Job ID = 4288900 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,765,816 reads read : 63,531,632 reads written : 31,765,816 reads 0-length : 31,765,816 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:29:44 31765816 reads; of these: 31765816 (100.00%) were unpaired; of these: 704093 (2.22%) aligned 0 times 21306728 (67.07%) aligned exactly 1 time 9754995 (30.71%) aligned >1 times 97.78% overall alignment rate Time searching: 00:29:45 Overall time: 00:29:45 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 16 files... [bam_rmdupse_core] 731597 / 31061723 = 0.0236 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:16:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.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 @ Tue, 10 Dec 2019 13:16:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:16:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:16:11: 1000000 INFO @ Tue, 10 Dec 2019 13:16:21: 2000000 INFO @ Tue, 10 Dec 2019 13:16:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.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 @ Tue, 10 Dec 2019 13:16:30: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:16:30: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:16:32: 3000000 INFO @ Tue, 10 Dec 2019 13:16:37: 1000000 INFO @ Tue, 10 Dec 2019 13:16:42: 4000000 INFO @ Tue, 10 Dec 2019 13:16:45: 2000000 INFO @ Tue, 10 Dec 2019 13:16:50: 5000000 INFO @ Tue, 10 Dec 2019 13:16:52: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:16:59: 6000000 INFO @ Tue, 10 Dec 2019 13:17:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.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 @ Tue, 10 Dec 2019 13:17:00: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:17:00: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:17:00: 4000000 INFO @ Tue, 10 Dec 2019 13:17:08: 5000000 INFO @ Tue, 10 Dec 2019 13:17:08: 7000000 INFO @ Tue, 10 Dec 2019 13:17:10: 1000000 INFO @ Tue, 10 Dec 2019 13:17:16: 6000000 INFO @ Tue, 10 Dec 2019 13:17:18: 8000000 INFO @ Tue, 10 Dec 2019 13:17:20: 2000000 INFO @ Tue, 10 Dec 2019 13:17:23: 7000000 INFO @ Tue, 10 Dec 2019 13:17:28: 9000000 INFO @ Tue, 10 Dec 2019 13:17:30: 3000000 INFO @ Tue, 10 Dec 2019 13:17:31: 8000000 INFO @ Tue, 10 Dec 2019 13:17:37: 10000000 INFO @ Tue, 10 Dec 2019 13:17:38: 9000000 INFO @ Tue, 10 Dec 2019 13:17:39: 4000000 INFO @ Tue, 10 Dec 2019 13:17:46: 10000000 INFO @ Tue, 10 Dec 2019 13:17:47: 11000000 INFO @ Tue, 10 Dec 2019 13:17:49: 5000000 INFO @ Tue, 10 Dec 2019 13:17:53: 11000000 INFO @ Tue, 10 Dec 2019 13:17:57: 12000000 INFO @ Tue, 10 Dec 2019 13:17:59: 6000000 INFO @ Tue, 10 Dec 2019 13:18:01: 12000000 INFO @ Tue, 10 Dec 2019 13:18:07: 13000000 INFO @ Tue, 10 Dec 2019 13:18:08: 13000000 INFO @ Tue, 10 Dec 2019 13:18:08: 7000000 INFO @ Tue, 10 Dec 2019 13:18:16: 14000000 INFO @ Tue, 10 Dec 2019 13:18:17: 14000000 INFO @ Tue, 10 Dec 2019 13:18:18: 8000000 INFO @ Tue, 10 Dec 2019 13:18:23: 15000000 INFO @ Tue, 10 Dec 2019 13:18:27: 15000000 INFO @ Tue, 10 Dec 2019 13:18:29: 9000000 INFO @ Tue, 10 Dec 2019 13:18:31: 16000000 INFO @ Tue, 10 Dec 2019 13:18:38: 16000000 INFO @ Tue, 10 Dec 2019 13:18:38: 17000000 INFO @ Tue, 10 Dec 2019 13:18:40: 10000000 INFO @ Tue, 10 Dec 2019 13:18:46: 18000000 INFO @ Tue, 10 Dec 2019 13:18:48: 17000000 INFO @ Tue, 10 Dec 2019 13:18:50: 11000000 INFO @ Tue, 10 Dec 2019 13:18:53: 19000000 INFO @ Tue, 10 Dec 2019 13:18:58: 18000000 INFO @ Tue, 10 Dec 2019 13:19:00: 12000000 INFO @ Tue, 10 Dec 2019 13:19:01: 20000000 INFO @ Tue, 10 Dec 2019 13:19:08: 21000000 INFO @ Tue, 10 Dec 2019 13:19:09: 19000000 INFO @ Tue, 10 Dec 2019 13:19:11: 13000000 INFO @ Tue, 10 Dec 2019 13:19:16: 22000000 INFO @ Tue, 10 Dec 2019 13:19:20: 20000000 INFO @ Tue, 10 Dec 2019 13:19:21: 14000000 INFO @ Tue, 10 Dec 2019 13:19:23: 23000000 INFO @ Tue, 10 Dec 2019 13:19:30: 21000000 INFO @ Tue, 10 Dec 2019 13:19:31: 24000000 INFO @ Tue, 10 Dec 2019 13:19:32: 15000000 INFO @ Tue, 10 Dec 2019 13:19:38: 25000000 INFO @ Tue, 10 Dec 2019 13:19:40: 22000000 INFO @ Tue, 10 Dec 2019 13:19:42: 16000000 INFO @ Tue, 10 Dec 2019 13:19:46: 26000000 INFO @ Tue, 10 Dec 2019 13:19:50: 23000000 INFO @ Tue, 10 Dec 2019 13:19:52: 17000000 INFO @ Tue, 10 Dec 2019 13:19:53: 27000000 INFO @ Tue, 10 Dec 2019 13:20:00: 24000000 INFO @ Tue, 10 Dec 2019 13:20:01: 28000000 INFO @ Tue, 10 Dec 2019 13:20:02: 18000000 INFO @ Tue, 10 Dec 2019 13:20:09: 29000000 INFO @ Tue, 10 Dec 2019 13:20:09: 25000000 INFO @ Tue, 10 Dec 2019 13:20:12: 19000000 INFO @ Tue, 10 Dec 2019 13:20:16: 30000000 INFO @ Tue, 10 Dec 2019 13:20:19: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:20:19: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:20:19: #1 total tags in treatment: 30330126 INFO @ Tue, 10 Dec 2019 13:20:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:20:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:20:19: 26000000 INFO @ Tue, 10 Dec 2019 13:20:20: #1 tags after filtering in treatment: 30330052 INFO @ Tue, 10 Dec 2019 13:20:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:20:20: #1 finished! INFO @ Tue, 10 Dec 2019 13:20:20: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:20:22: 20000000 INFO @ Tue, 10 Dec 2019 13:20:23: #2 number of paired peaks: 6114 INFO @ Tue, 10 Dec 2019 13:20:23: start model_add_line... INFO @ Tue, 10 Dec 2019 13:20:24: start X-correlation... INFO @ Tue, 10 Dec 2019 13:20:24: end of X-cor INFO @ Tue, 10 Dec 2019 13:20:24: #2 finished! INFO @ Tue, 10 Dec 2019 13:20:24: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 13:20:24: #2 alternative fragment length(s) may be 50,229,404 bps INFO @ Tue, 10 Dec 2019 13:20:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.10_model.r WARNING @ Tue, 10 Dec 2019 13:20:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:20:24: #2 You may need to consider one of the other alternative d(s): 50,229,404 WARNING @ Tue, 10 Dec 2019 13:20:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:20:24: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:20:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:20:29: 27000000 INFO @ Tue, 10 Dec 2019 13:20:31: 21000000 INFO @ Tue, 10 Dec 2019 13:20:39: 28000000 INFO @ Tue, 10 Dec 2019 13:20:41: 22000000 INFO @ Tue, 10 Dec 2019 13:20:49: 29000000 INFO @ Tue, 10 Dec 2019 13:20:51: 23000000 INFO @ Tue, 10 Dec 2019 13:20:58: 30000000 INFO @ Tue, 10 Dec 2019 13:21:01: 24000000 INFO @ Tue, 10 Dec 2019 13:21:02: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:21:02: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:21:02: #1 total tags in treatment: 30330126 INFO @ Tue, 10 Dec 2019 13:21:02: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:21:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:21:03: #1 tags after filtering in treatment: 30330052 INFO @ Tue, 10 Dec 2019 13:21:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:21:03: #1 finished! INFO @ Tue, 10 Dec 2019 13:21:03: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:21:06: #2 number of paired peaks: 6114 INFO @ Tue, 10 Dec 2019 13:21:06: start model_add_line... INFO @ Tue, 10 Dec 2019 13:21:07: start X-correlation... INFO @ Tue, 10 Dec 2019 13:21:07: end of X-cor INFO @ Tue, 10 Dec 2019 13:21:07: #2 finished! INFO @ Tue, 10 Dec 2019 13:21:07: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 13:21:07: #2 alternative fragment length(s) may be 50,229,404 bps INFO @ Tue, 10 Dec 2019 13:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.05_model.r WARNING @ Tue, 10 Dec 2019 13:21:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:21:07: #2 You may need to consider one of the other alternative d(s): 50,229,404 WARNING @ Tue, 10 Dec 2019 13:21:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:21:07: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:21:12: 25000000 INFO @ Tue, 10 Dec 2019 13:21:22: 26000000 INFO @ Tue, 10 Dec 2019 13:21:32: 27000000 INFO @ Tue, 10 Dec 2019 13:21:43: 28000000 INFO @ Tue, 10 Dec 2019 13:21:53: 29000000 INFO @ Tue, 10 Dec 2019 13:21:59: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:22:03: 30000000 INFO @ Tue, 10 Dec 2019 13:22:06: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 13:22:06: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 13:22:06: #1 total tags in treatment: 30330126 INFO @ Tue, 10 Dec 2019 13:22:06: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:22:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:22:07: #1 tags after filtering in treatment: 30330052 INFO @ Tue, 10 Dec 2019 13:22:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:22:07: #1 finished! INFO @ Tue, 10 Dec 2019 13:22:07: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:22:10: #2 number of paired peaks: 6114 INFO @ Tue, 10 Dec 2019 13:22:10: start model_add_line... INFO @ Tue, 10 Dec 2019 13:22:10: start X-correlation... INFO @ Tue, 10 Dec 2019 13:22:10: end of X-cor INFO @ Tue, 10 Dec 2019 13:22:10: #2 finished! INFO @ Tue, 10 Dec 2019 13:22:10: #2 predicted fragment length is 50 bps INFO @ Tue, 10 Dec 2019 13:22:10: #2 alternative fragment length(s) may be 50,229,404 bps INFO @ Tue, 10 Dec 2019 13:22:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.20_model.r WARNING @ Tue, 10 Dec 2019 13:22:10: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:22:10: #2 You may need to consider one of the other alternative d(s): 50,229,404 WARNING @ Tue, 10 Dec 2019 13:22:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:22:10: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:22:44: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:22:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:22:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:22:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.10_summits.bed INFO @ Tue, 10 Dec 2019 13:22:48: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (1072 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.05_summits.bed INFO @ Tue, 10 Dec 2019 13:23:36: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (1894 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:23:47: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4779825/SRX4779825.20_summits.bed INFO @ Tue, 10 Dec 2019 13:24:38: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (534 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。