Job ID = 2640574 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,242,314 reads read : 38,484,628 reads written : 19,242,314 reads 0-length : 19,242,314 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:23 19242314 reads; of these: 19242314 (100.00%) were unpaired; of these: 1934655 (10.05%) aligned 0 times 14150794 (73.54%) aligned exactly 1 time 3156865 (16.41%) aligned >1 times 89.95% overall alignment rate Time searching: 00:12:26 Overall time: 00:12:26 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] 2017674 / 17307659 = 0.1166 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.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 18:08:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:08:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:09:04: 1000000 INFO @ Sat, 24 Aug 2019 18:09:11: 2000000 INFO @ Sat, 24 Aug 2019 18:09:19: 3000000 INFO @ Sat, 24 Aug 2019 18:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.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 18:09:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:09:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:09:26: 4000000 INFO @ Sat, 24 Aug 2019 18:09:33: 5000000 INFO @ Sat, 24 Aug 2019 18:09:33: 1000000 INFO @ Sat, 24 Aug 2019 18:09:41: 2000000 INFO @ Sat, 24 Aug 2019 18:09:41: 6000000 INFO @ Sat, 24 Aug 2019 18:09:48: 7000000 INFO @ Sat, 24 Aug 2019 18:09:48: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:09:55: 8000000 INFO @ Sat, 24 Aug 2019 18:09:56: 4000000 INFO @ Sat, 24 Aug 2019 18:09:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.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 18:09:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:09:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:10:02: 9000000 INFO @ Sat, 24 Aug 2019 18:10:03: 5000000 INFO @ Sat, 24 Aug 2019 18:10:06: 1000000 INFO @ Sat, 24 Aug 2019 18:10:10: 10000000 INFO @ Sat, 24 Aug 2019 18:10:10: 6000000 INFO @ Sat, 24 Aug 2019 18:10:15: 2000000 INFO @ Sat, 24 Aug 2019 18:10:17: 7000000 INFO @ Sat, 24 Aug 2019 18:10:18: 11000000 INFO @ Sat, 24 Aug 2019 18:10:24: 3000000 INFO @ Sat, 24 Aug 2019 18:10:25: 8000000 INFO @ Sat, 24 Aug 2019 18:10:25: 12000000 INFO @ Sat, 24 Aug 2019 18:10:32: 4000000 INFO @ Sat, 24 Aug 2019 18:10:32: 9000000 INFO @ Sat, 24 Aug 2019 18:10:33: 13000000 INFO @ Sat, 24 Aug 2019 18:10:40: 10000000 INFO @ Sat, 24 Aug 2019 18:10:40: 5000000 INFO @ Sat, 24 Aug 2019 18:10:41: 14000000 INFO @ Sat, 24 Aug 2019 18:10:49: 6000000 INFO @ Sat, 24 Aug 2019 18:10:49: 15000000 INFO @ Sat, 24 Aug 2019 18:10:49: 11000000 INFO @ Sat, 24 Aug 2019 18:10:51: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:10:51: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:10:51: #1 total tags in treatment: 15289985 INFO @ Sat, 24 Aug 2019 18:10:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:10:51: #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 18:10:52: #1 tags after filtering in treatment: 15289765 INFO @ Sat, 24 Aug 2019 18:10:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:10:52: #1 finished! INFO @ Sat, 24 Aug 2019 18:10:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:10:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:10:56: #2 number of paired peaks: 70667 INFO @ Sat, 24 Aug 2019 18:10:56: start model_add_line... INFO @ Sat, 24 Aug 2019 18:10:57: start X-correlation... INFO @ Sat, 24 Aug 2019 18:10:57: end of X-cor INFO @ Sat, 24 Aug 2019 18:10:57: #2 finished! INFO @ Sat, 24 Aug 2019 18:10:57: #2 predicted fragment length is 168 bps INFO @ Sat, 24 Aug 2019 18:10:57: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 24 Aug 2019 18:10:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.05_model.r INFO @ Sat, 24 Aug 2019 18:10:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:10:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:10:57: 12000000 INFO @ Sat, 24 Aug 2019 18:10:57: 7000000 INFO @ Sat, 24 Aug 2019 18:11:04: 13000000 INFO @ Sat, 24 Aug 2019 18:11:05: 8000000 INFO @ Sat, 24 Aug 2019 18:11:11: 14000000 INFO @ Sat, 24 Aug 2019 18:11:14: 9000000 INFO @ Sat, 24 Aug 2019 18:11:18: 15000000 INFO @ Sat, 24 Aug 2019 18:11:20: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:11:20: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:11:20: #1 total tags in treatment: 15289985 INFO @ Sat, 24 Aug 2019 18:11:20: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:11:20: #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 18:11:21: #1 tags after filtering in treatment: 15289765 INFO @ Sat, 24 Aug 2019 18:11:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:11:21: #1 finished! INFO @ Sat, 24 Aug 2019 18:11:21: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:11:23: 10000000 INFO @ Sat, 24 Aug 2019 18:11:25: #2 number of paired peaks: 70667 INFO @ Sat, 24 Aug 2019 18:11:25: start model_add_line... INFO @ Sat, 24 Aug 2019 18:11:26: start X-correlation... INFO @ Sat, 24 Aug 2019 18:11:26: end of X-cor INFO @ Sat, 24 Aug 2019 18:11:26: #2 finished! INFO @ Sat, 24 Aug 2019 18:11:26: #2 predicted fragment length is 168 bps INFO @ Sat, 24 Aug 2019 18:11:26: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 24 Aug 2019 18:11:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.10_model.r INFO @ Sat, 24 Aug 2019 18:11:26: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:11:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:11:31: 11000000 INFO @ Sat, 24 Aug 2019 18:11:39: 12000000 INFO @ Sat, 24 Aug 2019 18:11:47: 13000000 INFO @ Sat, 24 Aug 2019 18:11:48: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:11:56: 14000000 INFO @ Sat, 24 Aug 2019 18:12:04: 15000000 INFO @ Sat, 24 Aug 2019 18:12:07: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:12:07: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:12:07: #1 total tags in treatment: 15289985 INFO @ Sat, 24 Aug 2019 18:12:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:12:07: #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 18:12:07: #1 tags after filtering in treatment: 15289765 INFO @ Sat, 24 Aug 2019 18:12:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:12:07: #1 finished! INFO @ Sat, 24 Aug 2019 18:12:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:12:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:12:12: #2 number of paired peaks: 70667 INFO @ Sat, 24 Aug 2019 18:12:12: start model_add_line... INFO @ Sat, 24 Aug 2019 18:12:12: start X-correlation... INFO @ Sat, 24 Aug 2019 18:12:12: end of X-cor INFO @ Sat, 24 Aug 2019 18:12:12: #2 finished! INFO @ Sat, 24 Aug 2019 18:12:12: #2 predicted fragment length is 168 bps INFO @ Sat, 24 Aug 2019 18:12:12: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 24 Aug 2019 18:12:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.20_model.r INFO @ Sat, 24 Aug 2019 18:12:12: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:12:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.05_summits.bed INFO @ Sat, 24 Aug 2019 18:12:15: Done! pass1 - making usageList (104 chroms): 10 millis pass2 - checking and writing primary data (20760 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:12:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:12:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:12:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.10_summits.bed INFO @ Sat, 24 Aug 2019 18:12:43: Done! pass1 - making usageList (79 chroms): 7 millis pass2 - checking and writing primary data (15043 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:13:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:13:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:13:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:13:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375018/SRX5375018.20_summits.bed INFO @ Sat, 24 Aug 2019 18:13:29: Done! pass1 - making usageList (52 chroms): 6 millis pass2 - checking and writing primary data (8744 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。