Job ID = 2590164 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,434,363 reads read : 24,434,363 reads written : 24,434,363 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:33 24434363 reads; of these: 24434363 (100.00%) were unpaired; of these: 3205441 (13.12%) aligned 0 times 17392691 (71.18%) aligned exactly 1 time 3836231 (15.70%) aligned >1 times 86.88% overall alignment rate Time searching: 00:06:33 Overall time: 00:06:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2473032 / 21228922 = 0.1165 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 20:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 20:13:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:13:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 20:13:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:13:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 12 Aug 2019 20:13:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:13:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:14:03: 1000000 INFO @ Mon, 12 Aug 2019 20:14:04: 1000000 INFO @ Mon, 12 Aug 2019 20:14:05: 1000000 INFO @ Mon, 12 Aug 2019 20:14:10: 2000000 INFO @ Mon, 12 Aug 2019 20:14:11: 2000000 INFO @ Mon, 12 Aug 2019 20:14:12: 2000000 INFO @ Mon, 12 Aug 2019 20:14:17: 3000000 INFO @ Mon, 12 Aug 2019 20:14:18: 3000000 INFO @ Mon, 12 Aug 2019 20:14:19: 3000000 INFO @ Mon, 12 Aug 2019 20:14:24: 4000000 INFO @ Mon, 12 Aug 2019 20:14:25: 4000000 INFO @ Mon, 12 Aug 2019 20:14:26: 4000000 INFO @ Mon, 12 Aug 2019 20:14:32: 5000000 INFO @ Mon, 12 Aug 2019 20:14:32: 5000000 INFO @ Mon, 12 Aug 2019 20:14:34: 5000000 INFO @ Mon, 12 Aug 2019 20:14:39: 6000000 INFO @ Mon, 12 Aug 2019 20:14:39: 6000000 INFO @ Mon, 12 Aug 2019 20:14:41: 6000000 INFO @ Mon, 12 Aug 2019 20:14:46: 7000000 INFO @ Mon, 12 Aug 2019 20:14:47: 7000000 INFO @ Mon, 12 Aug 2019 20:14:48: 7000000 INFO @ Mon, 12 Aug 2019 20:14:54: 8000000 INFO @ Mon, 12 Aug 2019 20:14:54: 8000000 INFO @ Mon, 12 Aug 2019 20:14:55: 8000000 INFO @ Mon, 12 Aug 2019 20:15:01: 9000000 INFO @ Mon, 12 Aug 2019 20:15:01: 9000000 INFO @ Mon, 12 Aug 2019 20:15:02: 9000000 INFO @ Mon, 12 Aug 2019 20:15:08: 10000000 INFO @ Mon, 12 Aug 2019 20:15:08: 10000000 INFO @ Mon, 12 Aug 2019 20:15:09: 10000000 INFO @ Mon, 12 Aug 2019 20:15:15: 11000000 INFO @ Mon, 12 Aug 2019 20:15:16: 11000000 INFO @ Mon, 12 Aug 2019 20:15:17: 11000000 INFO @ Mon, 12 Aug 2019 20:15:22: 12000000 INFO @ Mon, 12 Aug 2019 20:15:23: 12000000 INFO @ Mon, 12 Aug 2019 20:15:24: 12000000 INFO @ Mon, 12 Aug 2019 20:15:29: 13000000 INFO @ Mon, 12 Aug 2019 20:15:30: 13000000 INFO @ Mon, 12 Aug 2019 20:15:31: 13000000 INFO @ Mon, 12 Aug 2019 20:15:37: 14000000 INFO @ Mon, 12 Aug 2019 20:15:37: 14000000 INFO @ Mon, 12 Aug 2019 20:15:38: 14000000 INFO @ Mon, 12 Aug 2019 20:15:44: 15000000 INFO @ Mon, 12 Aug 2019 20:15:44: 15000000 INFO @ Mon, 12 Aug 2019 20:15:45: 15000000 INFO @ Mon, 12 Aug 2019 20:15:51: 16000000 INFO @ Mon, 12 Aug 2019 20:15:51: 16000000 INFO @ Mon, 12 Aug 2019 20:15:52: 16000000 INFO @ Mon, 12 Aug 2019 20:15:58: 17000000 INFO @ Mon, 12 Aug 2019 20:15:59: 17000000 INFO @ Mon, 12 Aug 2019 20:15:59: 17000000 INFO @ Mon, 12 Aug 2019 20:16:05: 18000000 INFO @ Mon, 12 Aug 2019 20:16:06: 18000000 INFO @ Mon, 12 Aug 2019 20:16:06: 18000000 INFO @ Mon, 12 Aug 2019 20:16:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:16:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:16:10: #1 total tags in treatment: 18755890 INFO @ Mon, 12 Aug 2019 20:16:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:16:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:16:10: #1 tags after filtering in treatment: 18755890 INFO @ Mon, 12 Aug 2019 20:16:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:16:10: #1 finished! INFO @ Mon, 12 Aug 2019 20:16:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:16:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:16:11: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:16:11: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:16:11: #1 total tags in treatment: 18755890 INFO @ Mon, 12 Aug 2019 20:16:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:16:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:16:12: #1 tags after filtering in treatment: 18755890 INFO @ Mon, 12 Aug 2019 20:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:16:12: #1 finished! INFO @ Mon, 12 Aug 2019 20:16:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:16:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:16:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:16:12: #1 total tags in treatment: 18755890 INFO @ Mon, 12 Aug 2019 20:16:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:16:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:16:12: #2 number of paired peaks: 257 WARNING @ Mon, 12 Aug 2019 20:16:12: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Mon, 12 Aug 2019 20:16:12: start model_add_line... INFO @ Mon, 12 Aug 2019 20:16:12: start X-correlation... INFO @ Mon, 12 Aug 2019 20:16:12: end of X-cor INFO @ Mon, 12 Aug 2019 20:16:12: #2 finished! INFO @ Mon, 12 Aug 2019 20:16:12: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 20:16:12: #2 alternative fragment length(s) may be 2,21,49 bps INFO @ Mon, 12 Aug 2019 20:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.10_model.r WARNING @ Mon, 12 Aug 2019 20:16:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:16:12: #2 You may need to consider one of the other alternative d(s): 2,21,49 WARNING @ Mon, 12 Aug 2019 20:16:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:16:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:16:12: #1 tags after filtering in treatment: 18755890 INFO @ Mon, 12 Aug 2019 20:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:16:12: #1 finished! INFO @ Mon, 12 Aug 2019 20:16:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:16:13: #2 number of paired peaks: 257 WARNING @ Mon, 12 Aug 2019 20:16:13: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Mon, 12 Aug 2019 20:16:13: start model_add_line... INFO @ Mon, 12 Aug 2019 20:16:13: start X-correlation... INFO @ Mon, 12 Aug 2019 20:16:13: end of X-cor INFO @ Mon, 12 Aug 2019 20:16:13: #2 finished! INFO @ Mon, 12 Aug 2019 20:16:13: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 20:16:13: #2 alternative fragment length(s) may be 2,21,49 bps INFO @ Mon, 12 Aug 2019 20:16:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.05_model.r WARNING @ Mon, 12 Aug 2019 20:16:13: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:16:13: #2 You may need to consider one of the other alternative d(s): 2,21,49 WARNING @ Mon, 12 Aug 2019 20:16:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:16:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:16:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:16:14: #2 number of paired peaks: 257 WARNING @ Mon, 12 Aug 2019 20:16:14: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Mon, 12 Aug 2019 20:16:14: start model_add_line... INFO @ Mon, 12 Aug 2019 20:16:14: start X-correlation... INFO @ Mon, 12 Aug 2019 20:16:14: end of X-cor INFO @ Mon, 12 Aug 2019 20:16:14: #2 finished! INFO @ Mon, 12 Aug 2019 20:16:14: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 20:16:14: #2 alternative fragment length(s) may be 2,21,49 bps INFO @ Mon, 12 Aug 2019 20:16:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.20_model.r WARNING @ Mon, 12 Aug 2019 20:16:14: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:16:14: #2 You may need to consider one of the other alternative d(s): 2,21,49 WARNING @ Mon, 12 Aug 2019 20:16:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:16:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:16:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:16:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:16:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:16:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:17:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:17:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:17:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.10_summits.bed INFO @ Mon, 12 Aug 2019 20:17:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:17:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:17:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:17:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.05_summits.bed INFO @ Mon, 12 Aug 2019 20:17:14: Done! INFO @ Mon, 12 Aug 2019 20:17:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:17:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:17:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495038/SRX495038.20_summits.bed INFO @ Mon, 12 Aug 2019 20:17:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。