Job ID = 2001701 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,938,953 reads read : 24,938,953 reads written : 24,938,953 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: 00:00:01 Multiseed full-index search: 00:09:59 24938953 reads; of these: 24938953 (100.00%) were unpaired; of these: 586118 (2.35%) aligned 0 times 18340114 (73.54%) aligned exactly 1 time 6012721 (24.11%) aligned >1 times 97.65% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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] 1698435 / 24352835 = 0.0697 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 09:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.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 09:29:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:29:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:29:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.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 09:29:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:29:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.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 09:29:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:29:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:29:15: 1000000 INFO @ Fri, 05 Jul 2019 09:29:16: 1000000 INFO @ Fri, 05 Jul 2019 09:29:19: 1000000 INFO @ Fri, 05 Jul 2019 09:29:22: 2000000 INFO @ Fri, 05 Jul 2019 09:29:26: 2000000 INFO @ Fri, 05 Jul 2019 09:29:28: 2000000 INFO @ Fri, 05 Jul 2019 09:29:30: 3000000 INFO @ Fri, 05 Jul 2019 09:29:36: 3000000 INFO @ Fri, 05 Jul 2019 09:29:37: 3000000 INFO @ Fri, 05 Jul 2019 09:29:37: 4000000 INFO @ Fri, 05 Jul 2019 09:29:44: 5000000 INFO @ Fri, 05 Jul 2019 09:29:46: 4000000 INFO @ Fri, 05 Jul 2019 09:29:46: 4000000 INFO @ Fri, 05 Jul 2019 09:29:52: 6000000 INFO @ Fri, 05 Jul 2019 09:29:55: 5000000 INFO @ Fri, 05 Jul 2019 09:29:56: 5000000 INFO @ Fri, 05 Jul 2019 09:29:59: 7000000 INFO @ Fri, 05 Jul 2019 09:30:04: 6000000 INFO @ Fri, 05 Jul 2019 09:30:05: 6000000 INFO @ Fri, 05 Jul 2019 09:30:06: 8000000 INFO @ Fri, 05 Jul 2019 09:30:13: 9000000 INFO @ Fri, 05 Jul 2019 09:30:14: 7000000 INFO @ Fri, 05 Jul 2019 09:30:14: 7000000 INFO @ Fri, 05 Jul 2019 09:30:20: 10000000 INFO @ Fri, 05 Jul 2019 09:30:20: 8000000 INFO @ Fri, 05 Jul 2019 09:30:22: 8000000 INFO @ Fri, 05 Jul 2019 09:30:27: 9000000 INFO @ Fri, 05 Jul 2019 09:30:27: 11000000 INFO @ Fri, 05 Jul 2019 09:30:31: 9000000 INFO @ Fri, 05 Jul 2019 09:30:33: 10000000 INFO @ Fri, 05 Jul 2019 09:30:34: 12000000 INFO @ Fri, 05 Jul 2019 09:30:39: 10000000 INFO @ Fri, 05 Jul 2019 09:30:40: 11000000 INFO @ Fri, 05 Jul 2019 09:30:42: 13000000 INFO @ Fri, 05 Jul 2019 09:30:47: 12000000 INFO @ Fri, 05 Jul 2019 09:30:47: 11000000 INFO @ Fri, 05 Jul 2019 09:30:49: 14000000 INFO @ Fri, 05 Jul 2019 09:30:53: 13000000 INFO @ Fri, 05 Jul 2019 09:30:56: 12000000 INFO @ Fri, 05 Jul 2019 09:30:56: 15000000 INFO @ Fri, 05 Jul 2019 09:31:00: 14000000 INFO @ Fri, 05 Jul 2019 09:31:03: 16000000 INFO @ Fri, 05 Jul 2019 09:31:04: 13000000 INFO @ Fri, 05 Jul 2019 09:31:06: 15000000 INFO @ Fri, 05 Jul 2019 09:31:11: 17000000 INFO @ Fri, 05 Jul 2019 09:31:13: 14000000 INFO @ Fri, 05 Jul 2019 09:31:13: 16000000 INFO @ Fri, 05 Jul 2019 09:31:18: 18000000 INFO @ Fri, 05 Jul 2019 09:31:20: 17000000 INFO @ Fri, 05 Jul 2019 09:31:21: 15000000 INFO @ Fri, 05 Jul 2019 09:31:25: 19000000 INFO @ Fri, 05 Jul 2019 09:31:27: 18000000 INFO @ Fri, 05 Jul 2019 09:31:30: 16000000 INFO @ Fri, 05 Jul 2019 09:31:32: 20000000 INFO @ Fri, 05 Jul 2019 09:31:33: 19000000 INFO @ Fri, 05 Jul 2019 09:31:39: 17000000 INFO @ Fri, 05 Jul 2019 09:31:39: 21000000 INFO @ Fri, 05 Jul 2019 09:31:40: 20000000 INFO @ Fri, 05 Jul 2019 09:31:47: 21000000 INFO @ Fri, 05 Jul 2019 09:31:47: 22000000 INFO @ Fri, 05 Jul 2019 09:31:47: 18000000 INFO @ Fri, 05 Jul 2019 09:31:52: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:31:52: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:31:52: #1 total tags in treatment: 22654400 INFO @ Fri, 05 Jul 2019 09:31:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:31:52: #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 09:31:52: #1 tags after filtering in treatment: 22654221 INFO @ Fri, 05 Jul 2019 09:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:31:52: #1 finished! INFO @ Fri, 05 Jul 2019 09:31:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:31:53: 22000000 INFO @ Fri, 05 Jul 2019 09:31:56: 19000000 INFO @ Fri, 05 Jul 2019 09:31:57: #2 number of paired peaks: 54253 INFO @ Fri, 05 Jul 2019 09:31:57: start model_add_line... INFO @ Fri, 05 Jul 2019 09:31:57: start X-correlation... INFO @ Fri, 05 Jul 2019 09:31:57: end of X-cor INFO @ Fri, 05 Jul 2019 09:31:57: #2 finished! INFO @ Fri, 05 Jul 2019 09:31:57: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 09:31:57: #2 alternative fragment length(s) may be 4,129,499 bps INFO @ Fri, 05 Jul 2019 09:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.10_model.r INFO @ Fri, 05 Jul 2019 09:31:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:31:58: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:31:58: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:31:58: #1 total tags in treatment: 22654400 INFO @ Fri, 05 Jul 2019 09:31:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:31:58: #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 09:31:59: #1 tags after filtering in treatment: 22654221 INFO @ Fri, 05 Jul 2019 09:31:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:31:59: #1 finished! INFO @ Fri, 05 Jul 2019 09:31:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:31:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:32:03: #2 number of paired peaks: 54253 INFO @ Fri, 05 Jul 2019 09:32:03: start model_add_line... INFO @ Fri, 05 Jul 2019 09:32:04: start X-correlation... INFO @ Fri, 05 Jul 2019 09:32:04: end of X-cor INFO @ Fri, 05 Jul 2019 09:32:04: #2 finished! INFO @ Fri, 05 Jul 2019 09:32:04: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 09:32:04: #2 alternative fragment length(s) may be 4,129,499 bps INFO @ Fri, 05 Jul 2019 09:32:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.05_model.r INFO @ Fri, 05 Jul 2019 09:32:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:32:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:32:05: 20000000 INFO @ Fri, 05 Jul 2019 09:32:14: 21000000 INFO @ Fri, 05 Jul 2019 09:32:22: 22000000 INFO @ Fri, 05 Jul 2019 09:32:28: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:32:28: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:32:28: #1 total tags in treatment: 22654400 INFO @ Fri, 05 Jul 2019 09:32:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:32:28: #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 09:32:29: #1 tags after filtering in treatment: 22654221 INFO @ Fri, 05 Jul 2019 09:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:32:29: #1 finished! INFO @ Fri, 05 Jul 2019 09:32:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:32:33: #2 number of paired peaks: 54253 INFO @ Fri, 05 Jul 2019 09:32:33: start model_add_line... INFO @ Fri, 05 Jul 2019 09:32:34: start X-correlation... INFO @ Fri, 05 Jul 2019 09:32:34: end of X-cor INFO @ Fri, 05 Jul 2019 09:32:34: #2 finished! INFO @ Fri, 05 Jul 2019 09:32:34: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 09:32:34: #2 alternative fragment length(s) may be 4,129,499 bps INFO @ Fri, 05 Jul 2019 09:32:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.20_model.r INFO @ Fri, 05 Jul 2019 09:32:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:32:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:33:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:33:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:33:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:33:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:33:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.10_summits.bed INFO @ Fri, 05 Jul 2019 09:33:44: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (1370 records, 4 fields): 7 millis INFO @ Fri, 05 Jul 2019 09:33:46: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:33:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:33:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:33:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.05_summits.bed INFO @ Fri, 05 Jul 2019 09:33:50: Done! pass1 - making usageList (67 chroms): 4 millis pass2 - checking and writing primary data (6002 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:34:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:34:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:34:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102011/ERX102011.20_summits.bed INFO @ Fri, 05 Jul 2019 09:34:23: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (141 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。