Job ID = 2590213 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,041,160 reads read : 29,041,160 reads written : 29,041,160 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: 00:04:35 29041160 reads; of these: 29041160 (100.00%) were unpaired; of these: 10751664 (37.02%) aligned 0 times 15212250 (52.38%) aligned exactly 1 time 3077246 (10.60%) aligned >1 times 62.98% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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 8 files... [bam_rmdupse_core] 1906158 / 18289496 = 0.1042 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 20:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.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 20:22:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:22:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:22:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.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 20:22:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:22:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.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 20:22:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:22:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:22:21: 1000000 INFO @ Mon, 12 Aug 2019 20:22:22: 1000000 INFO @ Mon, 12 Aug 2019 20:22:23: 1000000 INFO @ Mon, 12 Aug 2019 20:22:28: 2000000 INFO @ Mon, 12 Aug 2019 20:22:29: 2000000 INFO @ Mon, 12 Aug 2019 20:22:30: 2000000 INFO @ Mon, 12 Aug 2019 20:22:36: 3000000 INFO @ Mon, 12 Aug 2019 20:22:36: 3000000 INFO @ Mon, 12 Aug 2019 20:22:37: 3000000 INFO @ Mon, 12 Aug 2019 20:22:43: 4000000 INFO @ Mon, 12 Aug 2019 20:22:44: 4000000 INFO @ Mon, 12 Aug 2019 20:22:45: 4000000 INFO @ Mon, 12 Aug 2019 20:22:51: 5000000 INFO @ Mon, 12 Aug 2019 20:22:51: 5000000 INFO @ Mon, 12 Aug 2019 20:22:52: 5000000 INFO @ Mon, 12 Aug 2019 20:22:58: 6000000 INFO @ Mon, 12 Aug 2019 20:22:59: 6000000 INFO @ Mon, 12 Aug 2019 20:23:00: 6000000 INFO @ Mon, 12 Aug 2019 20:23:05: 7000000 INFO @ Mon, 12 Aug 2019 20:23:06: 7000000 INFO @ Mon, 12 Aug 2019 20:23:07: 7000000 INFO @ Mon, 12 Aug 2019 20:23:13: 8000000 INFO @ Mon, 12 Aug 2019 20:23:13: 8000000 INFO @ Mon, 12 Aug 2019 20:23:14: 8000000 INFO @ Mon, 12 Aug 2019 20:23:20: 9000000 INFO @ Mon, 12 Aug 2019 20:23:21: 9000000 INFO @ Mon, 12 Aug 2019 20:23:21: 9000000 INFO @ Mon, 12 Aug 2019 20:23:28: 10000000 INFO @ Mon, 12 Aug 2019 20:23:28: 10000000 INFO @ Mon, 12 Aug 2019 20:23:29: 10000000 INFO @ Mon, 12 Aug 2019 20:23:35: 11000000 INFO @ Mon, 12 Aug 2019 20:23:35: 11000000 INFO @ Mon, 12 Aug 2019 20:23:36: 11000000 INFO @ Mon, 12 Aug 2019 20:23:42: 12000000 INFO @ Mon, 12 Aug 2019 20:23:43: 12000000 INFO @ Mon, 12 Aug 2019 20:23:43: 12000000 INFO @ Mon, 12 Aug 2019 20:23:50: 13000000 INFO @ Mon, 12 Aug 2019 20:23:50: 13000000 INFO @ Mon, 12 Aug 2019 20:23:50: 13000000 INFO @ Mon, 12 Aug 2019 20:23:57: 14000000 INFO @ Mon, 12 Aug 2019 20:23:57: 14000000 INFO @ Mon, 12 Aug 2019 20:23:58: 14000000 INFO @ Mon, 12 Aug 2019 20:24:04: 15000000 INFO @ Mon, 12 Aug 2019 20:24:05: 15000000 INFO @ Mon, 12 Aug 2019 20:24:05: 15000000 INFO @ Mon, 12 Aug 2019 20:24:12: 16000000 INFO @ Mon, 12 Aug 2019 20:24:12: 16000000 INFO @ Mon, 12 Aug 2019 20:24:12: 16000000 INFO @ Mon, 12 Aug 2019 20:24:15: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:24:15: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:24:15: #1 total tags in treatment: 16383338 INFO @ Mon, 12 Aug 2019 20:24:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:24:15: #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 20:24:15: #1 tags after filtering in treatment: 16383338 INFO @ Mon, 12 Aug 2019 20:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:24:15: #1 finished! INFO @ Mon, 12 Aug 2019 20:24:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:24:15: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:24:15: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:24:15: #1 total tags in treatment: 16383338 INFO @ Mon, 12 Aug 2019 20:24:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:24:15: #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 20:24:15: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:24:15: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:24:15: #1 total tags in treatment: 16383338 INFO @ Mon, 12 Aug 2019 20:24:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:24:15: #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 20:24:15: #1 tags after filtering in treatment: 16383338 INFO @ Mon, 12 Aug 2019 20:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:24:15: #1 finished! INFO @ Mon, 12 Aug 2019 20:24:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:24:16: #1 tags after filtering in treatment: 16383338 INFO @ Mon, 12 Aug 2019 20:24:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:24:16: #1 finished! INFO @ Mon, 12 Aug 2019 20:24:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:24:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:24:16: #2 number of paired peaks: 225 WARNING @ Mon, 12 Aug 2019 20:24:16: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Mon, 12 Aug 2019 20:24:16: start model_add_line... INFO @ Mon, 12 Aug 2019 20:24:16: start X-correlation... INFO @ Mon, 12 Aug 2019 20:24:16: end of X-cor INFO @ Mon, 12 Aug 2019 20:24:16: #2 finished! INFO @ Mon, 12 Aug 2019 20:24:16: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 20:24:16: #2 alternative fragment length(s) may be 1,31,562 bps INFO @ Mon, 12 Aug 2019 20:24:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.05_model.r WARNING @ Mon, 12 Aug 2019 20:24:16: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:24:16: #2 You may need to consider one of the other alternative d(s): 1,31,562 WARNING @ Mon, 12 Aug 2019 20:24:16: #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 20:24:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:24:17: #2 number of paired peaks: 225 WARNING @ Mon, 12 Aug 2019 20:24:17: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Mon, 12 Aug 2019 20:24:17: start model_add_line... INFO @ Mon, 12 Aug 2019 20:24:17: start X-correlation... INFO @ Mon, 12 Aug 2019 20:24:17: end of X-cor INFO @ Mon, 12 Aug 2019 20:24:17: #2 finished! INFO @ Mon, 12 Aug 2019 20:24:17: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 20:24:17: #2 alternative fragment length(s) may be 1,31,562 bps INFO @ Mon, 12 Aug 2019 20:24:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.20_model.r WARNING @ Mon, 12 Aug 2019 20:24:17: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:24:17: #2 You may need to consider one of the other alternative d(s): 1,31,562 WARNING @ Mon, 12 Aug 2019 20:24:17: #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 20:24:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:24:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:24:17: #2 number of paired peaks: 225 WARNING @ Mon, 12 Aug 2019 20:24:17: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Mon, 12 Aug 2019 20:24:17: start model_add_line... INFO @ Mon, 12 Aug 2019 20:24:17: start X-correlation... INFO @ Mon, 12 Aug 2019 20:24:17: end of X-cor INFO @ Mon, 12 Aug 2019 20:24:17: #2 finished! INFO @ Mon, 12 Aug 2019 20:24:17: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 20:24:17: #2 alternative fragment length(s) may be 1,31,562 bps INFO @ Mon, 12 Aug 2019 20:24:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.10_model.r WARNING @ Mon, 12 Aug 2019 20:24:17: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:24:17: #2 You may need to consider one of the other alternative d(s): 1,31,562 WARNING @ Mon, 12 Aug 2019 20:24:17: #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 20:24:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:24:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:24:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:24:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:24:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:25:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.05_summits.bed INFO @ Mon, 12 Aug 2019 20:25:15: Done! INFO @ Mon, 12 Aug 2019 20:25:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.20_summits.bed INFO @ Mon, 12 Aug 2019 20:25:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 millis pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:25:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:25:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:25:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529219/SRX529219.10_summits.bed INFO @ Mon, 12 Aug 2019 20:25:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。