Job ID = 2589491 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,248,610 reads read : 5,248,610 reads written : 5,248,610 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR503573.sra.cache’: 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: 00:00:54 5248610 reads; of these: 5248610 (100.00%) were unpaired; of these: 315193 (6.01%) aligned 0 times 4183239 (79.70%) aligned exactly 1 time 750178 (14.29%) aligned >1 times 93.99% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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_rmdupse_core] 332724 / 4933417 = 0.0674 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 17:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.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 17:49:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:49:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.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 17:49:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:49:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.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 17:49:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:49:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:49:23: 1000000 INFO @ Mon, 12 Aug 2019 17:49:24: 1000000 INFO @ Mon, 12 Aug 2019 17:49:26: 1000000 INFO @ Mon, 12 Aug 2019 17:49:30: 2000000 INFO @ Mon, 12 Aug 2019 17:49:31: 2000000 INFO @ Mon, 12 Aug 2019 17:49:34: 2000000 INFO @ Mon, 12 Aug 2019 17:49:37: 3000000 INFO @ Mon, 12 Aug 2019 17:49:37: 3000000 INFO @ Mon, 12 Aug 2019 17:49:42: 3000000 INFO @ Mon, 12 Aug 2019 17:49:43: 4000000 INFO @ Mon, 12 Aug 2019 17:49:44: 4000000 INFO @ Mon, 12 Aug 2019 17:49:47: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:49:47: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:49:47: #1 total tags in treatment: 4600693 INFO @ Mon, 12 Aug 2019 17:49:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:49:47: #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 17:49:47: #1 tags after filtering in treatment: 4600693 INFO @ Mon, 12 Aug 2019 17:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:49:47: #1 finished! INFO @ Mon, 12 Aug 2019 17:49:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:49:48: #2 number of paired peaks: 360 WARNING @ Mon, 12 Aug 2019 17:49:48: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Mon, 12 Aug 2019 17:49:48: start model_add_line... INFO @ Mon, 12 Aug 2019 17:49:48: start X-correlation... INFO @ Mon, 12 Aug 2019 17:49:48: end of X-cor INFO @ Mon, 12 Aug 2019 17:49:48: #2 finished! INFO @ Mon, 12 Aug 2019 17:49:48: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 17:49:48: #2 alternative fragment length(s) may be 3,30,77,151,439,497,576 bps INFO @ Mon, 12 Aug 2019 17:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.05_model.r WARNING @ Mon, 12 Aug 2019 17:49:48: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:49:48: #2 You may need to consider one of the other alternative d(s): 3,30,77,151,439,497,576 WARNING @ Mon, 12 Aug 2019 17:49:48: #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 17:49:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:49:48: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:49:48: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:49:48: #1 total tags in treatment: 4600693 INFO @ Mon, 12 Aug 2019 17:49:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:49:48: #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 17:49:48: #1 tags after filtering in treatment: 4600693 INFO @ Mon, 12 Aug 2019 17:49:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:49:48: #1 finished! INFO @ Mon, 12 Aug 2019 17:49:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:49:48: #2 number of paired peaks: 360 WARNING @ Mon, 12 Aug 2019 17:49:48: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Mon, 12 Aug 2019 17:49:48: start model_add_line... INFO @ Mon, 12 Aug 2019 17:49:48: start X-correlation... INFO @ Mon, 12 Aug 2019 17:49:48: end of X-cor INFO @ Mon, 12 Aug 2019 17:49:48: #2 finished! INFO @ Mon, 12 Aug 2019 17:49:48: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 17:49:48: #2 alternative fragment length(s) may be 3,30,77,151,439,497,576 bps INFO @ Mon, 12 Aug 2019 17:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.10_model.r WARNING @ Mon, 12 Aug 2019 17:49:48: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:49:48: #2 You may need to consider one of the other alternative d(s): 3,30,77,151,439,497,576 WARNING @ Mon, 12 Aug 2019 17:49:48: #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 17:49:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:49:50: 4000000 INFO @ Mon, 12 Aug 2019 17:49:54: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:49:54: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:49:54: #1 total tags in treatment: 4600693 INFO @ Mon, 12 Aug 2019 17:49:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:49:54: #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 17:49:54: #1 tags after filtering in treatment: 4600693 INFO @ Mon, 12 Aug 2019 17:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:49:54: #1 finished! INFO @ Mon, 12 Aug 2019 17:49:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:49:55: #2 number of paired peaks: 360 WARNING @ Mon, 12 Aug 2019 17:49:55: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Mon, 12 Aug 2019 17:49:55: start model_add_line... INFO @ Mon, 12 Aug 2019 17:49:55: start X-correlation... INFO @ Mon, 12 Aug 2019 17:49:55: end of X-cor INFO @ Mon, 12 Aug 2019 17:49:55: #2 finished! INFO @ Mon, 12 Aug 2019 17:49:55: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 17:49:55: #2 alternative fragment length(s) may be 3,30,77,151,439,497,576 bps INFO @ Mon, 12 Aug 2019 17:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.20_model.r WARNING @ Mon, 12 Aug 2019 17:49:55: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:49:55: #2 You may need to consider one of the other alternative d(s): 3,30,77,151,439,497,576 WARNING @ Mon, 12 Aug 2019 17:49:55: #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 17:49:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:50:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:50:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:50:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:50:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:50:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.05_summits.bed INFO @ Mon, 12 Aug 2019 17:50:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:50:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:50:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:50:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:50:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.10_summits.bed INFO @ Mon, 12 Aug 2019 17:50:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX151405/SRX151405.20_summits.bed INFO @ Mon, 12 Aug 2019 17:50:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。