Job ID = 2640520 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,292,305 reads read : 44,584,610 reads written : 22,292,305 reads 0-length : 22,292,305 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: 00:17:12 22292305 reads; of these: 22292305 (100.00%) were unpaired; of these: 964702 (4.33%) aligned 0 times 15821624 (70.97%) aligned exactly 1 time 5505979 (24.70%) aligned >1 times 95.67% overall alignment rate Time searching: 00:17:15 Overall time: 00:17:15 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] 4572720 / 21327603 = 0.2144 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:53:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.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 17:53:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:53:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:53:40: 1000000 INFO @ Sat, 24 Aug 2019 17:53:49: 2000000 INFO @ Sat, 24 Aug 2019 17:53:58: 3000000 INFO @ Sat, 24 Aug 2019 17:54:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.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 17:54:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:54:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:54:08: 4000000 INFO @ Sat, 24 Aug 2019 17:54:12: 1000000 INFO @ Sat, 24 Aug 2019 17:54:19: 5000000 INFO @ Sat, 24 Aug 2019 17:54:22: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:54:30: 6000000 INFO @ Sat, 24 Aug 2019 17:54:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.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 17:54:30: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:54:30: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:54:33: 3000000 INFO @ Sat, 24 Aug 2019 17:54:41: 7000000 INFO @ Sat, 24 Aug 2019 17:54:44: 1000000 INFO @ Sat, 24 Aug 2019 17:54:45: 4000000 INFO @ Sat, 24 Aug 2019 17:54:52: 8000000 INFO @ Sat, 24 Aug 2019 17:54:56: 2000000 INFO @ Sat, 24 Aug 2019 17:54:58: 5000000 INFO @ Sat, 24 Aug 2019 17:55:03: 9000000 INFO @ Sat, 24 Aug 2019 17:55:08: 3000000 INFO @ Sat, 24 Aug 2019 17:55:11: 6000000 INFO @ Sat, 24 Aug 2019 17:55:14: 10000000 INFO @ Sat, 24 Aug 2019 17:55:20: 4000000 INFO @ Sat, 24 Aug 2019 17:55:23: 7000000 INFO @ Sat, 24 Aug 2019 17:55:24: 11000000 INFO @ Sat, 24 Aug 2019 17:55:33: 5000000 INFO @ Sat, 24 Aug 2019 17:55:35: 12000000 INFO @ Sat, 24 Aug 2019 17:55:35: 8000000 INFO @ Sat, 24 Aug 2019 17:55:44: 13000000 INFO @ Sat, 24 Aug 2019 17:55:45: 6000000 INFO @ Sat, 24 Aug 2019 17:55:47: 9000000 INFO @ Sat, 24 Aug 2019 17:55:55: 14000000 INFO @ Sat, 24 Aug 2019 17:55:57: 7000000 INFO @ Sat, 24 Aug 2019 17:55:59: 10000000 INFO @ Sat, 24 Aug 2019 17:56:05: 15000000 INFO @ Sat, 24 Aug 2019 17:56:09: 8000000 INFO @ Sat, 24 Aug 2019 17:56:10: 11000000 INFO @ Sat, 24 Aug 2019 17:56:13: 16000000 INFO @ Sat, 24 Aug 2019 17:56:19: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:56:19: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:56:19: #1 total tags in treatment: 16754883 INFO @ Sat, 24 Aug 2019 17:56:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:56:19: #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 17:56:20: #1 tags after filtering in treatment: 16754726 INFO @ Sat, 24 Aug 2019 17:56:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:56:20: #1 finished! INFO @ Sat, 24 Aug 2019 17:56:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:56:20: 9000000 INFO @ Sat, 24 Aug 2019 17:56:21: 12000000 INFO @ Sat, 24 Aug 2019 17:56:22: #2 number of paired peaks: 14879 INFO @ Sat, 24 Aug 2019 17:56:22: start model_add_line... INFO @ Sat, 24 Aug 2019 17:56:23: start X-correlation... INFO @ Sat, 24 Aug 2019 17:56:23: end of X-cor INFO @ Sat, 24 Aug 2019 17:56:23: #2 finished! INFO @ Sat, 24 Aug 2019 17:56:23: #2 predicted fragment length is 136 bps INFO @ Sat, 24 Aug 2019 17:56:23: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 24 Aug 2019 17:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.05_model.r INFO @ Sat, 24 Aug 2019 17:56:23: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:56:31: 10000000 INFO @ Sat, 24 Aug 2019 17:56:32: 13000000 INFO @ Sat, 24 Aug 2019 17:56:42: 11000000 INFO @ Sat, 24 Aug 2019 17:56:43: 14000000 INFO @ Sat, 24 Aug 2019 17:56:53: 12000000 INFO @ Sat, 24 Aug 2019 17:56:54: 15000000 INFO @ Sat, 24 Aug 2019 17:57:04: 13000000 INFO @ Sat, 24 Aug 2019 17:57:05: 16000000 INFO @ Sat, 24 Aug 2019 17:57:14: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:57:14: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:57:14: #1 total tags in treatment: 16754883 INFO @ Sat, 24 Aug 2019 17:57:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:57:14: #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 17:57:14: #1 tags after filtering in treatment: 16754726 INFO @ Sat, 24 Aug 2019 17:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:57:14: #1 finished! INFO @ Sat, 24 Aug 2019 17:57:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:57:14: 14000000 INFO @ Sat, 24 Aug 2019 17:57:16: #2 number of paired peaks: 14879 INFO @ Sat, 24 Aug 2019 17:57:16: start model_add_line... INFO @ Sat, 24 Aug 2019 17:57:17: start X-correlation... INFO @ Sat, 24 Aug 2019 17:57:17: end of X-cor INFO @ Sat, 24 Aug 2019 17:57:17: #2 finished! INFO @ Sat, 24 Aug 2019 17:57:17: #2 predicted fragment length is 136 bps INFO @ Sat, 24 Aug 2019 17:57:17: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 24 Aug 2019 17:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.10_model.r INFO @ Sat, 24 Aug 2019 17:57:17: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:57:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:57:23: 15000000 INFO @ Sat, 24 Aug 2019 17:57:33: 16000000 INFO @ Sat, 24 Aug 2019 17:57:40: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:57:40: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:57:40: #1 total tags in treatment: 16754883 INFO @ Sat, 24 Aug 2019 17:57:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:57:40: #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 17:57:40: #1 tags after filtering in treatment: 16754726 INFO @ Sat, 24 Aug 2019 17:57:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:57:40: #1 finished! INFO @ Sat, 24 Aug 2019 17:57:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:57:43: #2 number of paired peaks: 14879 INFO @ Sat, 24 Aug 2019 17:57:43: start model_add_line... INFO @ Sat, 24 Aug 2019 17:57:43: start X-correlation... INFO @ Sat, 24 Aug 2019 17:57:43: end of X-cor INFO @ Sat, 24 Aug 2019 17:57:43: #2 finished! INFO @ Sat, 24 Aug 2019 17:57:43: #2 predicted fragment length is 136 bps INFO @ Sat, 24 Aug 2019 17:57:43: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 24 Aug 2019 17:57:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.20_model.r INFO @ Sat, 24 Aug 2019 17:57:43: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:57:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:57:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:57:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:57:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.05_summits.bed INFO @ Sat, 24 Aug 2019 17:57:45: Done! pass1 - making usageList (72 chroms): 3 millis pass2 - checking and writing primary data (6887 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:58:10: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:58:36: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.10_summits.bed INFO @ Sat, 24 Aug 2019 17:58:37: Done! pass1 - making usageList (48 chroms): 3 millis pass2 - checking and writing primary data (3826 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375001/SRX5375001.20_summits.bed INFO @ Sat, 24 Aug 2019 17:59:04: Done! pass1 - making usageList (36 chroms): 2 millis pass2 - checking and writing primary data (1825 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。