2533883904
283 AEMK02000543.1 55144 2534146048
284 AEMK02000673.1 55089 2534408192
285 AEMK02000611.1 55069 2534670336
286 AEMK02000174.1 54656 2534932480
287 AEMK02000176.1 54489 2535194624
288 AEMK02000523.1 54345 2535456768
289 AEMK02000142.1 54115 2535718912
290 AEMK02000228.1 53671 2535981056
291 AEMK02000606.1 53195 2536243200
292 AEMK02000674.1 52974 2536505344
293 AEMK02000443.1 52466 2536767488
294 AEMK02000340.1 52374 2537029632
295 AEMK02000461.1 52294 2537291776
296 AEMK02000518.1 52274 2537553920
297 AEMK02000550.1 52058 2537816064
298 AEMK02000489.1 51932 2538078208
299 AEMK02000274.1 51665 2538340352
300 AEMK02000480.1 51625 2538602496
301 AEMK02000313.1 50759 2538864640
302 AEMK02000125.1 50575 2539126784
303 AEMK02000385.1 50567 2539388928
304 AEMK02000583.1 50335 2539651072
305 AEMK02000702.1 50243 2539913216
306 AEMK02000241.1 50081 2540175360
307 AEMK02000181.1 49406 2540437504
308 AEMK02000197.1 49329 2540699648
309 AEMK02000416.1 49126 2540961792
310 AEMK02000471.1 49050 2541223936
311 AEMK02000283.1 48980 2541486080
312 AEMK02000457.1 48413 2541748224
313 AEMK02000426.1 47889 2542010368
314 AEMK02000144.1 47643 2542272512
315 AEMK02000404.1 47524 2542534656
316 AEMK02000552.1 47289 2542796800
317 AEMK02000129.1 47123 2543058944
318 AEMK02000147.1 47030 2543321088
319 AEMK02000575.1 46903 2543583232
320 AEMK02000138.1 46849 2543845376
321 AEMK02000395.1 46845 2544107520
322 AEMK02000345.1 46301 2544369664
323 AEMK02000549.1 46115 2544631808
324 AEMK02000483.1 46114 2544893952
325 AEMK02000322.1 46061 2545156096
326 AEMK02000657.1 46053 2545418240
327 AEMK02000255.1 45734 2545680384
328 AEMK02000511.1 45692 2545942528
329 AEMK02000161.1 45522 2546204672
330 AEMK02000308.1 45474 2546466816
331 AEMK02000540.1 45163 2546728960
332 AEMK02000266.1 44947 2546991104
333 AEMK02000429.1 44863 2547253248
334 AEMK02000596.1 44774 2547515392
335 AEMK02000386.1 44543 2547777536
336 FPKY02000009.1 44425 2548039680
337 AEMK02000622.1 44010 2548301824
338 AEMK02000614.1 43888 2548563968
339 AEMK02000565.1 43773 2548826112
340 AEMK02000279.1 43530 2549088256
341 AEMK02000555.1 43188 2549350400
342 AEMK02000367.1 43143 2549612544
343 AEMK02000590.1 42628 2549874688
344 AEMK02000504.1 42619 2550136832
345 AEMK02000373.1 42492 2550398976
346 AEMK02000546.1 42190 2550661120
347 AEMK02000687.1 42170 2550923264
348 AEMK02000479.1 42029 2551185408
349 AEMK02000180.1 42006 2551447552
350 AEMK02000411.1 41893 2551709696
351 AEMK02000392.1 41701 2551971840
352 AEMK02000330.1 41407 2552233984
353 AEMK02000487.1 41262 2552496128
354 AEMK02000226.1 40713 2552758272
355 AEMK02000466.1 40414 2553020416
356 AEMK02000556.1 40390 2553282560
357 AEMK02000402.1 40091 2553544704
358 AEMK02000681.1 40048 2553806848
359 AEMK02000520.1 39997 2554068992
360 AEMK02000202.1 39923 2554331136
361 AEMK02000268.1 39828 2554593280
362 AEMK02000187.1 39765 2554855424
363 AEMK02000325.1 39598 2555117568
364 AEMK02000433.1 39522 2555379712
365 AEMK02000140.1 39503 2555641856
366 AEMK02000638.1 39448 2555904000
367 AEMK02000671.1 39267 2556166144
368 AEMK02000619.1 39236 2556428288
369 AEMK02000469.1 39098 2556690432
370 AEMK02000244.1 39063 2556952576
371 AEMK02000209.1 38942 2557214720
372 AEMK02000374.1 38887 2557476864
373 AEMK02000222.1 38859 2557739008
374 AEMK02000139.1 38775 2558001152
375 AEMK02000548.1 38669 2558263296
376 AEMK02000246.1 38453 2558525440
377 AEMK02000505.1 38289 2558787584
378 AEMK02000624.1 38262 2559049728
379 AEMK02000645.1 38247 2559311872
380 AEMK02000442.1 38108 2559574016
381 AEMK02000675.1 38099 2559836160
382 AEMK02000252.1 38060 2560098304
383 AEMK02000536.1 37985 2560360448
384 AEMK02000500.1 37867 2560622592
385 AEMK02000243.1 37675 2560884736
386 AEMK02000267.1 37674 2561146880
387 AEMK02000450.1 37546 2561409024
388 AEMK02000127.1 37414 2561671168
389 AEMK02000581.1 37293 2561933312
390 AEMK02000150.1 37252 2562195456
391 AEMK02000365.1 37050 2562457600
392 AEMK02000459.1 36996 2562719744
393 AEMK02000420.1 36859 2562981888
394 AEMK02000467.1 36784 2563244032
395 AEMK02000603.1 36608 2563506176
396 AEMK02000570.1 36425 2563768320
397 AEMK02000664.1 36264 2564030464
398 AEMK02000269.1 36105 2564292608
399 AEMK02000607.1 36098 2564554752
400 AEMK02000387.1 35978 2564816896
401 AEMK02000201.1 35839 2565079040
402 AEMK02000377.1 35800 2565341184
403 AEMK02000618.1 35796 2565603328
404 AEMK02000157.1 35768 2565865472
405 AEMK02000355.1 35698 2566127616
406 AEMK02000597.1 35610 2566389760
407 AEMK02000216.1 35435 2566651904
408 AEMK02000337.1 35413 2566914048
409 AEMK02000475.1 35399 2567176192
410 AEMK02000165.1 35256 2567438336
411 AEMK02000134.1 35132 2567700480
412 AEMK02000218.1 35090 2567962624
413 AEMK02000379.1 35033 2568224768
414 AEMK02000553.1 34945 2568486912
415 AEMK02000604.1 34712 2568749056
416 AEMK02000635.1 34704 2569011200
417 AEMK02000316.1 34675 2569273344
418 AEMK02000533.1 34572 2569535488
419 AEMK02000233.1 34570 2569797632
420 AEMK02000356.1 34299 2570059776
421 AEMK02000360.1 34294 2570321920
422 AEMK02000348.1 34187 2570584064
423 AEMK02000231.1 33498 2570846208
424 AEMK02000605.1 33397 2571108352
425 AEMK02000643.1 33108 2571370496
426 AEMK02000199.1 32990 2571632640
427 AEMK02000490.1 32989 2571894784
428 AEMK02000192.1 32780 2572156928
429 AEMK02000265.1 32772 2572419072
430 AEMK02000650.1 32614 2572681216
431 AEMK02000257.1 32545 2572943360
432 AEMK02000613.1 32495 2573205504
433 AEMK02000634.1 32492 2573467648
434 AEMK02000473.1 32348 2573729792
435 AEMK02000582.1 32249 2573991936
436 AEMK02000524.1 32207 2574254080
437 AEMK02000262.1 32067 2574516224
438 AEMK02000448.1 32062 2574778368
439 AEMK02000123.1 32000 2575040512
440 AEMK02000578.1 31967 2575302656
441 AEMK02000249.1 31957 2575564800
442 AEMK02000303.1 31897 2575826944
443 AEMK02000237.1 31858 2576089088
444 AEMK02000319.1 31818 2576351232
445 AEMK02000609.1 31792 2576613376
446 AEMK02000211.1 31659 2576875520
447 AEMK02000498.1 31599 2577137664
448 AEMK02000516.1 31562 2577399808
449 AEMK02000141.1 31401 2577661952
450 AEMK02000143.1 31175 2577924096
451 AEMK02000326.1 30837 2578186240
452 AEMK02000499.1 30824 2578448384
453 AEMK02000293.1 30558 2578710528
454 AEMK02000418.1 30547 2578972672
455 AEMK02000610.1 30466 2579234816
456 AEMK02000376.1 30397 2579496960
457 AEMK02000347.1 30289 2579759104
458 AEMK02000314.1 30249 2580021248
459 AEMK02000560.1 30120 2580283392
460 AEMK02000601.1 30048 2580545536
461 AEMK02000455.1 30003 2580807680
462 AEMK02000372.1 29770 2581069824
463 AEMK02000484.1 29734 2581331968
464 AEMK02000329.1 29544 2581594112
465 AEMK02000359.1 29315 2581856256
466 AEMK02000470.1 29154 2582118400
467 AEMK02000160.1 29131 2582380544
468 AEMK02000428.1 28902 2582642688
469 AEMK02000195.1 28777 2582904832
470 AEMK02000288.1 28312 2583166976
471 AEMK02000463.1 28245 2583429120
472 AEMK02000298.1 28220 2583691264
473 AEMK02000436.1 28062 2583953408
474 AEMK02000405.1 28054 2584215552
475 AEMK02000538.1 27978 2584477696
476 AEMK02000321.1 27922 2584739840
477 AEMK02000633.1 27743 2585001984
478 AEMK02000158.1 27693 2585264128
479 AEMK02000196.1 27681 2585526272
480 AEMK02000388.1 27663 2585788416
481 AEMK02000488.1 27635 2586050560
482 AEMK02000615.1 27455 2586312704
483 AEMK02000224.1 27355 2586574848
484 AEMK02000666.1 27124 2586836992
485 AEMK02000290.1 26999 2587099136
486 AEMK02000648.1 26953 2587361280
487 AEMK02000629.1 26916 2587623424
488 AEMK02000691.1 26904 2587885568
489 AEMK02000317.1 26654 2588147712
490 AEMK02000132.1 26642 2588409856
491 AEMK02000126.1 26602 2588672000
492 AEMK02000599.1 26507 2588934144
493 AEMK02000242.1 26351 2589196288
494 AEMK02000446.1 26304 2589458432
495 AEMK02000527.1 26146 2589720576
496 AEMK02000684.1 26145 2589982720
497 AEMK02000154.1 26018 2590244864
498 AEMK02000212.1 25912 2590507008
499 AEMK02000447.1 25908 2590769152
500 AEMK02000136.1 25867 2591031296
501 AEMK02000670.1 25784 2591293440
502 AEMK02000178.1 25711 2591555584
503 AEMK02000653.1 25690 2591817728
504 AEMK02000625.1 25476 2592079872
505 AEMK02000194.1 25467 2592342016
506 AEMK02000167.1 25463 2592604160
507 AEMK02000338.1 25373 2592866304
508 AEMK02000193.1 25358 2593128448
509 AEMK02000454.1 25241 2593390592
510 AEMK02000567.1 25217 2593652736
511 AEMK02000128.1 25182 2593914880
512 AEMK02000312.1 25057 2594177024
513 AEMK02000335.1 24880 2594439168
514 AEMK02000667.1 24873 2594701312
515 AEMK02000354.1 24819 2594963456
516 AEMK02000530.1 24729 2595225600
517 AEMK02000198.1 24675 2595487744
518 AEMK02000688.1 24670 2595749888
519 AEMK02000587.1 24651 2596012032
520 AEMK02000371.1 24648 2596274176
521 AEMK02000413.1 24645 2596536320
522 AEMK02000296.1 24616 2596798464
523 AEMK02000547.1 24575 2597060608
524 AEMK02000545.1 24571 2597322752
525 AEMK02000464.1 24501 2597584896
526 AEMK02000396.1 24422 2597847040
527 AEMK02000669.1 24413 2598109184
528 AEMK02000419.1 24396 2598371328
529 AEMK02000652.1 24338 2598633472
530 AEMK02000205.1 24313 2598895616
531 AEMK02000693.1 24178 2599157760
532 AEMK02000557.1 24118 2599419904
533 AEMK02000149.1 24060 2599682048
534 AEMK02000353.1 24015 2599944192
535 AEMK02000651.1 23994 2600206336
536 AEMK02000352.1 23971 2600468480
537 AEMK02000166.1 23908 2600730624
538 AEMK02000145.1 23883 2600992768
539 AEMK02000700.1 23737 2601254912
540 AEMK02000306.1 23710 2601517056
541 AEMK02000462.1 23690 2601779200
542 AEMK02000502.1 23675 2602041344
543 AEMK02000155.1 23493 2602303488
544 AEMK02000214.1 23279 2602565632
545 AEMK02000424.1 23240 2602827776
546 AEMK02000351.1 23110 2603089920
547 AEMK02000384.1 22885 2603352064
548 AEMK02000458.1 22707 2603614208
549 AEMK02000492.1 22673 2603876352
550 AEMK02000686.1 22650 2604138496
551 AEMK02000357.1 22457 2604400640
552 AEMK02000608.1 22393 2604662784
553 AEMK02000544.1 22327 2604924928
554 AEMK02000358.1 22269 2605187072
555 AEMK02000349.1 22254 2605449216
556 AEMK02000217.1 22216 2605711360
557 AEMK02000401.1 22208 2605973504
558 AEMK02000486.1 21821 2606235648
559 AEMK02000690.1 21690 2606497792
560 AEMK02000406.1 21463 2606759936
561 AEMK02000206.1 21439 2607022080
562 AEMK02000397.1 21409 2607284224
563 AEMK02000539.1 21264 2607546368
564 AEMK02000236.1 21107 2607808512
565 AEMK02000230.1 20938 2608070656
566 AEMK02000190.1 20938 2608332800
567 AEMK02000508.1 20819 2608594944
568 AEMK02000307.1 20771 2608857088
569 AEMK02000551.1 20589 2609119232
570 AEMK02000564.1 20419 2609381376
571 AEMK02000594.1 20300 2609643520
572 AEMK02000430.1 20230 2609905664
573 AEMK02000219.1 19883 2610167808
574 AEMK02000481.1 19728 2610429952
575 AEMK02000148.1 19496 2610692096
576 AEMK02000285.1 19482 2610954240
577 AEMK02000491.1 19466 2611216384
578 AEMK02000294.1 19443 2611478528
579 AEMK02000343.1 19362 2611740672
580 AEMK02000562.1 19341 2612002816
581 AEMK02000185.1 19277 2612264960
582 AEMK02000284.1 19274 2612527104
583 AEMK02000362.1 19234 2612789248
584 AEMK02000184.1 19005 2613051392
585 AEMK02000281.1 18788 2613313536
586 AEMK02000705.1 18345 2613575680
587 AEMK02000220.1 18189 2613837824
588 AEMK02000151.1 18134 2614099968
589 AEMK02000381.1 18081 2614362112
590 AEMK02000441.1 17962 2614624256
591 AEMK02000350.1 17924 2614886400
592 AEMK02000701.1 17846 2615148544
593 AEMK02000580.1 17747 2615410688
594 AEMK02000531.1 17708 2615672832
595 AEMK02000535.1 17699 2615934976
596 AEMK02000272.1 17331 2616197120
597 AEMK02000239.1 17318 2616459264
598 AEMK02000642.1 17027 2616721408
599 AEMK02000432.1 17025 2616983552
600 AEMK02000409.1 16500 2617245696
601 AEMK02000586.1 16304 2617507840
602 AEMK02000695.1 16266 2617769984
603 AEMK02000342.1 15919 2618032128
604 AEMK02000124.1 15784 2618294272
605 AEMK02000689.1 15689 2618556416
606 AEMK02000573.1 15624 2618818560
607 AEMK02000663.1 15547 2619080704
608 AEMK02000302.1 15543 2619342848
609 AEMK02000270.1 15496 2619604992
610 AEMK02000323.1 15455 2619867136
611 AEMK02000654.1 15107 2620129280
612 AEMK02000417.1 15107 2620391424
613 AEMK02000519.1 15096 2620653568
--sjdbOverhang = 100 taken from the generated genome
Started loading the genome: Sun Oct 28 13:00:04 2018
checking Genome sizefile size: 2664635021 bytes; state: good=1 eof=0 fail=0 bad=0
checking SA sizefile size: 3502243840 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=2664635021; nSAbyte=3502243840
GstrandBit=32 SA number of indices=849028809
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 2664635021 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 2664635021 bytes
SA file size: 3502243841 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=0 eof=1 fail=1 bad=0; loaded 3502243840 bytes
Loading SAindex ... done: 1565873619 bytes
Finished loading the genome: Sun Oct 28 13:01:40 2018
Processing splice junctions database sjdbN=217509, sjdbOverhang=100
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Created thread # 1
Created thread # 2
Created thread # 3
STAR compilation time,server,dir=Fri Sep 1 18:26:03 PDT 2017 :/mnt/home/jenkins/workspace/module-STAR-5dda596---latest/sake/modules/STAR/5dda596/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 -
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:
STAR --genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star --outSAMmultNmax -1 --runThreadN 4 --readNameSeparator space --outSAMunmapped Within --outSAMtype SAM --outStd SAM --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA --readFilesIn /dev/fd/63
##### Initial USER parameters from Command Line:
outStd SAM
###### All USER parameters from Command Line:
genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star ~RE-DEFINED
outSAMmultNmax 18446744073709551615 ~RE-DEFINED
runThreadN 4 ~RE-DEFINED
readNameSeparator space ~RE-DEFINED
outSAMunmapped Within ~RE-DEFINED
outSAMtype SAM ~RE-DEFINED
outStd SAM ~RE-DEFINED
outSAMorder PairedKeepInputOrder ~RE-DEFINED
outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA ~RE-DEFINED
readFilesIn /dev/fd/63 ~RE-DEFINED
##### Finished reading parameters from all sources
##### Final user re-defined parameters-----------------:
runThreadN 4
genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star
readFilesIn /dev/fd/63
readNameSeparator space
outStd SAM
outSAMtype SAM
outSAMunmapped Within
outSAMorder PairedKeepInputOrder
outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA
outSAMmultNmax 18446744073709551615
-------------------------------
##### Final effective command line:
STAR --runThreadN 4 --genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star --readFilesIn /dev/fd/63 --readNameSeparator space --outStd SAM --outSAMtype SAM --outSAMunmapped Within --outSAMorder PairedKeepInputOrder --outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA --outSAMmultNmax 18446744073709551615
##### Final parameters after user input--------------------------------:
versionSTAR 20201
versionGenome 20101 20200
parametersFiles -
sysShell -
runMode alignReads
runThreadN 4
runDirPerm User_RWX
runRNGseed 777
genomeDir /home/yong/Downloads/RFpig/Sscrofa11.1/star
genomeLoad NoSharedMemory
genomeFastaFiles -
genomeSAindexNbases 14
genomeChrBinNbits 18
genomeSAsparseD 1
genomeSuffixLengthMax 18446744073709551615
readFilesIn /dev/fd/63
readFilesCommand -
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 ./
outTmpDir -
outStd SAM
outReadsUnmapped None
outQSconversionAdd 0
outMultimapperOrder Old_2.4
outSAMtype SAM
outSAMmode Full
outSAMstrandField None
outSAMattributes Standard
outSAMunmapped Within
outSAMorder PairedKeepInputOrder
outSAMprimaryFlag OneBestScore
outSAMreadID Standard
outSAMmapqUnique 255
outSAMflagOR 0
outSAMflagAND 65535
outSAMattrRGline ID:exon_E70:MissingLibrary:1:HCHT5BGX7:1 SM:exon_E70 LB:MissingLibrary.1 PU:exon_E70:MissingLibrary:1:HCHT5BGX7:1 PL:ILLUMINA
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
----------------------------------------
WARNING --outSAMattrRG defines a read group, therefore STAR will output RG attribute
Finished loading and checking parameters
Reading genome generation parameters:
versionGenome 20201 ~RE-DEFINED
genomeFastaFiles /home/yong/Downloads/Sscrofa11.1/fasta/genome.fa ~RE-DEFINED
genomeSAindexNbases 14 ~RE-DEFINED
genomeChrBinNbits 18 ~RE-DEFINED
genomeSAsparseD 3 ~RE-DEFINED
sjdbOverhang 100 ~RE-DEFINED
sjdbFileChrStartEnd - ~RE-DEFINED
sjdbGTFfile /home/yong/Downloads/Sscrofa11.1/genes/genes.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= 613
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2 2 151935994 274464768
3 3 132848913 426508288
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7 7 121844099 966000640
8 8 138966237 1087897600
9 9 139512083 1227096064
10 10 69359453 1366818816
11 11 79169978 1436286976
12 12 61602749 1515716608
13 13 208334590 1577320448
14 14 141755446 1785724928
15 15 140412725 1927544832
16 16 79944280 2068054016
17 17 63494081 2148007936
18 18 55982971 2211708928
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20 Y 43547828 2393899008
21 MT 16613 2437677056
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301 AEMK02000313.1 50759 2538864640
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326 AEMK02000657.1 46053 2545418240
327 AEMK02000255.1 45734 2545680384
328 AEMK02000511.1 45692 2545942528
329 AEMK02000161.1 45522 2546204672
330 AEMK02000308.1 45474 2546466816
331 AEMK02000540.1 45163 2546728960
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335 AEMK02000386.1 44543 2547777536
336 FPKY02000009.1 44425 2548039680
337 AEMK02000622.1 44010 2548301824
338 AEMK02000614.1 43888 2548563968
339 AEMK02000565.1 43773 2548826112
340 AEMK02000279.1 43530 2549088256
341 AEMK02000555.1 43188 2549350400
342 AEMK02000367.1 43143 2549612544
343 AEMK02000590.1 42628 2549874688
344 AEMK02000504.1 42619 2550136832
345 AEMK02000373.1 42492 2550398976
346 AEMK02000546.1 42190 2550661120
347 AEMK02000687.1 42170 2550923264
348 AEMK02000479.1 42029 2551185408
349 AEMK02000180.1 42006 2551447552
350 AEMK02000411.1 41893 2551709696
351 AEMK02000392.1 41701 2551971840
352 AEMK02000330.1 41407 2552233984
353 AEMK02000487.1 41262 2552496128
354 AEMK02000226.1 40713 2552758272
355 AEMK02000466.1 40414 2553020416
356 AEMK02000556.1 40390 2553282560
357 AEMK02000402.1 40091 2553544704
358 AEMK02000681.1 40048 2553806848
359 AEMK02000520.1 39997 2554068992
360 AEMK02000202.1 39923 2554331136
361 AEMK02000268.1 39828 2554593280
362 AEMK02000187.1 39765 2554855424
363 AEMK02000325.1 39598 2555117568
364 AEMK02000433.1 39522 2555379712
365 AEMK02000140.1 39503 2555641856
366 AEMK02000638.1 39448 2555904000
367 AEMK02000671.1 39267 2556166144
368 AEMK02000619.1 39236 2556428288
369 AEMK02000469.1 39098 2556690432
370 AEMK02000244.1 39063 2556952576
371 AEMK02000209.1 38942 2557214720
372 AEMK02000374.1 38887 2557476864
373 AEMK02000222.1 38859 2557739008
374 AEMK02000139.1 38775 2558001152
375 AEMK02000548.1 38669 2558263296
376 AEMK02000246.1 38453 2558525440
377 AEMK02000505.1 38289 2558787584
378 AEMK02000624.1 38262 2559049728
379 AEMK02000645.1 38247 2559311872
380 AEMK02000442.1 38108 2559574016
381 AEMK02000675.1 38099 2559836160
382 AEMK02000252.1 38060 2560098304
383 AEMK02000536.1 37985 2560360448
384 AEMK02000500.1 37867 2560622592
385 AEMK02000243.1 37675 2560884736
386 AEMK02000267.1 37674 2561146880
387 AEMK02000450.1 37546 2561409024
388 AEMK02000127.1 37414 2561671168
389 AEMK02000581.1 37293 2561933312
390 AEMK02000150.1 37252 2562195456
391 AEMK02000365.1 37050 2562457600
392 AEMK02000459.1 36996 2562719744
393 AEMK02000420.1 36859 2562981888
394 AEMK02000467.1 36784 2563244032
395 AEMK02000603.1 36608 2563506176
396 AEMK02000570.1 36425 2563768320
397 AEMK02000664.1 36264 2564030464
398 AEMK02000269.1 36105 2564292608
399 AEMK02000607.1 36098 2564554752
400 AEMK02000387.1 35978 2564816896
401 AEMK02000201.1 35839 2565079040
402 AEMK02000377.1 35800 2565341184
403 AEMK02000618.1 35796 2565603328
404 AEMK02000157.1 35768 2565865472
405 AEMK02000355.1 35698 2566127616
406 AEMK02000597.1 35610 2566389760
407 AEMK02000216.1 35435 2566651904
408 AEMK02000337.1 35413 2566914048
409 AEMK02000475.1 35399 2567176192
410 AEMK02000165.1 35256 2567438336
411 AEMK02000134.1 35132 2567700480
412 AEMK02000218.1 35090 2567962624
413 AEMK02000379.1 35033 2568224768
414 AEMK02000553.1 34945 2568486912
415 AEMK02000604.1 34712 2568749056
416 AEMK02000635.1 34704 2569011200
417 AEMK02000316.1 34675 2569273344
418 AEMK02000533.1 34572 2569535488
419 AEMK02000233.1 34570 2569797632
420 AEMK02000356.1 34299 2570059776
421 AEMK02000360.1 34294 2570321920
422 AEMK02000348.1 34187 2570584064
423 AEMK02000231.1 33498 2570846208
424 AEMK02000605.1 33397 2571108352
425 AEMK02000643.1 33108 2571370496
426 AEMK02000199.1 32990 2571632640
427 AEMK02000490.1 32989 2571894784
428 AEMK02000192.1 32780 2572156928
429 AEMK02000265.1 32772 2572419072
430 AEMK02000650.1 32614 2572681216
431 AEMK02000257.1 32545 2572943360
432 AEMK02000613.1 32495 2573205504
433 AEMK02000634.1 32492 2573467648
434 AEMK02000473.1 32348 2573729792
435 AEMK02000582.1 32249 2573991936
436 AEMK02000524.1 32207 2574254080
437 AEMK02000262.1 32067 2574516224
438 AEMK02000448.1 32062 2574778368
439 AEMK02000123.1 32000 2575040512
440 AEMK02000578.1 31967 2575302656
441 AEMK02000249.1 31957 2575564800
442 AEMK02000303.1 31897 2575826944
443 AEMK02000237.1 31858 2576089088
444 AEMK02000319.1 31818 2576351232
445 AEMK02000609.1 31792 2576613376
446 AEMK02000211.1 31659 2576875520
447 AEMK02000498.1 31599 2577137664
448 AEMK02000516.1 31562 2577399808
449 AEMK02000141.1 31401 2577661952
450 AEMK02000143.1 31175 2577924096
451 AEMK02000326.1 30837 2578186240
452 AEMK02000499.1 30824 2578448384
453 AEMK02000293.1 30558 2578710528
454 AEMK02000418.1 30547 2578972672
455 AEMK02000610.1 30466 2579234816
456 AEMK02000376.1 30397 2579496960
457 AEMK02000347.1 30289 2579759104
458 AEMK02000314.1 30249 2580021248
459 AEMK02000560.1 30120 2580283392
460 AEMK02000601.1 30048 2580545536
461 AEMK02000455.1 30003 2580807680
462 AEMK02000372.1 29770 2581069824
463 AEMK02000484.1 29734 2581331968
464 AEMK02000329.1 29544 2581594112
465 AEMK02000359.1 29315 2581856256
466 AEMK02000470.1 29154 2582118400
467 AEMK02000160.1 29131 2582380544
468 AEMK02000428.1 28902 2582642688
469 AEMK02000195.1 28777 2582904832
470 AEMK02000288.1 28312 2583166976
471 AEMK02000463.1 28245 2583429120
472 AEMK02000298.1 28220 2583691264
473 AEMK02000436.1 28062 2583953408
474 AEMK02000405.1 28054 2584215552
475 AEMK02000538.1 27978 2584477696
476 AEMK02000321.1 27922 2584739840
477 AEMK02000633.1 27743 2585001984
478 AEMK02000158.1 27693 2585264128
479 AEMK02000196.1 27681 2585526272
480 AEMK02000388.1 27663 2585788416
481 AEMK02000488.1 27635 2586050560
482 AEMK02000615.1 27455 2586312704
483 AEMK02000224.1 27355 2586574848
484 AEMK02000666.1 27124 2586836992
485 AEMK02000290.1 26999 2587099136
486 AEMK02000648.1 26953 2587361280
487 AEMK02000629.1 26916 2587623424
488 AEMK02000691.1 26904 2587885568
489 AEMK02000317.1 26654 2588147712
490 AEMK02000132.1 26642 2588409856
491 AEMK02000126.1 26602 2588672000
492 AEMK02000599.1 26507 2588934144
493 AEMK02000242.1 26351 2589196288
494 AEMK02000446.1 26304 2589458432
495 AEMK02000527.1 26146 2589720576
496 AEMK02000684.1 26145 2589982720
497 AEMK02000154.1 26018 2590244864
498 AEMK02000212.1 25912 2590507008
499 AEMK02000447.1 25908 2590769152
500 AEMK02000136.1 25867 2591031296
501 AEMK02000670.1 25784 2591293440
502 AEMK02000178.1 25711 2591555584
503 AEMK02000653.1 25690 2591817728
504 AEMK02000625.1 25476 2592079872
505 AEMK02000194.1 25467 2592342016
506 AEMK02000167.1 25463 2592604160
507 AEMK02000338.1 25373 2592866304
508 AEMK02000193.1 25358 2593128448
509 AEMK02000454.1 25241 2593390592
510 AEMK02000567.1 25217 2593652736
511 AEMK02000128.1 25182 2593914880
512 AEMK02000312.1 25057 2594177024
513 AEMK02000335.1 24880 2594439168
514 AEMK02000667.1 24873 2594701312
515 AEMK02000354.1 24819 2594963456
516 AEMK02000530.1 24729 2595225600
517 AEMK02000198.1 24675 2595487744
518 AEMK02000688.1 24670 2595749888
519 AEMK02000587.1 24651 2596012032
520 AEMK02000371.1 24648 2596274176
521 AEMK02000413.1 24645 2596536320
522 AEMK02000296.1 24616 2596798464
523 AEMK02000547.1 24575 2597060608
524 AEMK02000545.1 24571 2597322752
525 AEMK02000464.1 24501 2597584896
526 AEMK02000396.1 24422 2597847040
527 AEMK02000669.1 24413 2598109184
528 AEMK02000419.1 24396 2598371328
529 AEMK02000652.1 24338 2598633472
530 AEMK02000205.1 24313 2598895616
531 AEMK02000693.1 24178 2599157760
532 AEMK02000557.1 24118 2599419904
533 AEMK02000149.1 24060 2599682048
534 AEMK02000353.1 24015 2599944192
535 AEMK02000651.1 23994 2600206336
536 AEMK02000352.1 23971 2600468480
537 AEMK02000166.1 23908 2600730624
538 AEMK02000145.1 23883 2600992768
539 AEMK02000700.1 23737 2601254912
540 AEMK02000306.1 23710 2601517056
541 AEMK02000462.1 23690 2601779200
542 AEMK02000502.1 23675 2602041344
543 AEMK02000155.1 23493 2602303488
544 AEMK02000214.1 23279 2602565632
545 AEMK02000424.1 23240 2602827776
546 AEMK02000351.1 23110 2603089920
547 AEMK02000384.1 22885 2603352064
548 AEMK02000458.1 22707 2603614208
549 AEMK02000492.1 22673 2603876352
550 AEMK02000686.1 22650 2604138496
551 AEMK02000357.1 22457 2604400640
552 AEMK02000608.1 22393 2604662784
553 AEMK02000544.1 22327 2604924928
554 AEMK02000358.1 22269 2605187072
555 AEMK02000349.1 22254 2605449216
556 AEMK02000217.1 22216 2605711360
557 AEMK02000401.1 22208 2605973504
558 AEMK02000486.1 21821 2606235648
559 AEMK02000690.1 21690 2606497792
560 AEMK02000406.1 21463 2606759936
561 AEMK02000206.1 21439 2607022080
562 AEMK02000397.1 21409 2607284224
563 AEMK02000539.1 21264 2607546368
564 AEMK02000236.1 21107 2607808512
565 AEMK02000230.1 20938 2608070656
566 AEMK02000190.1 20938 2608332800
567 AEMK02000508.1 20819 2608594944
568 AEMK02000307.1 20771 2608857088
569 AEMK02000551.1 20589 2609119232
570 AEMK02000564.1 20419 2609381376
571 AEMK02000594.1 20300 2609643520
572 AEMK02000430.1 20230 2609905664
573 AEMK02000219.1 19883 2610167808
574 AEMK02000481.1 19728 2610429952
575 AEMK02000148.1 19496 2610692096
576 AEMK02000285.1 19482 2610954240
577 AEMK02000491.1 19466 2611216384
578 AEMK02000294.1 19443 2611478528
579 AEMK02000343.1 19362 2611740672
580 AEMK02000562.1 19341 2612002816
581 AEMK02000185.1 19277 2612264960
582 AEMK02000284.1 19274 2612527104
583 AEMK02000362.1 19234 2612789248
584 AEMK02000184.1 19005 2613051392
585 AEMK02000281.1 18788 2613313536
586 AEMK02000705.1 18345 2613575680
587 AEMK02000220.1 18189 2613837824
588 AEMK02000151.1 18134 2614099968
589 AEMK02000381.1 18081 2614362112
590 AEMK02000441.1 17962 2614624256
591 AEMK02000350.1 17924 2614886400
592 AEMK02000701.1 17846 2615148544
593 AEMK02000580.1 17747 2615410688
594 AEMK02000531.1 17708 2615672832
595 AEMK02000535.1 17699 2615934976
596 AEMK02000272.1 17331 2616197120
597 AEMK02000239.1 17318 2616459264
598 AEMK02000642.1 17027 2616721408
599 AEMK02000432.1 17025 2616983552
600 AEMK02000409.1 16500 2617245696
601 AEMK02000586.1 16304 2617507840
602 AEMK02000695.1 16266 2617769984
603 AEMK02000342.1 15919 2618032128
604 AEMK02000124.1 15784 2618294272
605 AEMK02000689.1 15689 2618556416
606 AEMK02000573.1 15624 2618818560
607 AEMK02000663.1 15547 2619080704
608 AEMK02000302.1 15543 2619342848
609 AEMK02000270.1 15496 2619604992
610 AEMK02000323.1 15455 2619867136
611 AEMK02000654.1 15107 2620129280
612 AEMK02000417.1 15107 2620391424
613 AEMK02000519.1 15096 2620653568
--sjdbOverhang = 100 taken from the generated genome
Started loading the genome: Sun Oct 28 13:00:04 2018
checking Genome sizefile size: 2664635021 bytes; state: good=1 eof=0 fail=0 bad=0
checking SA sizefile size: 3502243840 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=2664635021; nSAbyte=3502243840
GstrandBit=32 SA number of indices=849028809
Shared memory is not used for genomes. Allocated a private copy of the genome.
Genome file size: 2664635021 bytes; state: good=1 eof=0 fail=0 bad=0
Loading Genome ... done! state: good=1 eof=0 fail=0 bad=0; loaded 2664635021 bytes
SA file size: 3502243841 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=0 eof=1 fail=1 bad=0; loaded 3502243840 bytes
Loading SAindex ... done: 1565873619 bytes
Finished loading the genome: Sun Oct 28 13:01:40 2018
Processing splice junctions database sjdbN=217509, sjdbOverhang=100
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Created thread # 1
Created thread # 2
Created thread # 3
Alexander Dobin
Oct 29, 2018, 11:49:33 AM10/29/18
to rna-star
Hi Yong,
how did you generate the genome index? You would need to use the same version as CellRanger, i.e. 2.5.1b
Cheers
Alex
Yong Liu
Oct 30, 2018, 7:19:00 AM10/30/18
to rna-star
Hi Alex,
Thanks.
在 2018年10月29日星期一 UTC+1下午4:49:33，Alexander Dobin写道：
It works well so far. I have remade the reference genome and run the cellranger2.20 count at the same linux system (it is CentOS at the moment).
I use the same version of Cellranger 2.2.0 to make the reference genome at both OS.
But there are issues presented when I use the reference genome which produced in the Ubuntu OS and run it with the cellranger2.20 count at the CentOS.
Cheers,
Yong
Here is the log which produced by cell ranger2.20
Here is the log which produced by cell ranger2.20
在 2018年10月29日星期一 UTC+1下午4:49:33，Alexander Dobin写道：
Alexander Dobin
Oct 30, 2018, 4:03:38 PM10/30/18
to rna-star
Hi Yong,
not sure why exactly this is happening, but there is one byte missing in the failed run, according to these two lines from the Log.out you sent:
SA file size: 3502243841 bytes; state: good=1 eof=0 fail=0 bad=0
Loading SA ... done! state: good=0 eof=1 fail=1 bad=0; loaded 3502243840 bytes
Loading SA ... done! state: good=0 eof=1 fail=1 bad=0; loaded 3502243840 bytes
I guess it's just safer to do everything on one machine.
Cheers
Alex
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