Job ID = 2002127 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,363,226 reads read : 31,363,226 reads written : 31,363,226 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: 00:12:06 31363226 reads; of these: 31363226 (100.00%) were unpaired; of these: 690087 (2.20%) aligned 0 times 23455286 (74.79%) aligned exactly 1 time 7217853 (23.01%) aligned >1 times 97.80% overall alignment rate Time searching: 00:12:07 Overall time: 00:12:07 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] 2290236 / 30673139 = 0.0747 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 10:21:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.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 10:21:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:21:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:21:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.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 10:21:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:21:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:21:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.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 10:21:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:21:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:21:47: 1000000 INFO @ Fri, 05 Jul 2019 10:21:50: 1000000 INFO @ Fri, 05 Jul 2019 10:21:50: 1000000 INFO @ Fri, 05 Jul 2019 10:21:54: 2000000 INFO @ Fri, 05 Jul 2019 10:21:59: 2000000 INFO @ Fri, 05 Jul 2019 10:21:59: 2000000 INFO @ Fri, 05 Jul 2019 10:22:01: 3000000 INFO @ Fri, 05 Jul 2019 10:22:07: 3000000 INFO @ Fri, 05 Jul 2019 10:22:08: 3000000 INFO @ Fri, 05 Jul 2019 10:22:09: 4000000 INFO @ Fri, 05 Jul 2019 10:22:15: 4000000 INFO @ Fri, 05 Jul 2019 10:22:16: 5000000 INFO @ Fri, 05 Jul 2019 10:22:17: 4000000 INFO @ Fri, 05 Jul 2019 10:22:22: 5000000 INFO @ Fri, 05 Jul 2019 10:22:23: 6000000 INFO @ Fri, 05 Jul 2019 10:22:26: 5000000 INFO @ Fri, 05 Jul 2019 10:22:30: 7000000 INFO @ Fri, 05 Jul 2019 10:22:30: 6000000 INFO @ Fri, 05 Jul 2019 10:22:33: 6000000 INFO @ Fri, 05 Jul 2019 10:22:37: 8000000 INFO @ Fri, 05 Jul 2019 10:22:38: 7000000 INFO @ Fri, 05 Jul 2019 10:22:42: 7000000 INFO @ Fri, 05 Jul 2019 10:22:44: 9000000 INFO @ Fri, 05 Jul 2019 10:22:46: 8000000 INFO @ Fri, 05 Jul 2019 10:22:51: 10000000 INFO @ Fri, 05 Jul 2019 10:22:52: 8000000 INFO @ Fri, 05 Jul 2019 10:22:55: 9000000 INFO @ Fri, 05 Jul 2019 10:22:58: 11000000 INFO @ Fri, 05 Jul 2019 10:23:01: 9000000 INFO @ Fri, 05 Jul 2019 10:23:02: 10000000 INFO @ Fri, 05 Jul 2019 10:23:05: 12000000 INFO @ Fri, 05 Jul 2019 10:23:10: 11000000 INFO @ Fri, 05 Jul 2019 10:23:12: 10000000 INFO @ Fri, 05 Jul 2019 10:23:12: 13000000 INFO @ Fri, 05 Jul 2019 10:23:18: 12000000 INFO @ Fri, 05 Jul 2019 10:23:19: 14000000 INFO @ Fri, 05 Jul 2019 10:23:21: 11000000 INFO @ Fri, 05 Jul 2019 10:23:26: 13000000 INFO @ Fri, 05 Jul 2019 10:23:26: 15000000 INFO @ Fri, 05 Jul 2019 10:23:30: 12000000 INFO @ Fri, 05 Jul 2019 10:23:33: 16000000 INFO @ Fri, 05 Jul 2019 10:23:34: 14000000 INFO @ Fri, 05 Jul 2019 10:23:39: 13000000 INFO @ Fri, 05 Jul 2019 10:23:41: 17000000 INFO @ Fri, 05 Jul 2019 10:23:41: 15000000 INFO @ Fri, 05 Jul 2019 10:23:48: 18000000 INFO @ Fri, 05 Jul 2019 10:23:49: 14000000 INFO @ Fri, 05 Jul 2019 10:23:49: 16000000 INFO @ Fri, 05 Jul 2019 10:23:55: 19000000 INFO @ Fri, 05 Jul 2019 10:23:57: 17000000 INFO @ Fri, 05 Jul 2019 10:23:58: 15000000 INFO @ Fri, 05 Jul 2019 10:24:02: 20000000 INFO @ Fri, 05 Jul 2019 10:24:05: 18000000 INFO @ Fri, 05 Jul 2019 10:24:07: 16000000 INFO @ Fri, 05 Jul 2019 10:24:09: 21000000 INFO @ Fri, 05 Jul 2019 10:24:12: 19000000 INFO @ Fri, 05 Jul 2019 10:24:16: 22000000 INFO @ Fri, 05 Jul 2019 10:24:16: 17000000 INFO @ Fri, 05 Jul 2019 10:24:20: 20000000 INFO @ Fri, 05 Jul 2019 10:24:23: 23000000 INFO @ Fri, 05 Jul 2019 10:24:25: 18000000 INFO @ Fri, 05 Jul 2019 10:24:28: 21000000 INFO @ Fri, 05 Jul 2019 10:24:30: 24000000 INFO @ Fri, 05 Jul 2019 10:24:34: 19000000 INFO @ Fri, 05 Jul 2019 10:24:36: 22000000 INFO @ Fri, 05 Jul 2019 10:24:37: 25000000 INFO @ Fri, 05 Jul 2019 10:24:43: 20000000 INFO @ Fri, 05 Jul 2019 10:24:43: 23000000 INFO @ Fri, 05 Jul 2019 10:24:44: 26000000 INFO @ Fri, 05 Jul 2019 10:24:51: 24000000 INFO @ Fri, 05 Jul 2019 10:24:51: 27000000 INFO @ Fri, 05 Jul 2019 10:24:52: 21000000 INFO @ Fri, 05 Jul 2019 10:24:59: 25000000 INFO @ Fri, 05 Jul 2019 10:24:59: 28000000 INFO @ Fri, 05 Jul 2019 10:25:01: 22000000 INFO @ Fri, 05 Jul 2019 10:25:02: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:25:02: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:25:02: #1 total tags in treatment: 28382903 INFO @ Fri, 05 Jul 2019 10:25:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:25:02: #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 10:25:02: #1 tags after filtering in treatment: 28382774 INFO @ Fri, 05 Jul 2019 10:25:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:25:02: #1 finished! INFO @ Fri, 05 Jul 2019 10:25:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:25:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:25:07: 26000000 INFO @ Fri, 05 Jul 2019 10:25:08: #2 number of paired peaks: 57217 INFO @ Fri, 05 Jul 2019 10:25:08: start model_add_line... INFO @ Fri, 05 Jul 2019 10:25:08: start X-correlation... INFO @ Fri, 05 Jul 2019 10:25:08: end of X-cor INFO @ Fri, 05 Jul 2019 10:25:08: #2 finished! INFO @ Fri, 05 Jul 2019 10:25:08: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:25:08: #2 alternative fragment length(s) may be 135,297,510 bps INFO @ Fri, 05 Jul 2019 10:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.05_model.r INFO @ Fri, 05 Jul 2019 10:25:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:25:10: 23000000 INFO @ Fri, 05 Jul 2019 10:25:15: 27000000 INFO @ Fri, 05 Jul 2019 10:25:19: 24000000 INFO @ Fri, 05 Jul 2019 10:25:23: 28000000 INFO @ Fri, 05 Jul 2019 10:25:26: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:25:26: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:25:26: #1 total tags in treatment: 28382903 INFO @ Fri, 05 Jul 2019 10:25:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:25:26: #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 10:25:27: #1 tags after filtering in treatment: 28382774 INFO @ Fri, 05 Jul 2019 10:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:25:27: #1 finished! INFO @ Fri, 05 Jul 2019 10:25:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:25:28: 25000000 INFO @ Fri, 05 Jul 2019 10:25:32: #2 number of paired peaks: 57217 INFO @ Fri, 05 Jul 2019 10:25:32: start model_add_line... INFO @ Fri, 05 Jul 2019 10:25:33: start X-correlation... INFO @ Fri, 05 Jul 2019 10:25:33: end of X-cor INFO @ Fri, 05 Jul 2019 10:25:33: #2 finished! INFO @ Fri, 05 Jul 2019 10:25:33: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:25:33: #2 alternative fragment length(s) may be 135,297,510 bps INFO @ Fri, 05 Jul 2019 10:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.20_model.r INFO @ Fri, 05 Jul 2019 10:25:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:25:37: 26000000 INFO @ Fri, 05 Jul 2019 10:25:46: 27000000 INFO @ Fri, 05 Jul 2019 10:25:55: 28000000 INFO @ Fri, 05 Jul 2019 10:25:58: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:25:58: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:25:58: #1 total tags in treatment: 28382903 INFO @ Fri, 05 Jul 2019 10:25:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:25:58: #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 10:25:59: #1 tags after filtering in treatment: 28382774 INFO @ Fri, 05 Jul 2019 10:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:25:59: #1 finished! INFO @ Fri, 05 Jul 2019 10:25:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:26:04: #2 number of paired peaks: 57217 INFO @ Fri, 05 Jul 2019 10:26:04: start model_add_line... INFO @ Fri, 05 Jul 2019 10:26:05: start X-correlation... INFO @ Fri, 05 Jul 2019 10:26:05: end of X-cor INFO @ Fri, 05 Jul 2019 10:26:05: #2 finished! INFO @ Fri, 05 Jul 2019 10:26:05: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:26:05: #2 alternative fragment length(s) may be 135,297,510 bps INFO @ Fri, 05 Jul 2019 10:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.10_model.r INFO @ Fri, 05 Jul 2019 10:26:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:26:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:26:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:27:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:27:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:27:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:27:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.05_summits.bed INFO @ Fri, 05 Jul 2019 10:27:24: Done! pass1 - making usageList (78 chroms): 2 millis pass2 - checking and writing primary data (5786 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:27:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.20_summits.bed INFO @ Fri, 05 Jul 2019 10:27:49: Done! pass1 - making usageList (29 chroms): 2 millis pass2 - checking and writing primary data (141 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:28:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102029/ERX102029.10_summits.bed INFO @ Fri, 05 Jul 2019 10:28:22: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1258 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。