Job ID = 2003726 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,452,859 reads read : 58,905,718 reads written : 29,452,859 reads 0-length : 29,452,859 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:29 29452859 reads; of these: 29452859 (100.00%) were unpaired; of these: 2483335 (8.43%) aligned 0 times 17382148 (59.02%) aligned exactly 1 time 9587376 (32.55%) aligned >1 times 91.57% overall alignment rate Time searching: 00:26:30 Overall time: 00:26:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5559263 / 26969524 = 0.2061 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 @ Fri, 05 Jul 2019 14:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 14:38:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:38:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:38:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 14:38:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:38:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:38:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 14:38:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:38:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:38:37: 1000000 INFO @ Fri, 05 Jul 2019 14:38:38: 1000000 INFO @ Fri, 05 Jul 2019 14:38:39: 1000000 INFO @ Fri, 05 Jul 2019 14:38:44: 2000000 INFO @ Fri, 05 Jul 2019 14:38:45: 2000000 INFO @ Fri, 05 Jul 2019 14:38:46: 2000000 INFO @ Fri, 05 Jul 2019 14:38:51: 3000000 INFO @ Fri, 05 Jul 2019 14:38:52: 3000000 INFO @ Fri, 05 Jul 2019 14:38:54: 3000000 INFO @ Fri, 05 Jul 2019 14:38:58: 4000000 INFO @ Fri, 05 Jul 2019 14:39:00: 4000000 INFO @ Fri, 05 Jul 2019 14:39:01: 4000000 INFO @ Fri, 05 Jul 2019 14:39:06: 5000000 INFO @ Fri, 05 Jul 2019 14:39:07: 5000000 INFO @ Fri, 05 Jul 2019 14:39:09: 5000000 INFO @ Fri, 05 Jul 2019 14:39:13: 6000000 INFO @ Fri, 05 Jul 2019 14:39:14: 6000000 INFO @ Fri, 05 Jul 2019 14:39:16: 6000000 INFO @ Fri, 05 Jul 2019 14:39:20: 7000000 INFO @ Fri, 05 Jul 2019 14:39:22: 7000000 INFO @ Fri, 05 Jul 2019 14:39:23: 7000000 INFO @ Fri, 05 Jul 2019 14:39:28: 8000000 INFO @ Fri, 05 Jul 2019 14:39:29: 8000000 INFO @ Fri, 05 Jul 2019 14:39:31: 8000000 INFO @ Fri, 05 Jul 2019 14:39:35: 9000000 INFO @ Fri, 05 Jul 2019 14:39:36: 9000000 INFO @ Fri, 05 Jul 2019 14:39:38: 9000000 INFO @ Fri, 05 Jul 2019 14:39:42: 10000000 INFO @ Fri, 05 Jul 2019 14:39:44: 10000000 INFO @ Fri, 05 Jul 2019 14:39:46: 10000000 INFO @ Fri, 05 Jul 2019 14:39:50: 11000000 INFO @ Fri, 05 Jul 2019 14:39:51: 11000000 INFO @ Fri, 05 Jul 2019 14:39:53: 11000000 INFO @ Fri, 05 Jul 2019 14:39:57: 12000000 INFO @ Fri, 05 Jul 2019 14:39:58: 12000000 INFO @ Fri, 05 Jul 2019 14:40:00: 12000000 INFO @ Fri, 05 Jul 2019 14:40:04: 13000000 INFO @ Fri, 05 Jul 2019 14:40:05: 13000000 INFO @ Fri, 05 Jul 2019 14:40:07: 13000000 INFO @ Fri, 05 Jul 2019 14:40:12: 14000000 INFO @ Fri, 05 Jul 2019 14:40:13: 14000000 INFO @ Fri, 05 Jul 2019 14:40:15: 14000000 INFO @ Fri, 05 Jul 2019 14:40:20: 15000000 INFO @ Fri, 05 Jul 2019 14:40:20: 15000000 INFO @ Fri, 05 Jul 2019 14:40:22: 15000000 INFO @ Fri, 05 Jul 2019 14:40:28: 16000000 INFO @ Fri, 05 Jul 2019 14:40:28: 16000000 INFO @ Fri, 05 Jul 2019 14:40:29: 16000000 INFO @ Fri, 05 Jul 2019 14:40:36: 17000000 INFO @ Fri, 05 Jul 2019 14:40:36: 17000000 INFO @ Fri, 05 Jul 2019 14:40:37: 17000000 INFO @ Fri, 05 Jul 2019 14:40:43: 18000000 INFO @ Fri, 05 Jul 2019 14:40:44: 18000000 INFO @ Fri, 05 Jul 2019 14:40:45: 18000000 INFO @ Fri, 05 Jul 2019 14:40:50: 19000000 INFO @ Fri, 05 Jul 2019 14:40:52: 19000000 INFO @ Fri, 05 Jul 2019 14:40:53: 19000000 INFO @ Fri, 05 Jul 2019 14:40:57: 20000000 INFO @ Fri, 05 Jul 2019 14:41:00: 20000000 INFO @ Fri, 05 Jul 2019 14:41:01: 20000000 INFO @ Fri, 05 Jul 2019 14:41:04: 21000000 INFO @ Fri, 05 Jul 2019 14:41:07: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:41:07: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:41:07: #1 total tags in treatment: 21410261 INFO @ Fri, 05 Jul 2019 14:41:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:41:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 14:41:08: 21000000 INFO @ Fri, 05 Jul 2019 14:41:08: #1 tags after filtering in treatment: 21410149 INFO @ Fri, 05 Jul 2019 14:41:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:41:08: #1 finished! INFO @ Fri, 05 Jul 2019 14:41:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:41:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:41:09: 21000000 INFO @ Fri, 05 Jul 2019 14:41:11: #2 number of paired peaks: 7246 INFO @ Fri, 05 Jul 2019 14:41:11: start model_add_line... INFO @ Fri, 05 Jul 2019 14:41:11: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:41:11: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:41:11: #1 total tags in treatment: 21410261 INFO @ Fri, 05 Jul 2019 14:41:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:41:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 14:41:11: start X-correlation... INFO @ Fri, 05 Jul 2019 14:41:11: end of X-cor INFO @ Fri, 05 Jul 2019 14:41:11: #2 finished! INFO @ Fri, 05 Jul 2019 14:41:11: #2 predicted fragment length is 49 bps INFO @ Fri, 05 Jul 2019 14:41:11: #2 alternative fragment length(s) may be 49,224,413 bps INFO @ Fri, 05 Jul 2019 14:41:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.05_model.r WARNING @ Fri, 05 Jul 2019 14:41:11: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 14:41:11: #2 You may need to consider one of the other alternative d(s): 49,224,413 WARNING @ Fri, 05 Jul 2019 14:41:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 14:41:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:41:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:41:12: #1 tags after filtering in treatment: 21410149 INFO @ Fri, 05 Jul 2019 14:41:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:41:12: #1 finished! INFO @ Fri, 05 Jul 2019 14:41:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:41:12: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:41:12: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:41:12: #1 total tags in treatment: 21410261 INFO @ Fri, 05 Jul 2019 14:41:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:41:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 14:41:12: #1 tags after filtering in treatment: 21410149 INFO @ Fri, 05 Jul 2019 14:41:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:41:12: #1 finished! INFO @ Fri, 05 Jul 2019 14:41:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:41:14: #2 number of paired peaks: 7246 INFO @ Fri, 05 Jul 2019 14:41:14: start model_add_line... INFO @ Fri, 05 Jul 2019 14:41:14: start X-correlation... INFO @ Fri, 05 Jul 2019 14:41:14: end of X-cor INFO @ Fri, 05 Jul 2019 14:41:14: #2 finished! INFO @ Fri, 05 Jul 2019 14:41:14: #2 predicted fragment length is 49 bps INFO @ Fri, 05 Jul 2019 14:41:14: #2 alternative fragment length(s) may be 49,224,413 bps INFO @ Fri, 05 Jul 2019 14:41:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.10_model.r WARNING @ Fri, 05 Jul 2019 14:41:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 14:41:14: #2 You may need to consider one of the other alternative d(s): 49,224,413 WARNING @ Fri, 05 Jul 2019 14:41:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 14:41:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:41:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:41:15: #2 number of paired peaks: 7246 INFO @ Fri, 05 Jul 2019 14:41:15: start model_add_line... INFO @ Fri, 05 Jul 2019 14:41:15: start X-correlation... INFO @ Fri, 05 Jul 2019 14:41:15: end of X-cor INFO @ Fri, 05 Jul 2019 14:41:15: #2 finished! INFO @ Fri, 05 Jul 2019 14:41:15: #2 predicted fragment length is 49 bps INFO @ Fri, 05 Jul 2019 14:41:15: #2 alternative fragment length(s) may be 49,224,413 bps INFO @ Fri, 05 Jul 2019 14:41:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.20_model.r WARNING @ Fri, 05 Jul 2019 14:41:15: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 14:41:15: #2 You may need to consider one of the other alternative d(s): 49,224,413 WARNING @ Fri, 05 Jul 2019 14:41:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 14:41:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:41:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:42:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:42:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:42:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.05_summits.bed INFO @ Fri, 05 Jul 2019 14:42:51: Done! pass1 - making usageList (69 chroms): 2 millis pass2 - checking and writing primary data (2004 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.10_summits.bed INFO @ Fri, 05 Jul 2019 14:42:54: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1275 records, 4 fields): 10 millis INFO @ Fri, 05 Jul 2019 14:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333726/SRX5333726.20_summits.bed INFO @ Fri, 05 Jul 2019 14:42:55: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (707 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。