Job ID = 2640608 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,643,433 reads read : 51,286,866 reads written : 25,643,433 reads 0-length : 25,643,433 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:33 25643433 reads; of these: 25643433 (100.00%) were unpaired; of these: 648069 (2.53%) aligned 0 times 19910974 (77.65%) aligned exactly 1 time 5084390 (19.83%) aligned >1 times 97.47% overall alignment rate Time searching: 00:17:34 Overall time: 00:17:34 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] 3051900 / 24995364 = 0.1221 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:34:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.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 18:34:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:34:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:34:10: 1000000 INFO @ Sat, 24 Aug 2019 18:34:18: 2000000 INFO @ Sat, 24 Aug 2019 18:34:26: 3000000 INFO @ Sat, 24 Aug 2019 18:34:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.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 18:34:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:34:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:34:34: 4000000 INFO @ Sat, 24 Aug 2019 18:34:41: 1000000 INFO @ Sat, 24 Aug 2019 18:34:42: 5000000 INFO @ Sat, 24 Aug 2019 18:34:49: 6000000 INFO @ Sat, 24 Aug 2019 18:34:49: 2000000 INFO @ Sat, 24 Aug 2019 18:34:57: 7000000 INFO @ Sat, 24 Aug 2019 18:34:58: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.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 18:35:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:35:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:35:05: 8000000 INFO @ Sat, 24 Aug 2019 18:35:06: 4000000 INFO @ Sat, 24 Aug 2019 18:35:10: 1000000 INFO @ Sat, 24 Aug 2019 18:35:13: 9000000 INFO @ Sat, 24 Aug 2019 18:35:15: 5000000 INFO @ Sat, 24 Aug 2019 18:35:19: 2000000 INFO @ Sat, 24 Aug 2019 18:35:21: 10000000 INFO @ Sat, 24 Aug 2019 18:35:24: 6000000 INFO @ Sat, 24 Aug 2019 18:35:27: 3000000 INFO @ Sat, 24 Aug 2019 18:35:30: 11000000 INFO @ Sat, 24 Aug 2019 18:35:32: 7000000 INFO @ Sat, 24 Aug 2019 18:35:35: 4000000 INFO @ Sat, 24 Aug 2019 18:35:38: 12000000 INFO @ Sat, 24 Aug 2019 18:35:40: 8000000 INFO @ Sat, 24 Aug 2019 18:35:42: 5000000 INFO @ Sat, 24 Aug 2019 18:35:46: 13000000 INFO @ Sat, 24 Aug 2019 18:35:48: 9000000 INFO @ Sat, 24 Aug 2019 18:35:50: 6000000 INFO @ Sat, 24 Aug 2019 18:35:55: 14000000 INFO @ Sat, 24 Aug 2019 18:35:56: 10000000 INFO @ Sat, 24 Aug 2019 18:35:58: 7000000 INFO @ Sat, 24 Aug 2019 18:36:03: 15000000 INFO @ Sat, 24 Aug 2019 18:36:04: 11000000 INFO @ Sat, 24 Aug 2019 18:36:06: 8000000 INFO @ Sat, 24 Aug 2019 18:36:11: 16000000 INFO @ Sat, 24 Aug 2019 18:36:12: 12000000 INFO @ Sat, 24 Aug 2019 18:36:14: 9000000 INFO @ Sat, 24 Aug 2019 18:36:19: 17000000 INFO @ Sat, 24 Aug 2019 18:36:20: 13000000 INFO @ Sat, 24 Aug 2019 18:36:22: 10000000 INFO @ Sat, 24 Aug 2019 18:36:28: 18000000 INFO @ Sat, 24 Aug 2019 18:36:28: 14000000 INFO @ Sat, 24 Aug 2019 18:36:30: 11000000 INFO @ Sat, 24 Aug 2019 18:36:36: 15000000 INFO @ Sat, 24 Aug 2019 18:36:36: 19000000 INFO @ Sat, 24 Aug 2019 18:36:38: 12000000 INFO @ Sat, 24 Aug 2019 18:36:44: 16000000 INFO @ Sat, 24 Aug 2019 18:36:44: 20000000 INFO @ Sat, 24 Aug 2019 18:36:46: 13000000 INFO @ Sat, 24 Aug 2019 18:36:52: 17000000 INFO @ Sat, 24 Aug 2019 18:36:52: 21000000 INFO @ Sat, 24 Aug 2019 18:36:53: 14000000 INFO @ Sat, 24 Aug 2019 18:37:00: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:37:00: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:37:00: #1 total tags in treatment: 21943464 INFO @ Sat, 24 Aug 2019 18:37:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:37:00: #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 18:37:00: 18000000 INFO @ Sat, 24 Aug 2019 18:37:00: #1 tags after filtering in treatment: 21943297 INFO @ Sat, 24 Aug 2019 18:37:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:37:00: #1 finished! INFO @ Sat, 24 Aug 2019 18:37:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:37:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:37:02: 15000000 INFO @ Sat, 24 Aug 2019 18:37:05: #2 number of paired peaks: 50917 INFO @ Sat, 24 Aug 2019 18:37:05: start model_add_line... INFO @ Sat, 24 Aug 2019 18:37:05: start X-correlation... INFO @ Sat, 24 Aug 2019 18:37:05: end of X-cor INFO @ Sat, 24 Aug 2019 18:37:05: #2 finished! INFO @ Sat, 24 Aug 2019 18:37:05: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 18:37:05: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 18:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.05_model.r INFO @ Sat, 24 Aug 2019 18:37:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:37:08: 19000000 INFO @ Sat, 24 Aug 2019 18:37:10: 16000000 INFO @ Sat, 24 Aug 2019 18:37:16: 20000000 INFO @ Sat, 24 Aug 2019 18:37:18: 17000000 INFO @ Sat, 24 Aug 2019 18:37:24: 21000000 INFO @ Sat, 24 Aug 2019 18:37:27: 18000000 INFO @ Sat, 24 Aug 2019 18:37:32: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:37:32: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:37:32: #1 total tags in treatment: 21943464 INFO @ Sat, 24 Aug 2019 18:37:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:37:32: #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 18:37:33: #1 tags after filtering in treatment: 21943297 INFO @ Sat, 24 Aug 2019 18:37:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:37:33: #1 finished! INFO @ Sat, 24 Aug 2019 18:37:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:37:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:37:35: 19000000 INFO @ Sat, 24 Aug 2019 18:37:37: #2 number of paired peaks: 50917 INFO @ Sat, 24 Aug 2019 18:37:37: start model_add_line... INFO @ Sat, 24 Aug 2019 18:37:38: start X-correlation... INFO @ Sat, 24 Aug 2019 18:37:38: end of X-cor INFO @ Sat, 24 Aug 2019 18:37:38: #2 finished! INFO @ Sat, 24 Aug 2019 18:37:38: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 18:37:38: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 18:37:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.10_model.r INFO @ Sat, 24 Aug 2019 18:37:38: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:37:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:37:44: 20000000 INFO @ Sat, 24 Aug 2019 18:37:52: 21000000 INFO @ Sat, 24 Aug 2019 18:38:01: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:38:01: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:38:01: #1 total tags in treatment: 21943464 INFO @ Sat, 24 Aug 2019 18:38:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:38:01: #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 18:38:01: #1 tags after filtering in treatment: 21943297 INFO @ Sat, 24 Aug 2019 18:38:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:38:01: #1 finished! INFO @ Sat, 24 Aug 2019 18:38:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:38:06: #2 number of paired peaks: 50917 INFO @ Sat, 24 Aug 2019 18:38:06: start model_add_line... INFO @ Sat, 24 Aug 2019 18:38:06: start X-correlation... INFO @ Sat, 24 Aug 2019 18:38:06: end of X-cor INFO @ Sat, 24 Aug 2019 18:38:06: #2 finished! INFO @ Sat, 24 Aug 2019 18:38:06: #2 predicted fragment length is 171 bps INFO @ Sat, 24 Aug 2019 18:38:06: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 24 Aug 2019 18:38:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.20_model.r INFO @ Sat, 24 Aug 2019 18:38:06: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:38:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:38:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:38:48: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:38:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:38:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:38:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.05_summits.bed INFO @ Sat, 24 Aug 2019 18:38:55: Done! pass1 - making usageList (104 chroms): 4 millis pass2 - checking and writing primary data (18769 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:39:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:39:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:39:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:39:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.10_summits.bed INFO @ Sat, 24 Aug 2019 18:39:26: Done! pass1 - making usageList (91 chroms): 4 millis pass2 - checking and writing primary data (15390 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:39:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:39:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:39:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375036/SRX5375036.20_summits.bed INFO @ Sat, 24 Aug 2019 18:39:54: Done! pass1 - making usageList (67 chroms): 3 millis pass2 - checking and writing primary data (11293 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。