Job ID = 2001148 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,432,989 reads read : 33,432,989 reads written : 33,432,989 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: 00:00:00 Multiseed full-index search: 00:15:00 33432989 reads; of these: 33432989 (100.00%) were unpaired; of these: 749810 (2.24%) aligned 0 times 25180822 (75.32%) aligned exactly 1 time 7502357 (22.44%) aligned >1 times 97.76% overall alignment rate Time searching: 00:15:03 Overall time: 00:15:03 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] 2844296 / 32683179 = 0.0870 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 04:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.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 04:20:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:20:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:20:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.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 04:20:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:20:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.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 04:20:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:20:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:20:35: 1000000 INFO @ Fri, 05 Jul 2019 04:20:36: 1000000 INFO @ Fri, 05 Jul 2019 04:20:36: 1000000 INFO @ Fri, 05 Jul 2019 04:20:44: 2000000 INFO @ Fri, 05 Jul 2019 04:20:45: 2000000 INFO @ Fri, 05 Jul 2019 04:20:45: 2000000 INFO @ Fri, 05 Jul 2019 04:20:51: 3000000 INFO @ Fri, 05 Jul 2019 04:20:53: 3000000 INFO @ Fri, 05 Jul 2019 04:20:54: 3000000 INFO @ Fri, 05 Jul 2019 04:20:59: 4000000 INFO @ Fri, 05 Jul 2019 04:21:01: 4000000 INFO @ Fri, 05 Jul 2019 04:21:03: 4000000 INFO @ Fri, 05 Jul 2019 04:21:07: 5000000 INFO @ Fri, 05 Jul 2019 04:21:09: 5000000 INFO @ Fri, 05 Jul 2019 04:21:12: 5000000 INFO @ Fri, 05 Jul 2019 04:21:14: 6000000 INFO @ Fri, 05 Jul 2019 04:21:17: 6000000 INFO @ Fri, 05 Jul 2019 04:21:21: 6000000 INFO @ Fri, 05 Jul 2019 04:21:22: 7000000 INFO @ Fri, 05 Jul 2019 04:21:25: 7000000 INFO @ Fri, 05 Jul 2019 04:21:30: 7000000 INFO @ Fri, 05 Jul 2019 04:21:30: 8000000 INFO @ Fri, 05 Jul 2019 04:21:33: 8000000 INFO @ Fri, 05 Jul 2019 04:21:38: 9000000 INFO @ Fri, 05 Jul 2019 04:21:39: 8000000 INFO @ Fri, 05 Jul 2019 04:21:41: 9000000 INFO @ Fri, 05 Jul 2019 04:21:47: 10000000 INFO @ Fri, 05 Jul 2019 04:21:48: 9000000 INFO @ Fri, 05 Jul 2019 04:21:49: 10000000 INFO @ Fri, 05 Jul 2019 04:21:54: 11000000 INFO @ Fri, 05 Jul 2019 04:21:57: 10000000 INFO @ Fri, 05 Jul 2019 04:21:57: 11000000 INFO @ Fri, 05 Jul 2019 04:22:02: 12000000 INFO @ Fri, 05 Jul 2019 04:22:05: 12000000 INFO @ Fri, 05 Jul 2019 04:22:06: 11000000 INFO @ Fri, 05 Jul 2019 04:22:09: 13000000 INFO @ Fri, 05 Jul 2019 04:22:13: 13000000 INFO @ Fri, 05 Jul 2019 04:22:15: 12000000 INFO @ Fri, 05 Jul 2019 04:22:17: 14000000 INFO @ Fri, 05 Jul 2019 04:22:21: 14000000 INFO @ Fri, 05 Jul 2019 04:22:23: 13000000 INFO @ Fri, 05 Jul 2019 04:22:25: 15000000 INFO @ Fri, 05 Jul 2019 04:22:29: 15000000 INFO @ Fri, 05 Jul 2019 04:22:32: 14000000 INFO @ Fri, 05 Jul 2019 04:22:33: 16000000 INFO @ Fri, 05 Jul 2019 04:22:37: 16000000 INFO @ Fri, 05 Jul 2019 04:22:41: 15000000 INFO @ Fri, 05 Jul 2019 04:22:41: 17000000 INFO @ Fri, 05 Jul 2019 04:22:46: 17000000 INFO @ Fri, 05 Jul 2019 04:22:50: 16000000 INFO @ Fri, 05 Jul 2019 04:22:50: 18000000 INFO @ Fri, 05 Jul 2019 04:22:55: 18000000 INFO @ Fri, 05 Jul 2019 04:22:59: 19000000 INFO @ Fri, 05 Jul 2019 04:22:59: 17000000 INFO @ Fri, 05 Jul 2019 04:23:03: 19000000 INFO @ Fri, 05 Jul 2019 04:23:07: 20000000 INFO @ Fri, 05 Jul 2019 04:23:08: 18000000 INFO @ Fri, 05 Jul 2019 04:23:12: 20000000 INFO @ Fri, 05 Jul 2019 04:23:15: 21000000 INFO @ Fri, 05 Jul 2019 04:23:17: 19000000 INFO @ Fri, 05 Jul 2019 04:23:20: 21000000 INFO @ Fri, 05 Jul 2019 04:23:24: 22000000 INFO @ Fri, 05 Jul 2019 04:23:26: 20000000 INFO @ Fri, 05 Jul 2019 04:23:29: 22000000 INFO @ Fri, 05 Jul 2019 04:23:33: 23000000 INFO @ Fri, 05 Jul 2019 04:23:35: 21000000 INFO @ Fri, 05 Jul 2019 04:23:38: 23000000 INFO @ Fri, 05 Jul 2019 04:23:42: 24000000 INFO @ Fri, 05 Jul 2019 04:23:44: 22000000 INFO @ Fri, 05 Jul 2019 04:23:47: 24000000 INFO @ Fri, 05 Jul 2019 04:23:50: 25000000 INFO @ Fri, 05 Jul 2019 04:23:53: 23000000 INFO @ Fri, 05 Jul 2019 04:23:55: 25000000 INFO @ Fri, 05 Jul 2019 04:23:59: 26000000 INFO @ Fri, 05 Jul 2019 04:24:02: 24000000 INFO @ Fri, 05 Jul 2019 04:24:04: 26000000 INFO @ Fri, 05 Jul 2019 04:24:08: 27000000 INFO @ Fri, 05 Jul 2019 04:24:10: 25000000 INFO @ Fri, 05 Jul 2019 04:24:13: 27000000 INFO @ Fri, 05 Jul 2019 04:24:16: 28000000 INFO @ Fri, 05 Jul 2019 04:24:19: 26000000 INFO @ Fri, 05 Jul 2019 04:24:21: 28000000 INFO @ Fri, 05 Jul 2019 04:24:25: 29000000 INFO @ Fri, 05 Jul 2019 04:24:28: 27000000 INFO @ Fri, 05 Jul 2019 04:24:29: 29000000 INFO @ Fri, 05 Jul 2019 04:24:32: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:24:32: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:24:32: #1 total tags in treatment: 29838883 INFO @ Fri, 05 Jul 2019 04:24:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:24:32: #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 04:24:33: #1 tags after filtering in treatment: 29838734 INFO @ Fri, 05 Jul 2019 04:24:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:24:33: #1 finished! INFO @ Fri, 05 Jul 2019 04:24:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:24:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:24:36: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:24:36: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:24:36: #1 total tags in treatment: 29838883 INFO @ Fri, 05 Jul 2019 04:24:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:24:36: #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 04:24:37: 28000000 INFO @ Fri, 05 Jul 2019 04:24:37: #1 tags after filtering in treatment: 29838734 INFO @ Fri, 05 Jul 2019 04:24:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:24:37: #1 finished! INFO @ Fri, 05 Jul 2019 04:24:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:24:39: #2 number of paired peaks: 66781 INFO @ Fri, 05 Jul 2019 04:24:39: start model_add_line... INFO @ Fri, 05 Jul 2019 04:24:39: start X-correlation... INFO @ Fri, 05 Jul 2019 04:24:39: end of X-cor INFO @ Fri, 05 Jul 2019 04:24:39: #2 finished! INFO @ Fri, 05 Jul 2019 04:24:39: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 04:24:39: #2 alternative fragment length(s) may be 1,127,289,503 bps INFO @ Fri, 05 Jul 2019 04:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.05_model.r INFO @ Fri, 05 Jul 2019 04:24:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:24:43: #2 number of paired peaks: 66781 INFO @ Fri, 05 Jul 2019 04:24:43: start model_add_line... INFO @ Fri, 05 Jul 2019 04:24:44: start X-correlation... INFO @ Fri, 05 Jul 2019 04:24:44: end of X-cor INFO @ Fri, 05 Jul 2019 04:24:44: #2 finished! INFO @ Fri, 05 Jul 2019 04:24:44: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 04:24:44: #2 alternative fragment length(s) may be 1,127,289,503 bps INFO @ Fri, 05 Jul 2019 04:24:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.20_model.r INFO @ Fri, 05 Jul 2019 04:24:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:24:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:24:45: 29000000 INFO @ Fri, 05 Jul 2019 04:24:53: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:24:53: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:24:53: #1 total tags in treatment: 29838883 INFO @ Fri, 05 Jul 2019 04:24:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:24:53: #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 04:24:54: #1 tags after filtering in treatment: 29838734 INFO @ Fri, 05 Jul 2019 04:24:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:24:54: #1 finished! INFO @ Fri, 05 Jul 2019 04:24:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:24:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:25:00: #2 number of paired peaks: 66781 INFO @ Fri, 05 Jul 2019 04:25:00: start model_add_line... INFO @ Fri, 05 Jul 2019 04:25:00: start X-correlation... INFO @ Fri, 05 Jul 2019 04:25:00: end of X-cor INFO @ Fri, 05 Jul 2019 04:25:00: #2 finished! INFO @ Fri, 05 Jul 2019 04:25:00: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 04:25:00: #2 alternative fragment length(s) may be 1,127,289,503 bps INFO @ Fri, 05 Jul 2019 04:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.10_model.r INFO @ Fri, 05 Jul 2019 04:25:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:26:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:26:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:26:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:27:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.05_summits.bed INFO @ Fri, 05 Jul 2019 04:27:21: Done! pass1 - making usageList (77 chroms): 4 millis pass2 - checking and writing primary data (7567 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:27:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:27:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:27:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.20_summits.bed INFO @ Fri, 05 Jul 2019 04:27:23: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:27:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:27:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:27:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101838/ERX101838.10_summits.bed INFO @ Fri, 05 Jul 2019 04:27:44: Done! pass1 - making usageList (48 chroms): 2 millis pass2 - checking and writing primary data (1778 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。