Job ID = 2003701 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 92,891,204 reads read : 185,782,408 reads written : 92,891,204 reads 0-length : 92,891,204 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:43:16 92891204 reads; of these: 92891204 (100.00%) were unpaired; of these: 4205288 (4.53%) aligned 0 times 68061083 (73.27%) aligned exactly 1 time 20624833 (22.20%) aligned >1 times 95.47% overall alignment rate Time searching: 01:43:20 Overall time: 01:43:20 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 40 files... [bam_rmdupse_core] 55935768 / 88685916 = 0.6307 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 16:25:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.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 16:25:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:25:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:25:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.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 16:25:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:25:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.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 16:25:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:25:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:25:24: 1000000 INFO @ Fri, 05 Jul 2019 16:25:25: 1000000 INFO @ Fri, 05 Jul 2019 16:25:26: 1000000 INFO @ Fri, 05 Jul 2019 16:25:32: 2000000 INFO @ Fri, 05 Jul 2019 16:25:32: 2000000 INFO @ Fri, 05 Jul 2019 16:25:35: 2000000 INFO @ Fri, 05 Jul 2019 16:25:39: 3000000 INFO @ Fri, 05 Jul 2019 16:25:40: 3000000 INFO @ Fri, 05 Jul 2019 16:25:45: 3000000 INFO @ Fri, 05 Jul 2019 16:25:47: 4000000 INFO @ Fri, 05 Jul 2019 16:25:48: 4000000 INFO @ Fri, 05 Jul 2019 16:25:55: 5000000 INFO @ Fri, 05 Jul 2019 16:25:55: 4000000 INFO @ Fri, 05 Jul 2019 16:25:55: 5000000 INFO @ Fri, 05 Jul 2019 16:26:02: 6000000 INFO @ Fri, 05 Jul 2019 16:26:03: 6000000 INFO @ Fri, 05 Jul 2019 16:26:05: 5000000 INFO @ Fri, 05 Jul 2019 16:26:10: 7000000 INFO @ Fri, 05 Jul 2019 16:26:10: 7000000 INFO @ Fri, 05 Jul 2019 16:26:14: 6000000 INFO @ Fri, 05 Jul 2019 16:26:17: 8000000 INFO @ Fri, 05 Jul 2019 16:26:18: 8000000 INFO @ Fri, 05 Jul 2019 16:26:24: 7000000 INFO @ Fri, 05 Jul 2019 16:26:25: 9000000 INFO @ Fri, 05 Jul 2019 16:26:26: 9000000 INFO @ Fri, 05 Jul 2019 16:26:33: 8000000 INFO @ Fri, 05 Jul 2019 16:26:33: 10000000 INFO @ Fri, 05 Jul 2019 16:26:34: 10000000 INFO @ Fri, 05 Jul 2019 16:26:41: 11000000 INFO @ Fri, 05 Jul 2019 16:26:41: 11000000 INFO @ Fri, 05 Jul 2019 16:26:42: 9000000 INFO @ Fri, 05 Jul 2019 16:26:48: 12000000 INFO @ Fri, 05 Jul 2019 16:26:49: 12000000 INFO @ Fri, 05 Jul 2019 16:26:52: 10000000 INFO @ Fri, 05 Jul 2019 16:26:56: 13000000 INFO @ Fri, 05 Jul 2019 16:26:56: 13000000 INFO @ Fri, 05 Jul 2019 16:27:01: 11000000 INFO @ Fri, 05 Jul 2019 16:27:03: 14000000 INFO @ Fri, 05 Jul 2019 16:27:04: 14000000 INFO @ Fri, 05 Jul 2019 16:27:11: 12000000 INFO @ Fri, 05 Jul 2019 16:27:11: 15000000 INFO @ Fri, 05 Jul 2019 16:27:12: 15000000 INFO @ Fri, 05 Jul 2019 16:27:19: 16000000 INFO @ Fri, 05 Jul 2019 16:27:19: 16000000 INFO @ Fri, 05 Jul 2019 16:27:20: 13000000 INFO @ Fri, 05 Jul 2019 16:27:27: 17000000 INFO @ Fri, 05 Jul 2019 16:27:27: 17000000 INFO @ Fri, 05 Jul 2019 16:27:30: 14000000 INFO @ Fri, 05 Jul 2019 16:27:34: 18000000 INFO @ Fri, 05 Jul 2019 16:27:35: 18000000 INFO @ Fri, 05 Jul 2019 16:27:39: 15000000 INFO @ Fri, 05 Jul 2019 16:27:42: 19000000 INFO @ Fri, 05 Jul 2019 16:27:43: 19000000 INFO @ Fri, 05 Jul 2019 16:27:49: 16000000 INFO @ Fri, 05 Jul 2019 16:27:50: 20000000 INFO @ Fri, 05 Jul 2019 16:27:50: 20000000 INFO @ Fri, 05 Jul 2019 16:27:57: 21000000 INFO @ Fri, 05 Jul 2019 16:27:58: 21000000 INFO @ Fri, 05 Jul 2019 16:27:59: 17000000 INFO @ Fri, 05 Jul 2019 16:28:04: 22000000 INFO @ Fri, 05 Jul 2019 16:28:05: 22000000 INFO @ Fri, 05 Jul 2019 16:28:08: 18000000 INFO @ Fri, 05 Jul 2019 16:28:12: 23000000 INFO @ Fri, 05 Jul 2019 16:28:12: 23000000 INFO @ Fri, 05 Jul 2019 16:28:17: 19000000 INFO @ Fri, 05 Jul 2019 16:28:19: 24000000 INFO @ Fri, 05 Jul 2019 16:28:20: 24000000 INFO @ Fri, 05 Jul 2019 16:28:27: 25000000 INFO @ Fri, 05 Jul 2019 16:28:27: 20000000 INFO @ Fri, 05 Jul 2019 16:28:27: 25000000 INFO @ Fri, 05 Jul 2019 16:28:34: 26000000 INFO @ Fri, 05 Jul 2019 16:28:35: 26000000 INFO @ Fri, 05 Jul 2019 16:28:36: 21000000 INFO @ Fri, 05 Jul 2019 16:28:42: 27000000 INFO @ Fri, 05 Jul 2019 16:28:43: 27000000 INFO @ Fri, 05 Jul 2019 16:28:46: 22000000 INFO @ Fri, 05 Jul 2019 16:28:50: 28000000 INFO @ Fri, 05 Jul 2019 16:28:51: 28000000 INFO @ Fri, 05 Jul 2019 16:28:55: 23000000 INFO @ Fri, 05 Jul 2019 16:28:57: 29000000 INFO @ Fri, 05 Jul 2019 16:28:58: 29000000 INFO @ Fri, 05 Jul 2019 16:29:04: 24000000 INFO @ Fri, 05 Jul 2019 16:29:05: 30000000 INFO @ Fri, 05 Jul 2019 16:29:06: 30000000 INFO @ Fri, 05 Jul 2019 16:29:13: 31000000 INFO @ Fri, 05 Jul 2019 16:29:14: 25000000 INFO @ Fri, 05 Jul 2019 16:29:14: 31000000 INFO @ Fri, 05 Jul 2019 16:29:22: 32000000 INFO @ Fri, 05 Jul 2019 16:29:23: 26000000 INFO @ Fri, 05 Jul 2019 16:29:24: 32000000 INFO @ Fri, 05 Jul 2019 16:29:28: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:29:28: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:29:28: #1 total tags in treatment: 32750148 INFO @ Fri, 05 Jul 2019 16:29:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:29:28: #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 16:29:29: #1 tags after filtering in treatment: 32750072 INFO @ Fri, 05 Jul 2019 16:29:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:29:29: #1 finished! INFO @ Fri, 05 Jul 2019 16:29:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:29:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:29:30: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:29:30: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:29:30: #1 total tags in treatment: 32750148 INFO @ Fri, 05 Jul 2019 16:29:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:29:30: #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 16:29:31: #1 tags after filtering in treatment: 32750072 INFO @ Fri, 05 Jul 2019 16:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:29:31: #1 finished! INFO @ Fri, 05 Jul 2019 16:29:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:29:33: 27000000 INFO @ Fri, 05 Jul 2019 16:29:34: #2 number of paired peaks: 22829 INFO @ Fri, 05 Jul 2019 16:29:34: start model_add_line... INFO @ Fri, 05 Jul 2019 16:29:34: start X-correlation... INFO @ Fri, 05 Jul 2019 16:29:34: end of X-cor INFO @ Fri, 05 Jul 2019 16:29:34: #2 finished! INFO @ Fri, 05 Jul 2019 16:29:34: #2 predicted fragment length is 126 bps INFO @ Fri, 05 Jul 2019 16:29:34: #2 alternative fragment length(s) may be 126 bps INFO @ Fri, 05 Jul 2019 16:29:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.10_model.r WARNING @ Fri, 05 Jul 2019 16:29:34: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:29:34: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Fri, 05 Jul 2019 16:29:34: #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 16:29:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:29:36: #2 number of paired peaks: 22829 INFO @ Fri, 05 Jul 2019 16:29:36: start model_add_line... INFO @ Fri, 05 Jul 2019 16:29:36: start X-correlation... INFO @ Fri, 05 Jul 2019 16:29:36: end of X-cor INFO @ Fri, 05 Jul 2019 16:29:36: #2 finished! INFO @ Fri, 05 Jul 2019 16:29:36: #2 predicted fragment length is 126 bps INFO @ Fri, 05 Jul 2019 16:29:36: #2 alternative fragment length(s) may be 126 bps INFO @ Fri, 05 Jul 2019 16:29:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.20_model.r WARNING @ Fri, 05 Jul 2019 16:29:36: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:29:36: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Fri, 05 Jul 2019 16:29:36: #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 16:29:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:29:42: 28000000 INFO @ Fri, 05 Jul 2019 16:29:51: 29000000 INFO @ Fri, 05 Jul 2019 16:30:01: 30000000 INFO @ Fri, 05 Jul 2019 16:30:11: 31000000 INFO @ Fri, 05 Jul 2019 16:30:21: 32000000 INFO @ Fri, 05 Jul 2019 16:30:28: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:30:28: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:30:28: #1 total tags in treatment: 32750148 INFO @ Fri, 05 Jul 2019 16:30:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:30:28: #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 16:30:29: #1 tags after filtering in treatment: 32750072 INFO @ Fri, 05 Jul 2019 16:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:30:29: #1 finished! INFO @ Fri, 05 Jul 2019 16:30:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:30:34: #2 number of paired peaks: 22829 INFO @ Fri, 05 Jul 2019 16:30:34: start model_add_line... INFO @ Fri, 05 Jul 2019 16:30:34: start X-correlation... INFO @ Fri, 05 Jul 2019 16:30:34: end of X-cor INFO @ Fri, 05 Jul 2019 16:30:34: #2 finished! INFO @ Fri, 05 Jul 2019 16:30:34: #2 predicted fragment length is 126 bps INFO @ Fri, 05 Jul 2019 16:30:34: #2 alternative fragment length(s) may be 126 bps INFO @ Fri, 05 Jul 2019 16:30:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.05_model.r WARNING @ Fri, 05 Jul 2019 16:30:39: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:30:39: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Fri, 05 Jul 2019 16:30:39: #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 16:30:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:31:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:31:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:32:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:32:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:32:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.10_summits.bed INFO @ Fri, 05 Jul 2019 16:32:12: Done! pass1 - making usageList (89 chroms): 3 millis pass2 - checking and writing primary data (6401 records, 4 fields): 16 millis INFO @ Fri, 05 Jul 2019 16:32:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:32:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:32:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.20_summits.bed INFO @ Fri, 05 Jul 2019 16:32:15: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (1161 records, 4 fields): 14 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:32:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:33:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:33:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:33:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370840/SRX4370840.05_summits.bed INFO @ Fri, 05 Jul 2019 16:33:19: Done! pass1 - making usageList (141 chroms): 6 millis pass2 - checking and writing primary data (24142 records, 4 fields): 41 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。