Job ID = 2640711 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,961,675 reads read : 43,923,350 reads written : 21,961,675 reads 0-length : 21,961,675 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: 00:00:01 Multiseed full-index search: 00:15:05 21961675 reads; of these: 21961675 (100.00%) were unpaired; of these: 432180 (1.97%) aligned 0 times 17767495 (80.90%) aligned exactly 1 time 3762000 (17.13%) aligned >1 times 98.03% overall alignment rate Time searching: 00:15:07 Overall time: 00:15:07 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 12 files... [bam_rmdupse_core] 2164019 / 21529495 = 0.1005 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.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 18:49:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:49:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:50:06: 1000000 INFO @ Sat, 24 Aug 2019 18:50:13: 2000000 INFO @ Sat, 24 Aug 2019 18:50:20: 3000000 INFO @ Sat, 24 Aug 2019 18:50:28: 4000000 INFO @ Sat, 24 Aug 2019 18:50:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.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 18:50:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:50:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:50:35: 1000000 INFO @ Sat, 24 Aug 2019 18:50:35: 5000000 INFO @ Sat, 24 Aug 2019 18:50:42: 2000000 INFO @ Sat, 24 Aug 2019 18:50:43: 6000000 INFO @ Sat, 24 Aug 2019 18:50:48: 3000000 INFO @ Sat, 24 Aug 2019 18:50:50: 7000000 INFO @ Sat, 24 Aug 2019 18:50:55: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:50:57: 8000000 INFO @ Sat, 24 Aug 2019 18:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.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 18:50:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:50:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:51:02: 5000000 INFO @ Sat, 24 Aug 2019 18:51:05: 9000000 INFO @ Sat, 24 Aug 2019 18:51:06: 1000000 INFO @ Sat, 24 Aug 2019 18:51:09: 6000000 INFO @ Sat, 24 Aug 2019 18:51:12: 10000000 INFO @ Sat, 24 Aug 2019 18:51:13: 2000000 INFO @ Sat, 24 Aug 2019 18:51:15: 7000000 INFO @ Sat, 24 Aug 2019 18:51:20: 11000000 INFO @ Sat, 24 Aug 2019 18:51:21: 3000000 INFO @ Sat, 24 Aug 2019 18:51:22: 8000000 INFO @ Sat, 24 Aug 2019 18:51:28: 12000000 INFO @ Sat, 24 Aug 2019 18:51:29: 9000000 INFO @ Sat, 24 Aug 2019 18:51:30: 4000000 INFO @ Sat, 24 Aug 2019 18:51:36: 10000000 INFO @ Sat, 24 Aug 2019 18:51:36: 13000000 INFO @ Sat, 24 Aug 2019 18:51:38: 5000000 INFO @ Sat, 24 Aug 2019 18:51:43: 11000000 INFO @ Sat, 24 Aug 2019 18:51:44: 14000000 INFO @ Sat, 24 Aug 2019 18:51:46: 6000000 INFO @ Sat, 24 Aug 2019 18:51:49: 12000000 INFO @ Sat, 24 Aug 2019 18:51:52: 15000000 INFO @ Sat, 24 Aug 2019 18:51:53: 7000000 INFO @ Sat, 24 Aug 2019 18:51:56: 13000000 INFO @ Sat, 24 Aug 2019 18:52:00: 16000000 INFO @ Sat, 24 Aug 2019 18:52:01: 8000000 INFO @ Sat, 24 Aug 2019 18:52:03: 14000000 INFO @ Sat, 24 Aug 2019 18:52:07: 17000000 INFO @ Sat, 24 Aug 2019 18:52:08: 9000000 INFO @ Sat, 24 Aug 2019 18:52:10: 15000000 INFO @ Sat, 24 Aug 2019 18:52:15: 18000000 INFO @ Sat, 24 Aug 2019 18:52:15: 10000000 INFO @ Sat, 24 Aug 2019 18:52:17: 16000000 INFO @ Sat, 24 Aug 2019 18:52:22: 19000000 INFO @ Sat, 24 Aug 2019 18:52:23: 11000000 INFO @ Sat, 24 Aug 2019 18:52:24: 17000000 INFO @ Sat, 24 Aug 2019 18:52:25: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:52:25: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:52:25: #1 total tags in treatment: 19365476 INFO @ Sat, 24 Aug 2019 18:52:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:52:25: #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 18:52:26: #1 tags after filtering in treatment: 19365278 INFO @ Sat, 24 Aug 2019 18:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:52:26: #1 finished! INFO @ Sat, 24 Aug 2019 18:52:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:52:30: 12000000 INFO @ Sat, 24 Aug 2019 18:52:31: 18000000 INFO @ Sat, 24 Aug 2019 18:52:31: #2 number of paired peaks: 84784 INFO @ Sat, 24 Aug 2019 18:52:31: start model_add_line... INFO @ Sat, 24 Aug 2019 18:52:32: start X-correlation... INFO @ Sat, 24 Aug 2019 18:52:32: end of X-cor INFO @ Sat, 24 Aug 2019 18:52:32: #2 finished! INFO @ Sat, 24 Aug 2019 18:52:32: #2 predicted fragment length is 172 bps INFO @ Sat, 24 Aug 2019 18:52:32: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 24 Aug 2019 18:52:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.05_model.r INFO @ Sat, 24 Aug 2019 18:52:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:52:37: 13000000 INFO @ Sat, 24 Aug 2019 18:52:38: 19000000 INFO @ Sat, 24 Aug 2019 18:52:40: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:52:40: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:52:40: #1 total tags in treatment: 19365476 INFO @ Sat, 24 Aug 2019 18:52:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:52:40: #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 18:52:41: #1 tags after filtering in treatment: 19365278 INFO @ Sat, 24 Aug 2019 18:52:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:52:41: #1 finished! INFO @ Sat, 24 Aug 2019 18:52:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:52:44: 14000000 INFO @ Sat, 24 Aug 2019 18:52:46: #2 number of paired peaks: 84784 INFO @ Sat, 24 Aug 2019 18:52:46: start model_add_line... INFO @ Sat, 24 Aug 2019 18:52:47: start X-correlation... INFO @ Sat, 24 Aug 2019 18:52:47: end of X-cor INFO @ Sat, 24 Aug 2019 18:52:47: #2 finished! INFO @ Sat, 24 Aug 2019 18:52:47: #2 predicted fragment length is 172 bps INFO @ Sat, 24 Aug 2019 18:52:47: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 24 Aug 2019 18:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.10_model.r INFO @ Sat, 24 Aug 2019 18:52:47: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:52:52: 15000000 INFO @ Sat, 24 Aug 2019 18:52:59: 16000000 INFO @ Sat, 24 Aug 2019 18:53:06: 17000000 INFO @ Sat, 24 Aug 2019 18:53:13: 18000000 INFO @ Sat, 24 Aug 2019 18:53:21: 19000000 INFO @ Sat, 24 Aug 2019 18:53:24: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:53:24: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:53:24: #1 total tags in treatment: 19365476 INFO @ Sat, 24 Aug 2019 18:53:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:53:24: #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 18:53:24: #1 tags after filtering in treatment: 19365278 INFO @ Sat, 24 Aug 2019 18:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:53:24: #1 finished! INFO @ Sat, 24 Aug 2019 18:53:24: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:53:30: #2 number of paired peaks: 84784 INFO @ Sat, 24 Aug 2019 18:53:30: start model_add_line... INFO @ Sat, 24 Aug 2019 18:53:30: start X-correlation... INFO @ Sat, 24 Aug 2019 18:53:30: end of X-cor INFO @ Sat, 24 Aug 2019 18:53:30: #2 finished! INFO @ Sat, 24 Aug 2019 18:53:30: #2 predicted fragment length is 172 bps INFO @ Sat, 24 Aug 2019 18:53:30: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 24 Aug 2019 18:53:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.20_model.r INFO @ Sat, 24 Aug 2019 18:53:30: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:53:35: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:53:51: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.05_summits.bed INFO @ Sat, 24 Aug 2019 18:54:11: Done! pass1 - making usageList (115 chroms): 14 millis pass2 - checking and writing primary data (39825 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:54:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.10_summits.bed INFO @ Sat, 24 Aug 2019 18:54:27: Done! pass1 - making usageList (87 chroms): 5 millis pass2 - checking and writing primary data (24110 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:54:33: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:55:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:55:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:55:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375067/SRX5375067.20_summits.bed INFO @ Sat, 24 Aug 2019 18:55:07: Done! pass1 - making usageList (58 chroms): 5 millis pass2 - checking and writing primary data (9615 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。