Job ID = 1292993 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,685,473 reads read : 12,685,473 reads written : 12,685,473 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:22 12685473 reads; of these: 12685473 (100.00%) were unpaired; of these: 2931954 (23.11%) aligned 0 times 8238384 (64.94%) aligned exactly 1 time 1515135 (11.94%) aligned >1 times 76.89% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 1707786 / 9753519 = 0.1751 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 @ Sun, 02 Jun 2019 21:24:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.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 @ Sun, 02 Jun 2019 21:24:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:24:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:24:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.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 @ Sun, 02 Jun 2019 21:24:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:24:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:24:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.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 @ Sun, 02 Jun 2019 21:24:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:24:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:24:34: 1000000 INFO @ Sun, 02 Jun 2019 21:24:37: 1000000 INFO @ Sun, 02 Jun 2019 21:24:37: 1000000 INFO @ Sun, 02 Jun 2019 21:24:42: 2000000 INFO @ Sun, 02 Jun 2019 21:24:47: 2000000 INFO @ Sun, 02 Jun 2019 21:24:47: 2000000 INFO @ Sun, 02 Jun 2019 21:24:49: 3000000 INFO @ Sun, 02 Jun 2019 21:24:57: 3000000 INFO @ Sun, 02 Jun 2019 21:24:57: 4000000 INFO @ Sun, 02 Jun 2019 21:24:58: 3000000 INFO @ Sun, 02 Jun 2019 21:25:05: 5000000 INFO @ Sun, 02 Jun 2019 21:25:07: 4000000 INFO @ Sun, 02 Jun 2019 21:25:08: 4000000 INFO @ Sun, 02 Jun 2019 21:25:14: 6000000 INFO @ Sun, 02 Jun 2019 21:25:17: 5000000 INFO @ Sun, 02 Jun 2019 21:25:18: 5000000 INFO @ Sun, 02 Jun 2019 21:25:22: 7000000 INFO @ Sun, 02 Jun 2019 21:25:26: 6000000 INFO @ Sun, 02 Jun 2019 21:25:28: 6000000 INFO @ Sun, 02 Jun 2019 21:25:30: 8000000 INFO @ Sun, 02 Jun 2019 21:25:30: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:25:30: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:25:30: #1 total tags in treatment: 8045733 INFO @ Sun, 02 Jun 2019 21:25:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:25:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:25:31: #1 tags after filtering in treatment: 8045733 INFO @ Sun, 02 Jun 2019 21:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:25:31: #1 finished! INFO @ Sun, 02 Jun 2019 21:25:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:25:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:25:31: #2 number of paired peaks: 494 WARNING @ Sun, 02 Jun 2019 21:25:31: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sun, 02 Jun 2019 21:25:31: start model_add_line... INFO @ Sun, 02 Jun 2019 21:25:31: start X-correlation... INFO @ Sun, 02 Jun 2019 21:25:31: end of X-cor INFO @ Sun, 02 Jun 2019 21:25:31: #2 finished! INFO @ Sun, 02 Jun 2019 21:25:31: #2 predicted fragment length is 90 bps INFO @ Sun, 02 Jun 2019 21:25:31: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 02 Jun 2019 21:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.10_model.r WARNING @ Sun, 02 Jun 2019 21:25:31: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:25:31: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sun, 02 Jun 2019 21:25:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:25:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:25:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:25:36: 7000000 INFO @ Sun, 02 Jun 2019 21:25:37: 7000000 INFO @ Sun, 02 Jun 2019 21:25:46: 8000000 INFO @ Sun, 02 Jun 2019 21:25:46: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:25:46: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:25:46: #1 total tags in treatment: 8045733 INFO @ Sun, 02 Jun 2019 21:25:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:25:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:25:47: #1 tags after filtering in treatment: 8045733 INFO @ Sun, 02 Jun 2019 21:25:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:25:47: #1 finished! INFO @ Sun, 02 Jun 2019 21:25:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:25:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:25:47: 8000000 INFO @ Sun, 02 Jun 2019 21:25:47: #2 number of paired peaks: 494 WARNING @ Sun, 02 Jun 2019 21:25:47: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sun, 02 Jun 2019 21:25:47: start model_add_line... INFO @ Sun, 02 Jun 2019 21:25:47: start X-correlation... INFO @ Sun, 02 Jun 2019 21:25:47: end of X-cor INFO @ Sun, 02 Jun 2019 21:25:47: #2 finished! INFO @ Sun, 02 Jun 2019 21:25:47: #2 predicted fragment length is 90 bps INFO @ Sun, 02 Jun 2019 21:25:47: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 02 Jun 2019 21:25:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.20_model.r WARNING @ Sun, 02 Jun 2019 21:25:47: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:25:47: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sun, 02 Jun 2019 21:25:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:25:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:25:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:25:48: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:25:48: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:25:48: #1 total tags in treatment: 8045733 INFO @ Sun, 02 Jun 2019 21:25:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:25:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:25:48: #1 tags after filtering in treatment: 8045733 INFO @ Sun, 02 Jun 2019 21:25:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:25:48: #1 finished! INFO @ Sun, 02 Jun 2019 21:25:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:25:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:25:48: #2 number of paired peaks: 494 WARNING @ Sun, 02 Jun 2019 21:25:48: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sun, 02 Jun 2019 21:25:48: start model_add_line... INFO @ Sun, 02 Jun 2019 21:25:49: start X-correlation... INFO @ Sun, 02 Jun 2019 21:25:49: end of X-cor INFO @ Sun, 02 Jun 2019 21:25:49: #2 finished! INFO @ Sun, 02 Jun 2019 21:25:49: #2 predicted fragment length is 90 bps INFO @ Sun, 02 Jun 2019 21:25:49: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 02 Jun 2019 21:25:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.05_model.r WARNING @ Sun, 02 Jun 2019 21:25:49: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:25:49: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sun, 02 Jun 2019 21:25:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:25:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:25:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:25:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.10_summits.bed INFO @ Sun, 02 Jun 2019 21:26:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (491 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:26:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:26:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:26:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:26:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:26:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.20_summits.bed INFO @ Sun, 02 Jun 2019 21:26:23: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (267 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020768/SRX5020768.05_summits.bed INFO @ Sun, 02 Jun 2019 21:26:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (897 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。