Job ID = 2001161 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,256,240 reads read : 30,256,240 reads written : 30,256,240 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: 00:00:00 Multiseed full-index search: 00:12:28 30256240 reads; of these: 30256240 (100.00%) were unpaired; of these: 636165 (2.10%) aligned 0 times 22378845 (73.96%) aligned exactly 1 time 7241230 (23.93%) aligned >1 times 97.90% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 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] 1720581 / 29620075 = 0.0581 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 04:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.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 04:27:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:27:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.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 04:27:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:27:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:27:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.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 04:27:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:27:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:27:29: 1000000 INFO @ Fri, 05 Jul 2019 04:27:30: 1000000 INFO @ Fri, 05 Jul 2019 04:27:30: 1000000 INFO @ Fri, 05 Jul 2019 04:27:39: 2000000 INFO @ Fri, 05 Jul 2019 04:27:39: 2000000 INFO @ Fri, 05 Jul 2019 04:27:40: 2000000 INFO @ Fri, 05 Jul 2019 04:27:48: 3000000 INFO @ Fri, 05 Jul 2019 04:27:49: 3000000 INFO @ Fri, 05 Jul 2019 04:27:50: 3000000 INFO @ Fri, 05 Jul 2019 04:27:58: 4000000 INFO @ Fri, 05 Jul 2019 04:27:58: 4000000 INFO @ Fri, 05 Jul 2019 04:28:00: 4000000 INFO @ Fri, 05 Jul 2019 04:28:07: 5000000 INFO @ Fri, 05 Jul 2019 04:28:08: 5000000 INFO @ Fri, 05 Jul 2019 04:28:09: 5000000 INFO @ Fri, 05 Jul 2019 04:28:16: 6000000 INFO @ Fri, 05 Jul 2019 04:28:17: 6000000 INFO @ Fri, 05 Jul 2019 04:28:18: 6000000 INFO @ Fri, 05 Jul 2019 04:28:25: 7000000 INFO @ Fri, 05 Jul 2019 04:28:26: 7000000 INFO @ Fri, 05 Jul 2019 04:28:27: 7000000 INFO @ Fri, 05 Jul 2019 04:28:35: 8000000 INFO @ Fri, 05 Jul 2019 04:28:36: 8000000 INFO @ Fri, 05 Jul 2019 04:28:36: 8000000 INFO @ Fri, 05 Jul 2019 04:28:44: 9000000 INFO @ Fri, 05 Jul 2019 04:28:46: 9000000 INFO @ Fri, 05 Jul 2019 04:28:46: 9000000 INFO @ Fri, 05 Jul 2019 04:28:54: 10000000 INFO @ Fri, 05 Jul 2019 04:28:56: 10000000 INFO @ Fri, 05 Jul 2019 04:28:56: 10000000 INFO @ Fri, 05 Jul 2019 04:29:03: 11000000 INFO @ Fri, 05 Jul 2019 04:29:05: 11000000 INFO @ Fri, 05 Jul 2019 04:29:06: 11000000 INFO @ Fri, 05 Jul 2019 04:29:13: 12000000 INFO @ Fri, 05 Jul 2019 04:29:15: 12000000 INFO @ Fri, 05 Jul 2019 04:29:16: 12000000 INFO @ Fri, 05 Jul 2019 04:29:22: 13000000 INFO @ Fri, 05 Jul 2019 04:29:25: 13000000 INFO @ Fri, 05 Jul 2019 04:29:26: 13000000 INFO @ Fri, 05 Jul 2019 04:29:32: 14000000 INFO @ Fri, 05 Jul 2019 04:29:35: 14000000 INFO @ Fri, 05 Jul 2019 04:29:36: 14000000 INFO @ Fri, 05 Jul 2019 04:29:41: 15000000 INFO @ Fri, 05 Jul 2019 04:29:44: 15000000 INFO @ Fri, 05 Jul 2019 04:29:45: 15000000 INFO @ Fri, 05 Jul 2019 04:29:50: 16000000 INFO @ Fri, 05 Jul 2019 04:29:53: 16000000 INFO @ Fri, 05 Jul 2019 04:29:54: 16000000 INFO @ Fri, 05 Jul 2019 04:29:59: 17000000 INFO @ Fri, 05 Jul 2019 04:30:03: 17000000 INFO @ Fri, 05 Jul 2019 04:30:03: 17000000 INFO @ Fri, 05 Jul 2019 04:30:09: 18000000 INFO @ Fri, 05 Jul 2019 04:30:12: 18000000 INFO @ Fri, 05 Jul 2019 04:30:13: 18000000 INFO @ Fri, 05 Jul 2019 04:30:18: 19000000 INFO @ Fri, 05 Jul 2019 04:30:21: 19000000 INFO @ Fri, 05 Jul 2019 04:30:21: 19000000 INFO @ Fri, 05 Jul 2019 04:30:28: 20000000 INFO @ Fri, 05 Jul 2019 04:30:31: 20000000 INFO @ Fri, 05 Jul 2019 04:30:31: 20000000 INFO @ Fri, 05 Jul 2019 04:30:37: 21000000 INFO @ Fri, 05 Jul 2019 04:30:40: 21000000 INFO @ Fri, 05 Jul 2019 04:30:40: 21000000 INFO @ Fri, 05 Jul 2019 04:30:46: 22000000 INFO @ Fri, 05 Jul 2019 04:30:49: 22000000 INFO @ Fri, 05 Jul 2019 04:30:50: 22000000 INFO @ Fri, 05 Jul 2019 04:30:56: 23000000 INFO @ Fri, 05 Jul 2019 04:30:59: 23000000 INFO @ Fri, 05 Jul 2019 04:30:59: 23000000 INFO @ Fri, 05 Jul 2019 04:31:05: 24000000 INFO @ Fri, 05 Jul 2019 04:31:08: 24000000 INFO @ Fri, 05 Jul 2019 04:31:09: 24000000 INFO @ Fri, 05 Jul 2019 04:31:15: 25000000 INFO @ Fri, 05 Jul 2019 04:31:18: 25000000 INFO @ Fri, 05 Jul 2019 04:31:18: 25000000 INFO @ Fri, 05 Jul 2019 04:31:25: 26000000 INFO @ Fri, 05 Jul 2019 04:31:28: 26000000 INFO @ Fri, 05 Jul 2019 04:31:28: 26000000 INFO @ Fri, 05 Jul 2019 04:31:35: 27000000 INFO @ Fri, 05 Jul 2019 04:31:38: 27000000 INFO @ Fri, 05 Jul 2019 04:31:39: 27000000 INFO @ Fri, 05 Jul 2019 04:31:44: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:31:44: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:31:44: #1 total tags in treatment: 27899494 INFO @ Fri, 05 Jul 2019 04:31:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:31:44: #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 04:31:45: #1 tags after filtering in treatment: 27899356 INFO @ Fri, 05 Jul 2019 04:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:31:45: #1 finished! INFO @ Fri, 05 Jul 2019 04:31:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:31:46: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:31:46: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:31:46: #1 total tags in treatment: 27899494 INFO @ Fri, 05 Jul 2019 04:31:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:31:46: #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 04:31:47: #1 tags after filtering in treatment: 27899356 INFO @ Fri, 05 Jul 2019 04:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:31:47: #1 finished! INFO @ Fri, 05 Jul 2019 04:31:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:31:48: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:31:48: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:31:48: #1 total tags in treatment: 27899494 INFO @ Fri, 05 Jul 2019 04:31:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:31:48: #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 04:31:49: #1 tags after filtering in treatment: 27899356 INFO @ Fri, 05 Jul 2019 04:31:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:31:49: #1 finished! INFO @ Fri, 05 Jul 2019 04:31:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:31:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:31:50: #2 number of paired peaks: 47026 INFO @ Fri, 05 Jul 2019 04:31:50: start model_add_line... INFO @ Fri, 05 Jul 2019 04:31:50: start X-correlation... INFO @ Fri, 05 Jul 2019 04:31:50: end of X-cor INFO @ Fri, 05 Jul 2019 04:31:50: #2 finished! INFO @ Fri, 05 Jul 2019 04:31:50: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 04:31:50: #2 alternative fragment length(s) may be 2,136,500 bps INFO @ Fri, 05 Jul 2019 04:31:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.05_model.r INFO @ Fri, 05 Jul 2019 04:31:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:31:52: #2 number of paired peaks: 47026 INFO @ Fri, 05 Jul 2019 04:31:52: start model_add_line... INFO @ Fri, 05 Jul 2019 04:31:53: start X-correlation... INFO @ Fri, 05 Jul 2019 04:31:53: end of X-cor INFO @ Fri, 05 Jul 2019 04:31:53: #2 finished! INFO @ Fri, 05 Jul 2019 04:31:53: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 04:31:53: #2 alternative fragment length(s) may be 2,136,500 bps INFO @ Fri, 05 Jul 2019 04:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.20_model.r INFO @ Fri, 05 Jul 2019 04:31:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:31:54: #2 number of paired peaks: 47026 INFO @ Fri, 05 Jul 2019 04:31:54: start model_add_line... INFO @ Fri, 05 Jul 2019 04:31:54: start X-correlation... INFO @ Fri, 05 Jul 2019 04:31:54: end of X-cor INFO @ Fri, 05 Jul 2019 04:31:54: #2 finished! INFO @ Fri, 05 Jul 2019 04:31:54: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 04:31:54: #2 alternative fragment length(s) may be 2,136,500 bps INFO @ Fri, 05 Jul 2019 04:31:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.10_model.r INFO @ Fri, 05 Jul 2019 04:31:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:31:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:33:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:33:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:33:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:34:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:34:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:34:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.05_summits.bed INFO @ Fri, 05 Jul 2019 04:34:11: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (3285 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.20_summits.bed INFO @ Fri, 05 Jul 2019 04:34:12: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:34:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:34:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:34:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101851/ERX101851.10_summits.bed INFO @ Fri, 05 Jul 2019 04:34:18: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (725 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。