Job ID = 5790631 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,812,527 reads read : 23,812,527 reads written : 23,812,527 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:37 23812527 reads; of these: 23812527 (100.00%) were unpaired; of these: 462390 (1.94%) aligned 0 times 17855599 (74.98%) aligned exactly 1 time 5494538 (23.07%) aligned >1 times 98.06% overall alignment rate Time searching: 00:07:39 Overall time: 00:07:39 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 8 files... [bam_rmdupse_core] 1496312 / 23350137 = 0.0641 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 04:41:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.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 04:41:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 04:41:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 04:41:07: 1000000 INFO @ Wed, 22 Apr 2020 04:41:12: 2000000 INFO @ Wed, 22 Apr 2020 04:41:17: 3000000 INFO @ Wed, 22 Apr 2020 04:41:22: 4000000 INFO @ Wed, 22 Apr 2020 04:41:26: 5000000 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 04:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.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 04:41:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 04:41:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 04:41:31: 6000000 INFO @ Wed, 22 Apr 2020 04:41:35: 1000000 INFO @ Wed, 22 Apr 2020 04:41:36: 7000000 INFO @ Wed, 22 Apr 2020 04:41:40: 2000000 INFO @ Wed, 22 Apr 2020 04:41:41: 8000000 INFO @ Wed, 22 Apr 2020 04:41:46: 3000000 INFO @ Wed, 22 Apr 2020 04:41:46: 9000000 INFO @ Wed, 22 Apr 2020 04:41:51: 4000000 INFO @ Wed, 22 Apr 2020 04:41:51: 10000000 INFO @ Wed, 22 Apr 2020 04:41:56: 5000000 INFO @ Wed, 22 Apr 2020 04:41:56: 11000000 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 04:42:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.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 04:42:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 04:42:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 04:42:01: 6000000 INFO @ Wed, 22 Apr 2020 04:42:02: 12000000 INFO @ Wed, 22 Apr 2020 04:42:06: 7000000 INFO @ Wed, 22 Apr 2020 04:42:06: 1000000 INFO @ Wed, 22 Apr 2020 04:42:07: 13000000 INFO @ Wed, 22 Apr 2020 04:42:12: 8000000 INFO @ Wed, 22 Apr 2020 04:42:12: 14000000 INFO @ Wed, 22 Apr 2020 04:42:12: 2000000 INFO @ Wed, 22 Apr 2020 04:42:17: 9000000 INFO @ Wed, 22 Apr 2020 04:42:17: 15000000 INFO @ Wed, 22 Apr 2020 04:42:19: 3000000 INFO @ Wed, 22 Apr 2020 04:42:22: 10000000 INFO @ Wed, 22 Apr 2020 04:42:23: 16000000 INFO @ Wed, 22 Apr 2020 04:42:25: 4000000 INFO @ Wed, 22 Apr 2020 04:42:28: 11000000 INFO @ Wed, 22 Apr 2020 04:42:28: 17000000 INFO @ Wed, 22 Apr 2020 04:42:31: 5000000 INFO @ Wed, 22 Apr 2020 04:42:33: 12000000 INFO @ Wed, 22 Apr 2020 04:42:33: 18000000 INFO @ Wed, 22 Apr 2020 04:42:37: 6000000 INFO @ Wed, 22 Apr 2020 04:42:38: 13000000 INFO @ Wed, 22 Apr 2020 04:42:39: 19000000 INFO @ Wed, 22 Apr 2020 04:42:43: 7000000 INFO @ Wed, 22 Apr 2020 04:42:43: 14000000 INFO @ Wed, 22 Apr 2020 04:42:44: 20000000 INFO @ Wed, 22 Apr 2020 04:42:48: 8000000 INFO @ Wed, 22 Apr 2020 04:42:49: 15000000 INFO @ Wed, 22 Apr 2020 04:42:49: 21000000 INFO @ Wed, 22 Apr 2020 04:42:54: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 04:42:54: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 04:42:54: #1 total tags in treatment: 21853825 INFO @ Wed, 22 Apr 2020 04:42:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 04:42:54: #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 04:42:54: 16000000 INFO @ Wed, 22 Apr 2020 04:42:54: 9000000 INFO @ Wed, 22 Apr 2020 04:42:55: #1 tags after filtering in treatment: 21853636 INFO @ Wed, 22 Apr 2020 04:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 04:42:55: #1 finished! INFO @ Wed, 22 Apr 2020 04:42:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 04:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 04:42:58: #2 number of paired peaks: 70781 INFO @ Wed, 22 Apr 2020 04:42:58: start model_add_line... INFO @ Wed, 22 Apr 2020 04:42:58: start X-correlation... INFO @ Wed, 22 Apr 2020 04:42:58: end of X-cor INFO @ Wed, 22 Apr 2020 04:42:58: #2 finished! INFO @ Wed, 22 Apr 2020 04:42:58: #2 predicted fragment length is 139 bps INFO @ Wed, 22 Apr 2020 04:42:58: #2 alternative fragment length(s) may be 1,139,298,508 bps INFO @ Wed, 22 Apr 2020 04:42:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.05_model.r INFO @ Wed, 22 Apr 2020 04:42:58: #3 Call peaks... INFO @ Wed, 22 Apr 2020 04:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 04:43:00: 17000000 INFO @ Wed, 22 Apr 2020 04:43:00: 10000000 INFO @ Wed, 22 Apr 2020 04:43:05: 18000000 INFO @ Wed, 22 Apr 2020 04:43:06: 11000000 INFO @ Wed, 22 Apr 2020 04:43:10: 19000000 INFO @ Wed, 22 Apr 2020 04:43:12: 12000000 INFO @ Wed, 22 Apr 2020 04:43:16: 20000000 INFO @ Wed, 22 Apr 2020 04:43:18: 13000000 INFO @ Wed, 22 Apr 2020 04:43:21: 21000000 INFO @ Wed, 22 Apr 2020 04:43:24: 14000000 INFO @ Wed, 22 Apr 2020 04:43:26: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 04:43:26: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 04:43:26: #1 total tags in treatment: 21853825 INFO @ Wed, 22 Apr 2020 04:43:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 04:43:26: #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 04:43:26: #1 tags after filtering in treatment: 21853636 INFO @ Wed, 22 Apr 2020 04:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 04:43:26: #1 finished! INFO @ Wed, 22 Apr 2020 04:43:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 04:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 04:43:30: 15000000 INFO @ Wed, 22 Apr 2020 04:43:30: #2 number of paired peaks: 70781 INFO @ Wed, 22 Apr 2020 04:43:30: start model_add_line... INFO @ Wed, 22 Apr 2020 04:43:30: start X-correlation... INFO @ Wed, 22 Apr 2020 04:43:30: end of X-cor INFO @ Wed, 22 Apr 2020 04:43:30: #2 finished! INFO @ Wed, 22 Apr 2020 04:43:30: #2 predicted fragment length is 139 bps INFO @ Wed, 22 Apr 2020 04:43:30: #2 alternative fragment length(s) may be 1,139,298,508 bps INFO @ Wed, 22 Apr 2020 04:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.10_model.r INFO @ Wed, 22 Apr 2020 04:43:30: #3 Call peaks... INFO @ Wed, 22 Apr 2020 04:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 04:43:35: 16000000 INFO @ Wed, 22 Apr 2020 04:43:41: 17000000 INFO @ Wed, 22 Apr 2020 04:43:47: 18000000 INFO @ Wed, 22 Apr 2020 04:43:47: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 04:43:52: 19000000 INFO @ Wed, 22 Apr 2020 04:43:58: 20000000 INFO @ Wed, 22 Apr 2020 04:44:03: 21000000 INFO @ Wed, 22 Apr 2020 04:44:08: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 04:44:08: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 04:44:08: #1 total tags in treatment: 21853825 INFO @ Wed, 22 Apr 2020 04:44:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 04:44:08: #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 04:44:09: #1 tags after filtering in treatment: 21853636 INFO @ Wed, 22 Apr 2020 04:44:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 04:44:09: #1 finished! INFO @ Wed, 22 Apr 2020 04:44:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 04:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 04:44:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.05_peaks.xls INFO @ Wed, 22 Apr 2020 04:44:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 04:44:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.05_summits.bed INFO @ Wed, 22 Apr 2020 04:44:12: Done! INFO @ Wed, 22 Apr 2020 04:44:13: #2 number of paired peaks: 70781 INFO @ Wed, 22 Apr 2020 04:44:13: start model_add_line... INFO @ Wed, 22 Apr 2020 04:44:13: start X-correlation... INFO @ Wed, 22 Apr 2020 04:44:13: end of X-cor INFO @ Wed, 22 Apr 2020 04:44:13: #2 finished! INFO @ Wed, 22 Apr 2020 04:44:13: #2 predicted fragment length is 139 bps INFO @ Wed, 22 Apr 2020 04:44:13: #2 alternative fragment length(s) may be 1,139,298,508 bps INFO @ Wed, 22 Apr 2020 04:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.20_model.r INFO @ Wed, 22 Apr 2020 04:44:13: #3 Call peaks... INFO @ Wed, 22 Apr 2020 04:44:13: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (3947 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 04:44:18: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 04:44:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.10_peaks.xls INFO @ Wed, 22 Apr 2020 04:44:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 04:44:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.10_summits.bed INFO @ Wed, 22 Apr 2020 04:44:43: Done! pass1 - making usageList (38 chroms): 0 millis pass2 - checking and writing primary data (814 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 04:44:59: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 04:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.20_peaks.xls INFO @ Wed, 22 Apr 2020 04:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 04:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101944/ERX101944.20_summits.bed INFO @ Wed, 22 Apr 2020 04:45:23: Done! pass1 - making usageList (28 chroms): 0 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。