Job ID = 2002125 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,287,955 reads read : 35,287,955 reads written : 35,287,955 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:42 35287955 reads; of these: 35287955 (100.00%) were unpaired; of these: 726347 (2.06%) aligned 0 times 26466494 (75.00%) aligned exactly 1 time 8095114 (22.94%) aligned >1 times 97.94% overall alignment rate Time searching: 00:13:44 Overall time: 00:13:44 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] 2639129 / 34561608 = 0.0764 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 10:17:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.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 10:17:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:17:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.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 10:17:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:17:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:17:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:17:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.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 10:17:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:17:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:17:24: 1000000 INFO @ Fri, 05 Jul 2019 10:17:25: 1000000 INFO @ Fri, 05 Jul 2019 10:17:25: 1000000 INFO @ Fri, 05 Jul 2019 10:17:31: 2000000 INFO @ Fri, 05 Jul 2019 10:17:32: 2000000 INFO @ Fri, 05 Jul 2019 10:17:33: 2000000 INFO @ Fri, 05 Jul 2019 10:17:38: 3000000 INFO @ Fri, 05 Jul 2019 10:17:39: 3000000 INFO @ Fri, 05 Jul 2019 10:17:42: 3000000 INFO @ Fri, 05 Jul 2019 10:17:46: 4000000 INFO @ Fri, 05 Jul 2019 10:17:47: 4000000 INFO @ Fri, 05 Jul 2019 10:17:50: 4000000 INFO @ Fri, 05 Jul 2019 10:17:54: 5000000 INFO @ Fri, 05 Jul 2019 10:17:54: 5000000 INFO @ Fri, 05 Jul 2019 10:17:58: 5000000 INFO @ Fri, 05 Jul 2019 10:18:01: 6000000 INFO @ Fri, 05 Jul 2019 10:18:01: 6000000 INFO @ Fri, 05 Jul 2019 10:18:06: 6000000 INFO @ Fri, 05 Jul 2019 10:18:07: 7000000 INFO @ Fri, 05 Jul 2019 10:18:08: 7000000 INFO @ Fri, 05 Jul 2019 10:18:14: 7000000 INFO @ Fri, 05 Jul 2019 10:18:14: 8000000 INFO @ Fri, 05 Jul 2019 10:18:16: 8000000 INFO @ Fri, 05 Jul 2019 10:18:21: 9000000 INFO @ Fri, 05 Jul 2019 10:18:22: 8000000 INFO @ Fri, 05 Jul 2019 10:18:24: 9000000 INFO @ Fri, 05 Jul 2019 10:18:28: 10000000 INFO @ Fri, 05 Jul 2019 10:18:31: 9000000 INFO @ Fri, 05 Jul 2019 10:18:32: 10000000 INFO @ Fri, 05 Jul 2019 10:18:35: 11000000 INFO @ Fri, 05 Jul 2019 10:18:39: 10000000 INFO @ Fri, 05 Jul 2019 10:18:40: 11000000 INFO @ Fri, 05 Jul 2019 10:18:42: 12000000 INFO @ Fri, 05 Jul 2019 10:18:47: 12000000 INFO @ Fri, 05 Jul 2019 10:18:47: 11000000 INFO @ Fri, 05 Jul 2019 10:18:49: 13000000 INFO @ Fri, 05 Jul 2019 10:18:55: 13000000 INFO @ Fri, 05 Jul 2019 10:18:56: 12000000 INFO @ Fri, 05 Jul 2019 10:18:56: 14000000 INFO @ Fri, 05 Jul 2019 10:19:03: 14000000 INFO @ Fri, 05 Jul 2019 10:19:03: 15000000 INFO @ Fri, 05 Jul 2019 10:19:04: 13000000 INFO @ Fri, 05 Jul 2019 10:19:10: 16000000 INFO @ Fri, 05 Jul 2019 10:19:10: 15000000 INFO @ Fri, 05 Jul 2019 10:19:12: 14000000 INFO @ Fri, 05 Jul 2019 10:19:16: 17000000 INFO @ Fri, 05 Jul 2019 10:19:18: 16000000 INFO @ Fri, 05 Jul 2019 10:19:21: 15000000 INFO @ Fri, 05 Jul 2019 10:19:23: 18000000 INFO @ Fri, 05 Jul 2019 10:19:25: 17000000 INFO @ Fri, 05 Jul 2019 10:19:29: 16000000 INFO @ Fri, 05 Jul 2019 10:19:30: 19000000 INFO @ Fri, 05 Jul 2019 10:19:33: 18000000 INFO @ Fri, 05 Jul 2019 10:19:37: 20000000 INFO @ Fri, 05 Jul 2019 10:19:38: 17000000 INFO @ Fri, 05 Jul 2019 10:19:40: 19000000 INFO @ Fri, 05 Jul 2019 10:19:43: 21000000 INFO @ Fri, 05 Jul 2019 10:19:47: 18000000 INFO @ Fri, 05 Jul 2019 10:19:47: 20000000 INFO @ Fri, 05 Jul 2019 10:19:50: 22000000 INFO @ Fri, 05 Jul 2019 10:19:55: 21000000 INFO @ Fri, 05 Jul 2019 10:19:55: 19000000 INFO @ Fri, 05 Jul 2019 10:19:56: 23000000 INFO @ Fri, 05 Jul 2019 10:20:02: 22000000 INFO @ Fri, 05 Jul 2019 10:20:03: 24000000 INFO @ Fri, 05 Jul 2019 10:20:04: 20000000 INFO @ Fri, 05 Jul 2019 10:20:09: 23000000 INFO @ Fri, 05 Jul 2019 10:20:09: 25000000 INFO @ Fri, 05 Jul 2019 10:20:12: 21000000 INFO @ Fri, 05 Jul 2019 10:20:16: 26000000 INFO @ Fri, 05 Jul 2019 10:20:16: 24000000 INFO @ Fri, 05 Jul 2019 10:20:20: 22000000 INFO @ Fri, 05 Jul 2019 10:20:23: 27000000 INFO @ Fri, 05 Jul 2019 10:20:23: 25000000 INFO @ Fri, 05 Jul 2019 10:20:28: 23000000 INFO @ Fri, 05 Jul 2019 10:20:29: 28000000 INFO @ Fri, 05 Jul 2019 10:20:31: 26000000 INFO @ Fri, 05 Jul 2019 10:20:36: 29000000 INFO @ Fri, 05 Jul 2019 10:20:36: 24000000 INFO @ Fri, 05 Jul 2019 10:20:38: 27000000 INFO @ Fri, 05 Jul 2019 10:20:43: 30000000 INFO @ Fri, 05 Jul 2019 10:20:45: 25000000 INFO @ Fri, 05 Jul 2019 10:20:45: 28000000 INFO @ Fri, 05 Jul 2019 10:20:49: 31000000 INFO @ Fri, 05 Jul 2019 10:20:52: 29000000 INFO @ Fri, 05 Jul 2019 10:20:53: 26000000 INFO @ Fri, 05 Jul 2019 10:20:57: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:20:57: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:20:57: #1 total tags in treatment: 31922479 INFO @ Fri, 05 Jul 2019 10:20:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:20:57: #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 10:20:57: #1 tags after filtering in treatment: 31922381 INFO @ Fri, 05 Jul 2019 10:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:20:57: #1 finished! INFO @ Fri, 05 Jul 2019 10:20:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:21:00: 30000000 INFO @ Fri, 05 Jul 2019 10:21:01: 27000000 INFO @ Fri, 05 Jul 2019 10:21:03: #2 number of paired peaks: 53807 INFO @ Fri, 05 Jul 2019 10:21:03: start model_add_line... INFO @ Fri, 05 Jul 2019 10:21:04: start X-correlation... INFO @ Fri, 05 Jul 2019 10:21:04: end of X-cor INFO @ Fri, 05 Jul 2019 10:21:04: #2 finished! INFO @ Fri, 05 Jul 2019 10:21:04: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 10:21:04: #2 alternative fragment length(s) may be 1,129,290,504 bps INFO @ Fri, 05 Jul 2019 10:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.10_model.r INFO @ Fri, 05 Jul 2019 10:21:07: 31000000 INFO @ Fri, 05 Jul 2019 10:21:09: 28000000 INFO @ Fri, 05 Jul 2019 10:21:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:21:14: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:21:14: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:21:14: #1 total tags in treatment: 31922479 INFO @ Fri, 05 Jul 2019 10:21:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:21:14: #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 10:21:15: #1 tags after filtering in treatment: 31922381 INFO @ Fri, 05 Jul 2019 10:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:21:15: #1 finished! INFO @ Fri, 05 Jul 2019 10:21:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:21:17: 29000000 INFO @ Fri, 05 Jul 2019 10:21:21: #2 number of paired peaks: 53807 INFO @ Fri, 05 Jul 2019 10:21:21: start model_add_line... INFO @ Fri, 05 Jul 2019 10:21:21: start X-correlation... INFO @ Fri, 05 Jul 2019 10:21:21: end of X-cor INFO @ Fri, 05 Jul 2019 10:21:21: #2 finished! INFO @ Fri, 05 Jul 2019 10:21:21: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 10:21:21: #2 alternative fragment length(s) may be 1,129,290,504 bps INFO @ Fri, 05 Jul 2019 10:21:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.05_model.r INFO @ Fri, 05 Jul 2019 10:21:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:21:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:21:25: 30000000 INFO @ Fri, 05 Jul 2019 10:21:33: 31000000 INFO @ Fri, 05 Jul 2019 10:21:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:21:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:21:40: #1 total tags in treatment: 31922479 INFO @ Fri, 05 Jul 2019 10:21:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:21:40: #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 10:21:41: #1 tags after filtering in treatment: 31922381 INFO @ Fri, 05 Jul 2019 10:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:21:41: #1 finished! INFO @ Fri, 05 Jul 2019 10:21:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:21:47: #2 number of paired peaks: 53807 INFO @ Fri, 05 Jul 2019 10:21:47: start model_add_line... INFO @ Fri, 05 Jul 2019 10:21:47: start X-correlation... INFO @ Fri, 05 Jul 2019 10:21:47: end of X-cor INFO @ Fri, 05 Jul 2019 10:21:47: #2 finished! INFO @ Fri, 05 Jul 2019 10:21:47: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 10:21:47: #2 alternative fragment length(s) may be 1,129,290,504 bps INFO @ Fri, 05 Jul 2019 10:21:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.20_model.r INFO @ Fri, 05 Jul 2019 10:21:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:22:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:23:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:23:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.10_summits.bed INFO @ Fri, 05 Jul 2019 10:24:01: Done! pass1 - making usageList (44 chroms): 4 millis pass2 - checking and writing primary data (1107 records, 4 fields): 3090 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:24:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:24:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.05_summits.bed INFO @ Fri, 05 Jul 2019 10:24:36: Done! INFO @ Fri, 05 Jul 2019 10:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.20_peaks.xls pass1 - making usageList (65 chroms): 3 millis INFO @ Fri, 05 Jul 2019 10:24:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:24:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102027/ERX102027.20_summits.bed pass2 - checking and writing primary data (5168 records, 4 fields): 59 millis INFO @ Fri, 05 Jul 2019 10:24:47: Done! CompletedMACS2peakCalling pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。