Job ID = 2002139 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 116,783,140 reads read : 116,783,140 reads written : 116,783,140 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:58:57 116783140 reads; of these: 116783140 (100.00%) were unpaired; of these: 2101879 (1.80%) aligned 0 times 103317884 (88.47%) aligned exactly 1 time 11363377 (9.73%) aligned >1 times 98.20% overall alignment rate Time searching: 00:59:01 Overall time: 00:59:01 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 48 files... [bam_rmdupse_core] 76924366 / 114681261 = 0.6708 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 12:44:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.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 12:44:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:44:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.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 12:44:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:44:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:44:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.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 12:44:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:44:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:45:04: 1000000 INFO @ Fri, 05 Jul 2019 12:45:06: 1000000 INFO @ Fri, 05 Jul 2019 12:45:06: 1000000 INFO @ Fri, 05 Jul 2019 12:45:12: 2000000 INFO @ Fri, 05 Jul 2019 12:45:15: 2000000 INFO @ Fri, 05 Jul 2019 12:45:16: 2000000 INFO @ Fri, 05 Jul 2019 12:45:20: 3000000 INFO @ Fri, 05 Jul 2019 12:45:22: 3000000 INFO @ Fri, 05 Jul 2019 12:45:25: 3000000 INFO @ Fri, 05 Jul 2019 12:45:28: 4000000 INFO @ Fri, 05 Jul 2019 12:45:30: 4000000 INFO @ Fri, 05 Jul 2019 12:45:35: 4000000 INFO @ Fri, 05 Jul 2019 12:45:36: 5000000 INFO @ Fri, 05 Jul 2019 12:45:38: 5000000 INFO @ Fri, 05 Jul 2019 12:45:43: 6000000 INFO @ Fri, 05 Jul 2019 12:45:44: 5000000 INFO @ Fri, 05 Jul 2019 12:45:45: 6000000 INFO @ Fri, 05 Jul 2019 12:45:51: 7000000 INFO @ Fri, 05 Jul 2019 12:45:53: 7000000 INFO @ Fri, 05 Jul 2019 12:45:53: 6000000 INFO @ Fri, 05 Jul 2019 12:45:59: 8000000 INFO @ Fri, 05 Jul 2019 12:46:01: 8000000 INFO @ Fri, 05 Jul 2019 12:46:02: 7000000 INFO @ Fri, 05 Jul 2019 12:46:07: 9000000 INFO @ Fri, 05 Jul 2019 12:46:09: 9000000 INFO @ Fri, 05 Jul 2019 12:46:12: 8000000 INFO @ Fri, 05 Jul 2019 12:46:14: 10000000 INFO @ Fri, 05 Jul 2019 12:46:16: 10000000 INFO @ Fri, 05 Jul 2019 12:46:21: 9000000 INFO @ Fri, 05 Jul 2019 12:46:22: 11000000 INFO @ Fri, 05 Jul 2019 12:46:24: 11000000 INFO @ Fri, 05 Jul 2019 12:46:30: 12000000 INFO @ Fri, 05 Jul 2019 12:46:30: 10000000 INFO @ Fri, 05 Jul 2019 12:46:32: 12000000 INFO @ Fri, 05 Jul 2019 12:46:38: 13000000 INFO @ Fri, 05 Jul 2019 12:46:40: 11000000 INFO @ Fri, 05 Jul 2019 12:46:40: 13000000 INFO @ Fri, 05 Jul 2019 12:46:46: 14000000 INFO @ Fri, 05 Jul 2019 12:46:48: 14000000 INFO @ Fri, 05 Jul 2019 12:46:49: 12000000 INFO @ Fri, 05 Jul 2019 12:46:54: 15000000 INFO @ Fri, 05 Jul 2019 12:46:56: 15000000 INFO @ Fri, 05 Jul 2019 12:46:58: 13000000 INFO @ Fri, 05 Jul 2019 12:47:01: 16000000 INFO @ Fri, 05 Jul 2019 12:47:03: 16000000 INFO @ Fri, 05 Jul 2019 12:47:07: 14000000 INFO @ Fri, 05 Jul 2019 12:47:09: 17000000 INFO @ Fri, 05 Jul 2019 12:47:11: 17000000 INFO @ Fri, 05 Jul 2019 12:47:16: 15000000 INFO @ Fri, 05 Jul 2019 12:47:17: 18000000 INFO @ Fri, 05 Jul 2019 12:47:19: 18000000 INFO @ Fri, 05 Jul 2019 12:47:24: 19000000 INFO @ Fri, 05 Jul 2019 12:47:26: 16000000 INFO @ Fri, 05 Jul 2019 12:47:27: 19000000 INFO @ Fri, 05 Jul 2019 12:47:32: 20000000 INFO @ Fri, 05 Jul 2019 12:47:34: 20000000 INFO @ Fri, 05 Jul 2019 12:47:34: 17000000 INFO @ Fri, 05 Jul 2019 12:47:40: 21000000 INFO @ Fri, 05 Jul 2019 12:47:42: 21000000 INFO @ Fri, 05 Jul 2019 12:47:43: 18000000 INFO @ Fri, 05 Jul 2019 12:47:48: 22000000 INFO @ Fri, 05 Jul 2019 12:47:50: 22000000 INFO @ Fri, 05 Jul 2019 12:47:53: 19000000 INFO @ Fri, 05 Jul 2019 12:47:56: 23000000 INFO @ Fri, 05 Jul 2019 12:47:58: 23000000 INFO @ Fri, 05 Jul 2019 12:48:02: 20000000 INFO @ Fri, 05 Jul 2019 12:48:04: 24000000 INFO @ Fri, 05 Jul 2019 12:48:05: 24000000 INFO @ Fri, 05 Jul 2019 12:48:11: 21000000 INFO @ Fri, 05 Jul 2019 12:48:12: 25000000 INFO @ Fri, 05 Jul 2019 12:48:13: 25000000 INFO @ Fri, 05 Jul 2019 12:48:20: 26000000 INFO @ Fri, 05 Jul 2019 12:48:20: 22000000 INFO @ Fri, 05 Jul 2019 12:48:21: 26000000 INFO @ Fri, 05 Jul 2019 12:48:27: 27000000 INFO @ Fri, 05 Jul 2019 12:48:30: 27000000 INFO @ Fri, 05 Jul 2019 12:48:30: 23000000 INFO @ Fri, 05 Jul 2019 12:48:35: 28000000 INFO @ Fri, 05 Jul 2019 12:48:37: 28000000 INFO @ Fri, 05 Jul 2019 12:48:39: 24000000 INFO @ Fri, 05 Jul 2019 12:48:43: 29000000 INFO @ Fri, 05 Jul 2019 12:48:45: 29000000 INFO @ Fri, 05 Jul 2019 12:48:48: 25000000 INFO @ Fri, 05 Jul 2019 12:48:51: 30000000 INFO @ Fri, 05 Jul 2019 12:48:52: 30000000 INFO @ Fri, 05 Jul 2019 12:48:57: 26000000 INFO @ Fri, 05 Jul 2019 12:48:59: 31000000 INFO @ Fri, 05 Jul 2019 12:49:00: 31000000 INFO @ Fri, 05 Jul 2019 12:49:06: 27000000 INFO @ Fri, 05 Jul 2019 12:49:07: 32000000 INFO @ Fri, 05 Jul 2019 12:49:08: 32000000 INFO @ Fri, 05 Jul 2019 12:49:15: 33000000 INFO @ Fri, 05 Jul 2019 12:49:15: 33000000 INFO @ Fri, 05 Jul 2019 12:49:16: 28000000 INFO @ Fri, 05 Jul 2019 12:49:22: 34000000 INFO @ Fri, 05 Jul 2019 12:49:23: 34000000 INFO @ Fri, 05 Jul 2019 12:49:25: 29000000 INFO @ Fri, 05 Jul 2019 12:49:30: 35000000 INFO @ Fri, 05 Jul 2019 12:49:30: 35000000 INFO @ Fri, 05 Jul 2019 12:49:34: 30000000 INFO @ Fri, 05 Jul 2019 12:49:38: 36000000 INFO @ Fri, 05 Jul 2019 12:49:38: 36000000 INFO @ Fri, 05 Jul 2019 12:49:43: 31000000 INFO @ Fri, 05 Jul 2019 12:49:45: 37000000 INFO @ Fri, 05 Jul 2019 12:49:46: 37000000 INFO @ Fri, 05 Jul 2019 12:49:51: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:49:51: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:49:51: #1 total tags in treatment: 37756895 INFO @ Fri, 05 Jul 2019 12:49:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:49:51: #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 12:49:52: #1 tags after filtering in treatment: 37756685 INFO @ Fri, 05 Jul 2019 12:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:49:52: #1 finished! INFO @ Fri, 05 Jul 2019 12:49:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:49:53: 32000000 INFO @ Fri, 05 Jul 2019 12:49:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:49:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:49:53: #1 total tags in treatment: 37756895 INFO @ Fri, 05 Jul 2019 12:49:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:49:53: #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 12:49:54: #1 tags after filtering in treatment: 37756685 INFO @ Fri, 05 Jul 2019 12:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:49:54: #1 finished! INFO @ Fri, 05 Jul 2019 12:49:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:50:01: #2 number of paired peaks: 66687 INFO @ Fri, 05 Jul 2019 12:50:01: start model_add_line... INFO @ Fri, 05 Jul 2019 12:50:02: 33000000 INFO @ Fri, 05 Jul 2019 12:50:02: start X-correlation... INFO @ Fri, 05 Jul 2019 12:50:02: end of X-cor INFO @ Fri, 05 Jul 2019 12:50:02: #2 finished! INFO @ Fri, 05 Jul 2019 12:50:02: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 12:50:02: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 12:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.10_model.r INFO @ Fri, 05 Jul 2019 12:50:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:50:03: #2 number of paired peaks: 66687 INFO @ Fri, 05 Jul 2019 12:50:03: start model_add_line... INFO @ Fri, 05 Jul 2019 12:50:04: start X-correlation... INFO @ Fri, 05 Jul 2019 12:50:04: end of X-cor INFO @ Fri, 05 Jul 2019 12:50:04: #2 finished! INFO @ Fri, 05 Jul 2019 12:50:04: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 12:50:04: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 12:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.05_model.r INFO @ Fri, 05 Jul 2019 12:50:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:50:11: 34000000 INFO @ Fri, 05 Jul 2019 12:50:20: 35000000 INFO @ Fri, 05 Jul 2019 12:50:29: 36000000 INFO @ Fri, 05 Jul 2019 12:50:39: 37000000 INFO @ Fri, 05 Jul 2019 12:50:46: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:50:46: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:50:46: #1 total tags in treatment: 37756895 INFO @ Fri, 05 Jul 2019 12:50:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:50:46: #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 12:50:47: #1 tags after filtering in treatment: 37756685 INFO @ Fri, 05 Jul 2019 12:50:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:50:47: #1 finished! INFO @ Fri, 05 Jul 2019 12:50:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:50:56: #2 number of paired peaks: 66687 INFO @ Fri, 05 Jul 2019 12:50:56: start model_add_line... INFO @ Fri, 05 Jul 2019 12:50:57: start X-correlation... INFO @ Fri, 05 Jul 2019 12:50:57: end of X-cor INFO @ Fri, 05 Jul 2019 12:50:57: #2 finished! INFO @ Fri, 05 Jul 2019 12:50:57: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 12:50:57: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 12:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.20_model.r INFO @ Fri, 05 Jul 2019 12:50:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:50:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:52:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:52:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:52:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.10_summits.bed INFO @ Fri, 05 Jul 2019 12:53:10: Done! INFO @ Fri, 05 Jul 2019 12:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.05_peaks.xls pass1 - making usageList (144 chroms): 12 millis pass2 - checking and writing primary data (49388 records, 4 fields): 75 millis INFO @ Fri, 05 Jul 2019 12:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.05_summits.bed INFO @ Fri, 05 Jul 2019 12:53:12: Done! pass1 - making usageList (164 chroms): 14 millis pass2 - checking and writing primary data (59695 records, 4 fields): 90 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:54:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:54:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:54:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102039/ERX102039.20_summits.bed INFO @ Fri, 05 Jul 2019 12:54:07: Done! pass1 - making usageList (124 chroms): 9 millis pass2 - checking and writing primary data (38289 records, 4 fields): 59 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。