Job ID = 2640700 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 44,172,260 reads read : 88,344,520 reads written : 44,172,260 reads 0-length : 44,172,260 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: 00:32:44 44172260 reads; of these: 44172260 (100.00%) were unpaired; of these: 1251419 (2.83%) aligned 0 times 31782819 (71.95%) aligned exactly 1 time 11138022 (25.21%) aligned >1 times 97.17% overall alignment rate Time searching: 00:32:47 Overall time: 00:32:47 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 20 files... [bam_rmdupse_core] 2666611 / 42920841 = 0.0621 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.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 @ Sat, 24 Aug 2019 19:15:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:15:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:15:17: 1000000 INFO @ Sat, 24 Aug 2019 19:15:27: 2000000 INFO @ Sat, 24 Aug 2019 19:15:36: 3000000 INFO @ Sat, 24 Aug 2019 19:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.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 @ Sat, 24 Aug 2019 19:15:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:15:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:15:45: 4000000 INFO @ Sat, 24 Aug 2019 19:15:47: 1000000 INFO @ Sat, 24 Aug 2019 19:15:55: 5000000 INFO @ Sat, 24 Aug 2019 19:15:57: 2000000 INFO @ Sat, 24 Aug 2019 19:16:04: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:16:06: 3000000 INFO @ Sat, 24 Aug 2019 19:16:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.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 @ Sat, 24 Aug 2019 19:16:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:16:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:16:13: 7000000 INFO @ Sat, 24 Aug 2019 19:16:15: 4000000 INFO @ Sat, 24 Aug 2019 19:16:18: 1000000 INFO @ Sat, 24 Aug 2019 19:16:23: 8000000 INFO @ Sat, 24 Aug 2019 19:16:25: 5000000 INFO @ Sat, 24 Aug 2019 19:16:27: 2000000 INFO @ Sat, 24 Aug 2019 19:16:32: 9000000 INFO @ Sat, 24 Aug 2019 19:16:34: 6000000 INFO @ Sat, 24 Aug 2019 19:16:37: 3000000 INFO @ Sat, 24 Aug 2019 19:16:42: 10000000 INFO @ Sat, 24 Aug 2019 19:16:44: 7000000 INFO @ Sat, 24 Aug 2019 19:16:46: 4000000 INFO @ Sat, 24 Aug 2019 19:16:51: 11000000 INFO @ Sat, 24 Aug 2019 19:16:53: 8000000 INFO @ Sat, 24 Aug 2019 19:16:56: 5000000 INFO @ Sat, 24 Aug 2019 19:17:00: 12000000 INFO @ Sat, 24 Aug 2019 19:17:02: 9000000 INFO @ Sat, 24 Aug 2019 19:17:05: 6000000 INFO @ Sat, 24 Aug 2019 19:17:10: 13000000 INFO @ Sat, 24 Aug 2019 19:17:12: 10000000 INFO @ Sat, 24 Aug 2019 19:17:15: 7000000 INFO @ Sat, 24 Aug 2019 19:17:19: 14000000 INFO @ Sat, 24 Aug 2019 19:17:21: 11000000 INFO @ Sat, 24 Aug 2019 19:17:24: 8000000 INFO @ Sat, 24 Aug 2019 19:17:29: 15000000 INFO @ Sat, 24 Aug 2019 19:17:31: 12000000 INFO @ Sat, 24 Aug 2019 19:17:34: 9000000 INFO @ Sat, 24 Aug 2019 19:17:38: 16000000 INFO @ Sat, 24 Aug 2019 19:17:40: 13000000 INFO @ Sat, 24 Aug 2019 19:17:43: 10000000 INFO @ Sat, 24 Aug 2019 19:17:47: 17000000 INFO @ Sat, 24 Aug 2019 19:17:49: 14000000 INFO @ Sat, 24 Aug 2019 19:17:52: 11000000 INFO @ Sat, 24 Aug 2019 19:17:57: 18000000 INFO @ Sat, 24 Aug 2019 19:17:59: 15000000 INFO @ Sat, 24 Aug 2019 19:18:02: 12000000 INFO @ Sat, 24 Aug 2019 19:18:06: 19000000 INFO @ Sat, 24 Aug 2019 19:18:08: 16000000 INFO @ Sat, 24 Aug 2019 19:18:11: 13000000 INFO @ Sat, 24 Aug 2019 19:18:16: 20000000 INFO @ Sat, 24 Aug 2019 19:18:18: 17000000 INFO @ Sat, 24 Aug 2019 19:18:20: 14000000 INFO @ Sat, 24 Aug 2019 19:18:25: 21000000 INFO @ Sat, 24 Aug 2019 19:18:27: 18000000 INFO @ Sat, 24 Aug 2019 19:18:30: 15000000 INFO @ Sat, 24 Aug 2019 19:18:35: 22000000 INFO @ Sat, 24 Aug 2019 19:18:36: 19000000 INFO @ Sat, 24 Aug 2019 19:18:39: 16000000 INFO @ Sat, 24 Aug 2019 19:18:44: 23000000 INFO @ Sat, 24 Aug 2019 19:18:46: 20000000 INFO @ Sat, 24 Aug 2019 19:18:48: 17000000 INFO @ Sat, 24 Aug 2019 19:18:53: 24000000 INFO @ Sat, 24 Aug 2019 19:18:55: 21000000 INFO @ Sat, 24 Aug 2019 19:18:58: 18000000 INFO @ Sat, 24 Aug 2019 19:19:03: 25000000 INFO @ Sat, 24 Aug 2019 19:19:05: 22000000 INFO @ Sat, 24 Aug 2019 19:19:07: 19000000 INFO @ Sat, 24 Aug 2019 19:19:12: 26000000 INFO @ Sat, 24 Aug 2019 19:19:14: 23000000 INFO @ Sat, 24 Aug 2019 19:19:16: 20000000 INFO @ Sat, 24 Aug 2019 19:19:22: 27000000 INFO @ Sat, 24 Aug 2019 19:19:24: 24000000 INFO @ Sat, 24 Aug 2019 19:19:26: 21000000 INFO @ Sat, 24 Aug 2019 19:19:31: 28000000 INFO @ Sat, 24 Aug 2019 19:19:33: 25000000 INFO @ Sat, 24 Aug 2019 19:19:35: 22000000 INFO @ Sat, 24 Aug 2019 19:19:41: 29000000 INFO @ Sat, 24 Aug 2019 19:19:43: 26000000 INFO @ Sat, 24 Aug 2019 19:19:44: 23000000 INFO @ Sat, 24 Aug 2019 19:19:50: 30000000 INFO @ Sat, 24 Aug 2019 19:19:52: 27000000 INFO @ Sat, 24 Aug 2019 19:19:54: 24000000 INFO @ Sat, 24 Aug 2019 19:20:00: 31000000 INFO @ Sat, 24 Aug 2019 19:20:01: 28000000 INFO @ Sat, 24 Aug 2019 19:20:03: 25000000 INFO @ Sat, 24 Aug 2019 19:20:09: 32000000 INFO @ Sat, 24 Aug 2019 19:20:11: 29000000 INFO @ Sat, 24 Aug 2019 19:20:13: 26000000 INFO @ Sat, 24 Aug 2019 19:20:18: 33000000 INFO @ Sat, 24 Aug 2019 19:20:20: 30000000 INFO @ Sat, 24 Aug 2019 19:20:22: 27000000 INFO @ Sat, 24 Aug 2019 19:20:28: 34000000 INFO @ Sat, 24 Aug 2019 19:20:30: 31000000 INFO @ Sat, 24 Aug 2019 19:20:31: 28000000 INFO @ Sat, 24 Aug 2019 19:20:37: 35000000 INFO @ Sat, 24 Aug 2019 19:20:39: 32000000 INFO @ Sat, 24 Aug 2019 19:20:41: 29000000 INFO @ Sat, 24 Aug 2019 19:20:47: 36000000 INFO @ Sat, 24 Aug 2019 19:20:48: 33000000 INFO @ Sat, 24 Aug 2019 19:20:50: 30000000 INFO @ Sat, 24 Aug 2019 19:20:56: 37000000 INFO @ Sat, 24 Aug 2019 19:20:58: 34000000 INFO @ Sat, 24 Aug 2019 19:20:59: 31000000 INFO @ Sat, 24 Aug 2019 19:21:05: 38000000 INFO @ Sat, 24 Aug 2019 19:21:07: 35000000 INFO @ Sat, 24 Aug 2019 19:21:09: 32000000 INFO @ Sat, 24 Aug 2019 19:21:15: 39000000 INFO @ Sat, 24 Aug 2019 19:21:17: 36000000 INFO @ Sat, 24 Aug 2019 19:21:18: 33000000 INFO @ Sat, 24 Aug 2019 19:21:25: 40000000 INFO @ Sat, 24 Aug 2019 19:21:26: 37000000 INFO @ Sat, 24 Aug 2019 19:21:27: 34000000 INFO @ Sat, 24 Aug 2019 19:21:27: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:21:27: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:21:27: #1 total tags in treatment: 40254230 INFO @ Sat, 24 Aug 2019 19:21:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:21:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:21:28: #1 tags after filtering in treatment: 40254134 INFO @ Sat, 24 Aug 2019 19:21:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:21:28: #1 finished! INFO @ Sat, 24 Aug 2019 19:21:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:21:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:21:33: #2 number of paired peaks: 16334 INFO @ Sat, 24 Aug 2019 19:21:33: start model_add_line... INFO @ Sat, 24 Aug 2019 19:21:34: start X-correlation... INFO @ Sat, 24 Aug 2019 19:21:34: end of X-cor INFO @ Sat, 24 Aug 2019 19:21:34: #2 finished! INFO @ Sat, 24 Aug 2019 19:21:34: #2 predicted fragment length is 169 bps INFO @ Sat, 24 Aug 2019 19:21:34: #2 alternative fragment length(s) may be 169 bps INFO @ Sat, 24 Aug 2019 19:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.05_model.r INFO @ Sat, 24 Aug 2019 19:21:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:21:35: 38000000 INFO @ Sat, 24 Aug 2019 19:21:37: 35000000 INFO @ Sat, 24 Aug 2019 19:21:45: 39000000 INFO @ Sat, 24 Aug 2019 19:21:46: 36000000 INFO @ Sat, 24 Aug 2019 19:21:54: 40000000 INFO @ Sat, 24 Aug 2019 19:21:55: 37000000 INFO @ Sat, 24 Aug 2019 19:21:57: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:21:57: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:21:57: #1 total tags in treatment: 40254230 INFO @ Sat, 24 Aug 2019 19:21:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:21:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:21:58: #1 tags after filtering in treatment: 40254134 INFO @ Sat, 24 Aug 2019 19:21:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:21:58: #1 finished! INFO @ Sat, 24 Aug 2019 19:21:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:21:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:03: #2 number of paired peaks: 16334 INFO @ Sat, 24 Aug 2019 19:22:03: start model_add_line... INFO @ Sat, 24 Aug 2019 19:22:03: start X-correlation... INFO @ Sat, 24 Aug 2019 19:22:03: end of X-cor INFO @ Sat, 24 Aug 2019 19:22:03: #2 finished! INFO @ Sat, 24 Aug 2019 19:22:03: #2 predicted fragment length is 169 bps INFO @ Sat, 24 Aug 2019 19:22:03: #2 alternative fragment length(s) may be 169 bps INFO @ Sat, 24 Aug 2019 19:22:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.10_model.r INFO @ Sat, 24 Aug 2019 19:22:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:22:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:22:04: 38000000 INFO @ Sat, 24 Aug 2019 19:22:14: 39000000 INFO @ Sat, 24 Aug 2019 19:22:23: 40000000 INFO @ Sat, 24 Aug 2019 19:22:26: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:22:26: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:22:26: #1 total tags in treatment: 40254230 INFO @ Sat, 24 Aug 2019 19:22:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:22:27: #1 tags after filtering in treatment: 40254134 INFO @ Sat, 24 Aug 2019 19:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:22:27: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:32: #2 number of paired peaks: 16334 INFO @ Sat, 24 Aug 2019 19:22:32: start model_add_line... INFO @ Sat, 24 Aug 2019 19:22:32: start X-correlation... INFO @ Sat, 24 Aug 2019 19:22:32: end of X-cor INFO @ Sat, 24 Aug 2019 19:22:32: #2 finished! INFO @ Sat, 24 Aug 2019 19:22:32: #2 predicted fragment length is 169 bps INFO @ Sat, 24 Aug 2019 19:22:32: #2 alternative fragment length(s) may be 169 bps INFO @ Sat, 24 Aug 2019 19:22:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.20_model.r INFO @ Sat, 24 Aug 2019 19:22:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:22:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:23:41: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:24:11: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:24:39: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:24:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:24:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:24:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.05_summits.bed INFO @ Sat, 24 Aug 2019 19:24:48: Done! pass1 - making usageList (94 chroms): 6 millis pass2 - checking and writing primary data (14039 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:25:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.10_summits.bed INFO @ Sat, 24 Aug 2019 19:25:17: Done! pass1 - making usageList (77 chroms): 5 millis pass2 - checking and writing primary data (9166 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:25:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:25:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:25:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375057/SRX5375057.20_summits.bed INFO @ Sat, 24 Aug 2019 19:25:45: Done! pass1 - making usageList (55 chroms): 3 millis pass2 - checking and writing primary data (5538 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。