Job ID = 2640706 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,740,074 reads read : 29,480,148 reads written : 14,740,074 reads 0-length : 14,740,074 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: 00:00:01 Multiseed full-index search: 00:10:26 14740074 reads; of these: 14740074 (100.00%) were unpaired; of these: 299459 (2.03%) aligned 0 times 11914909 (80.83%) aligned exactly 1 time 2525706 (17.13%) aligned >1 times 97.97% overall alignment rate Time searching: 00:10:29 Overall time: 00:10:29 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] 818092 / 14440615 = 0.0567 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:39:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.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 @ Sat, 24 Aug 2019 18:39:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:39:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:39:10: 1000000 INFO @ Sat, 24 Aug 2019 18:39:18: 2000000 INFO @ Sat, 24 Aug 2019 18:39:26: 3000000 INFO @ Sat, 24 Aug 2019 18:39:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.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 @ Sat, 24 Aug 2019 18:39:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:39:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:39:34: 4000000 INFO @ Sat, 24 Aug 2019 18:39:40: 1000000 INFO @ Sat, 24 Aug 2019 18:39:42: 5000000 INFO @ Sat, 24 Aug 2019 18:39:49: 2000000 INFO @ Sat, 24 Aug 2019 18:39:49: 6000000 INFO @ Sat, 24 Aug 2019 18:39:57: 7000000 INFO @ Sat, 24 Aug 2019 18:39:57: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:40:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.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 @ Sat, 24 Aug 2019 18:40:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:40:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:40:04: 8000000 INFO @ Sat, 24 Aug 2019 18:40:06: 4000000 INFO @ Sat, 24 Aug 2019 18:40:10: 1000000 INFO @ Sat, 24 Aug 2019 18:40:11: 9000000 INFO @ Sat, 24 Aug 2019 18:40:15: 5000000 INFO @ Sat, 24 Aug 2019 18:40:18: 10000000 INFO @ Sat, 24 Aug 2019 18:40:20: 2000000 INFO @ Sat, 24 Aug 2019 18:40:24: 6000000 INFO @ Sat, 24 Aug 2019 18:40:25: 11000000 INFO @ Sat, 24 Aug 2019 18:40:29: 3000000 INFO @ Sat, 24 Aug 2019 18:40:32: 12000000 INFO @ Sat, 24 Aug 2019 18:40:34: 7000000 INFO @ Sat, 24 Aug 2019 18:40:38: 4000000 INFO @ Sat, 24 Aug 2019 18:40:39: 13000000 INFO @ Sat, 24 Aug 2019 18:40:43: 8000000 INFO @ Sat, 24 Aug 2019 18:40:43: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:40:43: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:40:43: #1 total tags in treatment: 13622523 INFO @ Sat, 24 Aug 2019 18:40:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:40:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:40:44: #1 tags after filtering in treatment: 13622294 INFO @ Sat, 24 Aug 2019 18:40:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:40:44: #1 finished! INFO @ Sat, 24 Aug 2019 18:40:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:40:47: 5000000 INFO @ Sat, 24 Aug 2019 18:40:48: #2 number of paired peaks: 74384 INFO @ Sat, 24 Aug 2019 18:40:48: start model_add_line... INFO @ Sat, 24 Aug 2019 18:40:48: start X-correlation... INFO @ Sat, 24 Aug 2019 18:40:48: end of X-cor INFO @ Sat, 24 Aug 2019 18:40:48: #2 finished! INFO @ Sat, 24 Aug 2019 18:40:48: #2 predicted fragment length is 174 bps INFO @ Sat, 24 Aug 2019 18:40:48: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 24 Aug 2019 18:40:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.05_model.r INFO @ Sat, 24 Aug 2019 18:40:48: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:40:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:40:52: 9000000 INFO @ Sat, 24 Aug 2019 18:40:56: 6000000 INFO @ Sat, 24 Aug 2019 18:41:00: 10000000 INFO @ Sat, 24 Aug 2019 18:41:05: 7000000 INFO @ Sat, 24 Aug 2019 18:41:09: 11000000 INFO @ Sat, 24 Aug 2019 18:41:14: 8000000 INFO @ Sat, 24 Aug 2019 18:41:19: 12000000 INFO @ Sat, 24 Aug 2019 18:41:23: 9000000 INFO @ Sat, 24 Aug 2019 18:41:28: 13000000 INFO @ Sat, 24 Aug 2019 18:41:32: 10000000 INFO @ Sat, 24 Aug 2019 18:41:33: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:41:33: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:41:33: #1 total tags in treatment: 13622523 INFO @ Sat, 24 Aug 2019 18:41:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:41:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:41:33: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:41:34: #1 tags after filtering in treatment: 13622294 INFO @ Sat, 24 Aug 2019 18:41:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:41:34: #1 finished! INFO @ Sat, 24 Aug 2019 18:41:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:41:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:41:38: #2 number of paired peaks: 74384 INFO @ Sat, 24 Aug 2019 18:41:38: start model_add_line... INFO @ Sat, 24 Aug 2019 18:41:38: start X-correlation... INFO @ Sat, 24 Aug 2019 18:41:38: end of X-cor INFO @ Sat, 24 Aug 2019 18:41:38: #2 finished! INFO @ Sat, 24 Aug 2019 18:41:38: #2 predicted fragment length is 174 bps INFO @ Sat, 24 Aug 2019 18:41:38: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 24 Aug 2019 18:41:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.10_model.r INFO @ Sat, 24 Aug 2019 18:41:38: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:41:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:41:41: 11000000 INFO @ Sat, 24 Aug 2019 18:41:49: 12000000 INFO @ Sat, 24 Aug 2019 18:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:41:58: 13000000 INFO @ Sat, 24 Aug 2019 18:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.05_summits.bed INFO @ Sat, 24 Aug 2019 18:41:58: Done! pass1 - making usageList (101 chroms): 8 millis pass2 - checking and writing primary data (30575 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:42:03: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:42:03: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:42:03: #1 total tags in treatment: 13622523 INFO @ Sat, 24 Aug 2019 18:42:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:42:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:42:03: #1 tags after filtering in treatment: 13622294 INFO @ Sat, 24 Aug 2019 18:42:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:42:03: #1 finished! INFO @ Sat, 24 Aug 2019 18:42:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:42:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:42:07: #2 number of paired peaks: 74384 INFO @ Sat, 24 Aug 2019 18:42:07: start model_add_line... INFO @ Sat, 24 Aug 2019 18:42:08: start X-correlation... INFO @ Sat, 24 Aug 2019 18:42:08: end of X-cor INFO @ Sat, 24 Aug 2019 18:42:08: #2 finished! INFO @ Sat, 24 Aug 2019 18:42:08: #2 predicted fragment length is 174 bps INFO @ Sat, 24 Aug 2019 18:42:08: #2 alternative fragment length(s) may be 174 bps INFO @ Sat, 24 Aug 2019 18:42:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.20_model.r INFO @ Sat, 24 Aug 2019 18:42:08: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:42:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:42:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.10_summits.bed INFO @ Sat, 24 Aug 2019 18:42:45: Done! pass1 - making usageList (74 chroms): 7 millis pass2 - checking and writing primary data (17507 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:42:53: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:43:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375063/SRX5375063.20_summits.bed INFO @ Sat, 24 Aug 2019 18:43:17: Done! pass1 - making usageList (42 chroms): 4 millis pass2 - checking and writing primary data (6427 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。