Job ID = 5790630 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 111,056,270 reads read : 111,056,270 reads written : 111,056,270 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: 00:47:39 111056270 reads; of these: 111056270 (100.00%) were unpaired; of these: 1931988 (1.74%) aligned 0 times 97370317 (87.68%) aligned exactly 1 time 11753965 (10.58%) aligned >1 times 98.26% overall alignment rate Time searching: 00:47:42 Overall time: 00:47:42 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] 65318909 / 109124282 = 0.5986 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 06:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.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 @ Wed, 22 Apr 2020 06:20:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:20:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:20:31: 1000000 INFO @ Wed, 22 Apr 2020 06:20:36: 2000000 INFO @ Wed, 22 Apr 2020 06:20:43: 3000000 INFO @ Wed, 22 Apr 2020 06:20:49: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 06:20:55: 5000000 INFO @ Wed, 22 Apr 2020 06:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.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 @ Wed, 22 Apr 2020 06:20:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:20:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:21:01: 6000000 INFO @ Wed, 22 Apr 2020 06:21:02: 1000000 INFO @ Wed, 22 Apr 2020 06:21:08: 7000000 INFO @ Wed, 22 Apr 2020 06:21:09: 2000000 INFO @ Wed, 22 Apr 2020 06:21:14: 8000000 INFO @ Wed, 22 Apr 2020 06:21:18: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 06:21:21: 9000000 INFO @ Wed, 22 Apr 2020 06:21:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.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 @ Wed, 22 Apr 2020 06:21:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:21:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:21:27: 4000000 INFO @ Wed, 22 Apr 2020 06:21:28: 10000000 INFO @ Wed, 22 Apr 2020 06:21:32: 1000000 INFO @ Wed, 22 Apr 2020 06:21:34: 11000000 INFO @ Wed, 22 Apr 2020 06:21:36: 5000000 INFO @ Wed, 22 Apr 2020 06:21:38: 2000000 INFO @ Wed, 22 Apr 2020 06:21:41: 12000000 INFO @ Wed, 22 Apr 2020 06:21:44: 3000000 INFO @ Wed, 22 Apr 2020 06:21:45: 6000000 INFO @ Wed, 22 Apr 2020 06:21:48: 13000000 INFO @ Wed, 22 Apr 2020 06:21:51: 4000000 INFO @ Wed, 22 Apr 2020 06:21:53: 7000000 INFO @ Wed, 22 Apr 2020 06:21:55: 14000000 INFO @ Wed, 22 Apr 2020 06:21:57: 5000000 INFO @ Wed, 22 Apr 2020 06:22:02: 8000000 INFO @ Wed, 22 Apr 2020 06:22:02: 15000000 INFO @ Wed, 22 Apr 2020 06:22:04: 6000000 INFO @ Wed, 22 Apr 2020 06:22:08: 16000000 INFO @ Wed, 22 Apr 2020 06:22:10: 7000000 INFO @ Wed, 22 Apr 2020 06:22:10: 9000000 INFO @ Wed, 22 Apr 2020 06:22:15: 17000000 INFO @ Wed, 22 Apr 2020 06:22:17: 8000000 INFO @ Wed, 22 Apr 2020 06:22:19: 10000000 INFO @ Wed, 22 Apr 2020 06:22:22: 18000000 INFO @ Wed, 22 Apr 2020 06:22:23: 9000000 INFO @ Wed, 22 Apr 2020 06:22:27: 11000000 INFO @ Wed, 22 Apr 2020 06:22:28: 19000000 INFO @ Wed, 22 Apr 2020 06:22:29: 10000000 INFO @ Wed, 22 Apr 2020 06:22:35: 20000000 INFO @ Wed, 22 Apr 2020 06:22:36: 12000000 INFO @ Wed, 22 Apr 2020 06:22:36: 11000000 INFO @ Wed, 22 Apr 2020 06:22:42: 21000000 INFO @ Wed, 22 Apr 2020 06:22:42: 13000000 INFO @ Wed, 22 Apr 2020 06:22:42: 12000000 INFO @ Wed, 22 Apr 2020 06:22:48: 22000000 INFO @ Wed, 22 Apr 2020 06:22:48: 14000000 INFO @ Wed, 22 Apr 2020 06:22:49: 13000000 INFO @ Wed, 22 Apr 2020 06:22:54: 23000000 INFO @ Wed, 22 Apr 2020 06:22:55: 15000000 INFO @ Wed, 22 Apr 2020 06:22:55: 14000000 INFO @ Wed, 22 Apr 2020 06:23:01: 24000000 INFO @ Wed, 22 Apr 2020 06:23:01: 16000000 INFO @ Wed, 22 Apr 2020 06:23:01: 15000000 INFO @ Wed, 22 Apr 2020 06:23:07: 25000000 INFO @ Wed, 22 Apr 2020 06:23:08: 17000000 INFO @ Wed, 22 Apr 2020 06:23:08: 16000000 INFO @ Wed, 22 Apr 2020 06:23:14: 26000000 INFO @ Wed, 22 Apr 2020 06:23:14: 18000000 INFO @ Wed, 22 Apr 2020 06:23:14: 17000000 INFO @ Wed, 22 Apr 2020 06:23:20: 19000000 INFO @ Wed, 22 Apr 2020 06:23:20: 27000000 INFO @ Wed, 22 Apr 2020 06:23:20: 18000000 INFO @ Wed, 22 Apr 2020 06:23:27: 20000000 INFO @ Wed, 22 Apr 2020 06:23:27: 19000000 INFO @ Wed, 22 Apr 2020 06:23:27: 28000000 INFO @ Wed, 22 Apr 2020 06:23:33: 21000000 INFO @ Wed, 22 Apr 2020 06:23:33: 20000000 INFO @ Wed, 22 Apr 2020 06:23:33: 29000000 INFO @ Wed, 22 Apr 2020 06:23:39: 22000000 INFO @ Wed, 22 Apr 2020 06:23:40: 21000000 INFO @ Wed, 22 Apr 2020 06:23:40: 30000000 INFO @ Wed, 22 Apr 2020 06:23:46: 23000000 INFO @ Wed, 22 Apr 2020 06:23:46: 22000000 INFO @ Wed, 22 Apr 2020 06:23:46: 31000000 INFO @ Wed, 22 Apr 2020 06:23:52: 24000000 INFO @ Wed, 22 Apr 2020 06:23:52: 23000000 INFO @ Wed, 22 Apr 2020 06:23:53: 32000000 INFO @ Wed, 22 Apr 2020 06:23:59: 25000000 INFO @ Wed, 22 Apr 2020 06:23:59: 24000000 INFO @ Wed, 22 Apr 2020 06:23:59: 33000000 INFO @ Wed, 22 Apr 2020 06:24:05: 26000000 INFO @ Wed, 22 Apr 2020 06:24:05: 25000000 INFO @ Wed, 22 Apr 2020 06:24:06: 34000000 INFO @ Wed, 22 Apr 2020 06:24:11: 26000000 INFO @ Wed, 22 Apr 2020 06:24:11: 27000000 INFO @ Wed, 22 Apr 2020 06:24:12: 35000000 INFO @ Wed, 22 Apr 2020 06:24:18: 27000000 INFO @ Wed, 22 Apr 2020 06:24:18: 28000000 INFO @ Wed, 22 Apr 2020 06:24:19: 36000000 INFO @ Wed, 22 Apr 2020 06:24:24: 28000000 INFO @ Wed, 22 Apr 2020 06:24:24: 29000000 INFO @ Wed, 22 Apr 2020 06:24:25: 37000000 INFO @ Wed, 22 Apr 2020 06:24:31: 29000000 INFO @ Wed, 22 Apr 2020 06:24:31: 30000000 INFO @ Wed, 22 Apr 2020 06:24:32: 38000000 INFO @ Wed, 22 Apr 2020 06:24:37: 30000000 INFO @ Wed, 22 Apr 2020 06:24:37: 31000000 INFO @ Wed, 22 Apr 2020 06:24:38: 39000000 INFO @ Wed, 22 Apr 2020 06:24:43: 31000000 INFO @ Wed, 22 Apr 2020 06:24:43: 32000000 INFO @ Wed, 22 Apr 2020 06:24:45: 40000000 INFO @ Wed, 22 Apr 2020 06:24:50: 32000000 INFO @ Wed, 22 Apr 2020 06:24:50: 33000000 INFO @ Wed, 22 Apr 2020 06:24:51: 41000000 INFO @ Wed, 22 Apr 2020 06:24:56: 33000000 INFO @ Wed, 22 Apr 2020 06:24:56: 34000000 INFO @ Wed, 22 Apr 2020 06:24:57: 42000000 INFO @ Wed, 22 Apr 2020 06:25:03: 35000000 INFO @ Wed, 22 Apr 2020 06:25:03: 34000000 INFO @ Wed, 22 Apr 2020 06:25:04: 43000000 INFO @ Wed, 22 Apr 2020 06:25:09: 36000000 INFO @ Wed, 22 Apr 2020 06:25:09: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 06:25:09: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 06:25:09: #1 total tags in treatment: 43805373 INFO @ Wed, 22 Apr 2020 06:25:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:25:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:25:09: 35000000 INFO @ Wed, 22 Apr 2020 06:25:10: #1 tags after filtering in treatment: 43805177 INFO @ Wed, 22 Apr 2020 06:25:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:25:10: #1 finished! INFO @ Wed, 22 Apr 2020 06:25:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:25:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:25:15: 37000000 INFO @ Wed, 22 Apr 2020 06:25:16: 36000000 INFO @ Wed, 22 Apr 2020 06:25:19: #2 number of paired peaks: 109100 INFO @ Wed, 22 Apr 2020 06:25:19: start model_add_line... INFO @ Wed, 22 Apr 2020 06:25:20: start X-correlation... INFO @ Wed, 22 Apr 2020 06:25:20: end of X-cor INFO @ Wed, 22 Apr 2020 06:25:20: #2 finished! INFO @ Wed, 22 Apr 2020 06:25:20: #2 predicted fragment length is 138 bps INFO @ Wed, 22 Apr 2020 06:25:20: #2 alternative fragment length(s) may be 3,138 bps INFO @ Wed, 22 Apr 2020 06:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.05_model.r INFO @ Wed, 22 Apr 2020 06:25:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:25:22: 38000000 INFO @ Wed, 22 Apr 2020 06:25:22: 37000000 INFO @ Wed, 22 Apr 2020 06:25:28: 39000000 INFO @ Wed, 22 Apr 2020 06:25:28: 38000000 INFO @ Wed, 22 Apr 2020 06:25:34: 40000000 INFO @ Wed, 22 Apr 2020 06:25:35: 39000000 INFO @ Wed, 22 Apr 2020 06:25:41: 41000000 INFO @ Wed, 22 Apr 2020 06:25:41: 40000000 INFO @ Wed, 22 Apr 2020 06:25:47: 42000000 INFO @ Wed, 22 Apr 2020 06:25:47: 41000000 INFO @ Wed, 22 Apr 2020 06:25:53: 42000000 INFO @ Wed, 22 Apr 2020 06:25:54: 43000000 INFO @ Wed, 22 Apr 2020 06:25:59: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 06:25:59: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 06:25:59: #1 total tags in treatment: 43805373 INFO @ Wed, 22 Apr 2020 06:25:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:25:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:26:00: 43000000 INFO @ Wed, 22 Apr 2020 06:26:00: #1 tags after filtering in treatment: 43805177 INFO @ Wed, 22 Apr 2020 06:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:26:00: #1 finished! INFO @ Wed, 22 Apr 2020 06:26:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:26:05: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 06:26:05: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 06:26:05: #1 total tags in treatment: 43805373 INFO @ Wed, 22 Apr 2020 06:26:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:26:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:26:06: #1 tags after filtering in treatment: 43805177 INFO @ Wed, 22 Apr 2020 06:26:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:26:06: #1 finished! INFO @ Wed, 22 Apr 2020 06:26:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:26:08: #2 number of paired peaks: 109100 INFO @ Wed, 22 Apr 2020 06:26:08: start model_add_line... INFO @ Wed, 22 Apr 2020 06:26:09: start X-correlation... INFO @ Wed, 22 Apr 2020 06:26:09: end of X-cor INFO @ Wed, 22 Apr 2020 06:26:09: #2 finished! INFO @ Wed, 22 Apr 2020 06:26:09: #2 predicted fragment length is 138 bps INFO @ Wed, 22 Apr 2020 06:26:09: #2 alternative fragment length(s) may be 3,138 bps INFO @ Wed, 22 Apr 2020 06:26:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.10_model.r INFO @ Wed, 22 Apr 2020 06:26:09: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:26:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:26:14: #2 number of paired peaks: 109100 INFO @ Wed, 22 Apr 2020 06:26:14: start model_add_line... INFO @ Wed, 22 Apr 2020 06:26:15: start X-correlation... INFO @ Wed, 22 Apr 2020 06:26:15: end of X-cor INFO @ Wed, 22 Apr 2020 06:26:15: #2 finished! INFO @ Wed, 22 Apr 2020 06:26:15: #2 predicted fragment length is 138 bps INFO @ Wed, 22 Apr 2020 06:26:15: #2 alternative fragment length(s) may be 3,138 bps INFO @ Wed, 22 Apr 2020 06:26:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.20_model.r INFO @ Wed, 22 Apr 2020 06:26:15: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:26:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:27:07: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:27:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:28:07: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:28:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:28:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:28:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.05_summits.bed INFO @ Wed, 22 Apr 2020 06:28:11: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (188 chroms): 12 millis pass2 - checking and writing primary data (87791 records, 4 fields): 84 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:29:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:29:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.10_summits.bed INFO @ Wed, 22 Apr 2020 06:29:02: Done! pass1 - making usageList (159 chroms): 9 millis pass2 - checking and writing primary data (66232 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:29:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:29:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:29:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101930/ERX101930.20_summits.bed INFO @ Wed, 22 Apr 2020 06:29:12: Done! pass1 - making usageList (132 chroms): 7 millis pass2 - checking and writing primary data (44529 records, 4 fields): 42 millis CompletedMACS2peakCalling BigWig に変換しました。