Job ID = 2001656 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,070,733 reads read : 20,070,733 reads written : 20,070,733 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:49 20070733 reads; of these: 20070733 (100.00%) were unpaired; of these: 497320 (2.48%) aligned 0 times 13629773 (67.91%) aligned exactly 1 time 5943640 (29.61%) aligned >1 times 97.52% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 462792 / 19573413 = 0.0236 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 07:39:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.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 07:39:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:39:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.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 07:39:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:39:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.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 07:39:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:39:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:39:24: 1000000 INFO @ Fri, 05 Jul 2019 07:39:25: 1000000 INFO @ Fri, 05 Jul 2019 07:39:25: 1000000 INFO @ Fri, 05 Jul 2019 07:39:31: 2000000 INFO @ Fri, 05 Jul 2019 07:39:32: 2000000 INFO @ Fri, 05 Jul 2019 07:39:33: 2000000 INFO @ Fri, 05 Jul 2019 07:39:38: 3000000 INFO @ Fri, 05 Jul 2019 07:39:38: 3000000 INFO @ Fri, 05 Jul 2019 07:39:41: 3000000 INFO @ Fri, 05 Jul 2019 07:39:45: 4000000 INFO @ Fri, 05 Jul 2019 07:39:45: 4000000 INFO @ Fri, 05 Jul 2019 07:39:48: 4000000 INFO @ Fri, 05 Jul 2019 07:39:51: 5000000 INFO @ Fri, 05 Jul 2019 07:39:52: 5000000 INFO @ Fri, 05 Jul 2019 07:39:56: 5000000 INFO @ Fri, 05 Jul 2019 07:39:58: 6000000 INFO @ Fri, 05 Jul 2019 07:39:59: 6000000 INFO @ Fri, 05 Jul 2019 07:40:03: 6000000 INFO @ Fri, 05 Jul 2019 07:40:05: 7000000 INFO @ Fri, 05 Jul 2019 07:40:06: 7000000 INFO @ Fri, 05 Jul 2019 07:40:11: 7000000 INFO @ Fri, 05 Jul 2019 07:40:12: 8000000 INFO @ Fri, 05 Jul 2019 07:40:12: 8000000 INFO @ Fri, 05 Jul 2019 07:40:19: 8000000 INFO @ Fri, 05 Jul 2019 07:40:19: 9000000 INFO @ Fri, 05 Jul 2019 07:40:19: 9000000 INFO @ Fri, 05 Jul 2019 07:40:26: 10000000 INFO @ Fri, 05 Jul 2019 07:40:27: 10000000 INFO @ Fri, 05 Jul 2019 07:40:27: 9000000 INFO @ Fri, 05 Jul 2019 07:40:34: 11000000 INFO @ Fri, 05 Jul 2019 07:40:34: 11000000 INFO @ Fri, 05 Jul 2019 07:40:36: 10000000 INFO @ Fri, 05 Jul 2019 07:40:41: 12000000 INFO @ Fri, 05 Jul 2019 07:40:42: 12000000 INFO @ Fri, 05 Jul 2019 07:40:45: 11000000 INFO @ Fri, 05 Jul 2019 07:40:48: 13000000 INFO @ Fri, 05 Jul 2019 07:40:49: 13000000 INFO @ Fri, 05 Jul 2019 07:40:54: 12000000 INFO @ Fri, 05 Jul 2019 07:40:55: 14000000 INFO @ Fri, 05 Jul 2019 07:40:56: 14000000 INFO @ Fri, 05 Jul 2019 07:41:02: 13000000 INFO @ Fri, 05 Jul 2019 07:41:02: 15000000 INFO @ Fri, 05 Jul 2019 07:41:03: 15000000 INFO @ Fri, 05 Jul 2019 07:41:09: 16000000 INFO @ Fri, 05 Jul 2019 07:41:09: 16000000 INFO @ Fri, 05 Jul 2019 07:41:10: 14000000 INFO @ Fri, 05 Jul 2019 07:41:15: 17000000 INFO @ Fri, 05 Jul 2019 07:41:16: 17000000 INFO @ Fri, 05 Jul 2019 07:41:19: 15000000 INFO @ Fri, 05 Jul 2019 07:41:22: 18000000 INFO @ Fri, 05 Jul 2019 07:41:23: 18000000 INFO @ Fri, 05 Jul 2019 07:41:27: 16000000 INFO @ Fri, 05 Jul 2019 07:41:30: 19000000 INFO @ Fri, 05 Jul 2019 07:41:30: 19000000 INFO @ Fri, 05 Jul 2019 07:41:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:41:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:41:31: #1 total tags in treatment: 19110621 INFO @ Fri, 05 Jul 2019 07:41:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:41:31: #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 07:41:31: #1 tags after filtering in treatment: 19110465 INFO @ Fri, 05 Jul 2019 07:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:41:31: #1 finished! INFO @ Fri, 05 Jul 2019 07:41:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:41:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:41:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:41:31: #1 total tags in treatment: 19110621 INFO @ Fri, 05 Jul 2019 07:41:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:41:31: #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 07:41:32: #1 tags after filtering in treatment: 19110465 INFO @ Fri, 05 Jul 2019 07:41:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:41:32: #1 finished! INFO @ Fri, 05 Jul 2019 07:41:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:41:34: #2 number of paired peaks: 6841 INFO @ Fri, 05 Jul 2019 07:41:34: start model_add_line... INFO @ Fri, 05 Jul 2019 07:41:34: start X-correlation... INFO @ Fri, 05 Jul 2019 07:41:34: end of X-cor INFO @ Fri, 05 Jul 2019 07:41:34: #2 finished! INFO @ Fri, 05 Jul 2019 07:41:34: #2 predicted fragment length is 89 bps INFO @ Fri, 05 Jul 2019 07:41:34: #2 alternative fragment length(s) may be 40,89 bps INFO @ Fri, 05 Jul 2019 07:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.05_model.r INFO @ Fri, 05 Jul 2019 07:41:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:41:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:41:34: #2 number of paired peaks: 6841 INFO @ Fri, 05 Jul 2019 07:41:34: start model_add_line... INFO @ Fri, 05 Jul 2019 07:41:34: start X-correlation... INFO @ Fri, 05 Jul 2019 07:41:34: end of X-cor INFO @ Fri, 05 Jul 2019 07:41:34: #2 finished! INFO @ Fri, 05 Jul 2019 07:41:34: #2 predicted fragment length is 89 bps INFO @ Fri, 05 Jul 2019 07:41:34: #2 alternative fragment length(s) may be 40,89 bps INFO @ Fri, 05 Jul 2019 07:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.10_model.r INFO @ Fri, 05 Jul 2019 07:41:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:41:35: 17000000 INFO @ Fri, 05 Jul 2019 07:41:42: 18000000 INFO @ Fri, 05 Jul 2019 07:41:51: 19000000 INFO @ Fri, 05 Jul 2019 07:41:53: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:41:53: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:41:53: #1 total tags in treatment: 19110621 INFO @ Fri, 05 Jul 2019 07:41:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:41:53: #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 07:41:53: #1 tags after filtering in treatment: 19110465 INFO @ Fri, 05 Jul 2019 07:41:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:41:53: #1 finished! INFO @ Fri, 05 Jul 2019 07:41:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:41:56: #2 number of paired peaks: 6841 INFO @ Fri, 05 Jul 2019 07:41:56: start model_add_line... INFO @ Fri, 05 Jul 2019 07:41:56: start X-correlation... INFO @ Fri, 05 Jul 2019 07:41:56: end of X-cor INFO @ Fri, 05 Jul 2019 07:41:56: #2 finished! INFO @ Fri, 05 Jul 2019 07:41:56: #2 predicted fragment length is 89 bps INFO @ Fri, 05 Jul 2019 07:41:56: #2 alternative fragment length(s) may be 40,89 bps INFO @ Fri, 05 Jul 2019 07:41:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.20_model.r INFO @ Fri, 05 Jul 2019 07:41:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:41:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:42:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:42:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:43:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:43:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:43:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:43:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.05_summits.bed INFO @ Fri, 05 Jul 2019 07:43:10: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1330 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:43:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:43:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:43:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.10_summits.bed INFO @ Fri, 05 Jul 2019 07:43:11: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (520 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:43:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:43:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:43:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101971/ERX101971.20_summits.bed INFO @ Fri, 05 Jul 2019 07:43:30: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。