Job ID = 2002533 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,266,225 reads read : 26,266,225 reads written : 26,266,225 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR572186.sra.cache’: 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: 00:00:02 Multiseed full-index search: 00:23:45 26266225 reads; of these: 26266225 (100.00%) were unpaired; of these: 595644 (2.27%) aligned 0 times 21511502 (81.90%) aligned exactly 1 time 4159079 (15.83%) aligned >1 times 97.73% overall alignment rate Time searching: 00:23:49 Overall time: 00:23:49 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] 1074766 / 25670581 = 0.0419 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 12:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.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 @ Fri, 05 Jul 2019 12:19:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:19:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.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 @ Fri, 05 Jul 2019 12:19:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:19:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.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 @ Fri, 05 Jul 2019 12:19:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:19:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:19:40: 1000000 INFO @ Fri, 05 Jul 2019 12:19:40: 1000000 INFO @ Fri, 05 Jul 2019 12:19:41: 1000000 INFO @ Fri, 05 Jul 2019 12:19:49: 2000000 INFO @ Fri, 05 Jul 2019 12:19:49: 2000000 INFO @ Fri, 05 Jul 2019 12:19:49: 2000000 INFO @ Fri, 05 Jul 2019 12:19:58: 3000000 INFO @ Fri, 05 Jul 2019 12:19:58: 3000000 INFO @ Fri, 05 Jul 2019 12:19:59: 3000000 INFO @ Fri, 05 Jul 2019 12:20:07: 4000000 INFO @ Fri, 05 Jul 2019 12:20:07: 4000000 INFO @ Fri, 05 Jul 2019 12:20:08: 4000000 INFO @ Fri, 05 Jul 2019 12:20:15: 5000000 INFO @ Fri, 05 Jul 2019 12:20:16: 5000000 INFO @ Fri, 05 Jul 2019 12:20:17: 5000000 INFO @ Fri, 05 Jul 2019 12:20:24: 6000000 INFO @ Fri, 05 Jul 2019 12:20:25: 6000000 INFO @ Fri, 05 Jul 2019 12:20:27: 6000000 INFO @ Fri, 05 Jul 2019 12:20:32: 7000000 INFO @ Fri, 05 Jul 2019 12:20:34: 7000000 INFO @ Fri, 05 Jul 2019 12:20:36: 7000000 INFO @ Fri, 05 Jul 2019 12:20:41: 8000000 INFO @ Fri, 05 Jul 2019 12:20:43: 8000000 INFO @ Fri, 05 Jul 2019 12:20:46: 8000000 INFO @ Fri, 05 Jul 2019 12:20:50: 9000000 INFO @ Fri, 05 Jul 2019 12:20:53: 9000000 INFO @ Fri, 05 Jul 2019 12:20:55: 9000000 INFO @ Fri, 05 Jul 2019 12:20:59: 10000000 INFO @ Fri, 05 Jul 2019 12:21:02: 10000000 INFO @ Fri, 05 Jul 2019 12:21:04: 10000000 INFO @ Fri, 05 Jul 2019 12:21:08: 11000000 INFO @ Fri, 05 Jul 2019 12:21:11: 11000000 INFO @ Fri, 05 Jul 2019 12:21:15: 11000000 INFO @ Fri, 05 Jul 2019 12:21:16: 12000000 INFO @ Fri, 05 Jul 2019 12:21:20: 12000000 INFO @ Fri, 05 Jul 2019 12:21:24: 12000000 INFO @ Fri, 05 Jul 2019 12:21:25: 13000000 INFO @ Fri, 05 Jul 2019 12:21:29: 13000000 INFO @ Fri, 05 Jul 2019 12:21:33: 13000000 INFO @ Fri, 05 Jul 2019 12:21:33: 14000000 INFO @ Fri, 05 Jul 2019 12:21:38: 14000000 INFO @ Fri, 05 Jul 2019 12:21:42: 14000000 INFO @ Fri, 05 Jul 2019 12:21:42: 15000000 INFO @ Fri, 05 Jul 2019 12:21:48: 15000000 INFO @ Fri, 05 Jul 2019 12:21:53: 16000000 INFO @ Fri, 05 Jul 2019 12:21:54: 15000000 INFO @ Fri, 05 Jul 2019 12:21:57: 16000000 INFO @ Fri, 05 Jul 2019 12:22:02: 17000000 INFO @ Fri, 05 Jul 2019 12:22:03: 16000000 INFO @ Fri, 05 Jul 2019 12:22:06: 17000000 INFO @ Fri, 05 Jul 2019 12:22:11: 18000000 INFO @ Fri, 05 Jul 2019 12:22:13: 17000000 INFO @ Fri, 05 Jul 2019 12:22:16: 18000000 INFO @ Fri, 05 Jul 2019 12:22:20: 19000000 INFO @ Fri, 05 Jul 2019 12:22:23: 18000000 INFO @ Fri, 05 Jul 2019 12:22:25: 19000000 INFO @ Fri, 05 Jul 2019 12:22:29: 20000000 INFO @ Fri, 05 Jul 2019 12:22:32: 19000000 INFO @ Fri, 05 Jul 2019 12:22:34: 20000000 INFO @ Fri, 05 Jul 2019 12:22:37: 21000000 INFO @ Fri, 05 Jul 2019 12:22:42: 20000000 INFO @ Fri, 05 Jul 2019 12:22:44: 21000000 INFO @ Fri, 05 Jul 2019 12:22:46: 22000000 INFO @ Fri, 05 Jul 2019 12:22:52: 21000000 INFO @ Fri, 05 Jul 2019 12:22:53: 22000000 INFO @ Fri, 05 Jul 2019 12:22:55: 23000000 INFO @ Fri, 05 Jul 2019 12:23:01: 22000000 INFO @ Fri, 05 Jul 2019 12:23:03: 23000000 INFO @ Fri, 05 Jul 2019 12:23:04: 24000000 INFO @ Fri, 05 Jul 2019 12:23:10: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:23:10: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:23:10: #1 total tags in treatment: 24595815 INFO @ Fri, 05 Jul 2019 12:23:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:23:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:23:11: #1 tags after filtering in treatment: 24595593 INFO @ Fri, 05 Jul 2019 12:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:23:11: #1 finished! INFO @ Fri, 05 Jul 2019 12:23:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:23:11: 23000000 INFO @ Fri, 05 Jul 2019 12:23:12: 24000000 INFO @ Fri, 05 Jul 2019 12:23:18: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:23:18: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:23:18: #1 total tags in treatment: 24595815 INFO @ Fri, 05 Jul 2019 12:23:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:23:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:23:19: #2 number of paired peaks: 115198 INFO @ Fri, 05 Jul 2019 12:23:19: start model_add_line... INFO @ Fri, 05 Jul 2019 12:23:19: #1 tags after filtering in treatment: 24595593 INFO @ Fri, 05 Jul 2019 12:23:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:23:19: #1 finished! INFO @ Fri, 05 Jul 2019 12:23:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:23:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:23:20: 24000000 INFO @ Fri, 05 Jul 2019 12:23:20: start X-correlation... INFO @ Fri, 05 Jul 2019 12:23:20: end of X-cor INFO @ Fri, 05 Jul 2019 12:23:20: #2 finished! INFO @ Fri, 05 Jul 2019 12:23:20: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 12:23:20: #2 alternative fragment length(s) may be 226 bps INFO @ Fri, 05 Jul 2019 12:23:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.20_model.r INFO @ Fri, 05 Jul 2019 12:23:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:23:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:23:25: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:23:25: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:23:25: #1 total tags in treatment: 24595815 INFO @ Fri, 05 Jul 2019 12:23:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:23:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:23:26: #1 tags after filtering in treatment: 24595593 INFO @ Fri, 05 Jul 2019 12:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:23:26: #1 finished! INFO @ Fri, 05 Jul 2019 12:23:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:23:27: #2 number of paired peaks: 115198 INFO @ Fri, 05 Jul 2019 12:23:28: start model_add_line... INFO @ Fri, 05 Jul 2019 12:23:29: start X-correlation... INFO @ Fri, 05 Jul 2019 12:23:29: end of X-cor INFO @ Fri, 05 Jul 2019 12:23:29: #2 finished! INFO @ Fri, 05 Jul 2019 12:23:29: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 12:23:29: #2 alternative fragment length(s) may be 226 bps INFO @ Fri, 05 Jul 2019 12:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.05_model.r INFO @ Fri, 05 Jul 2019 12:23:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:23:34: #2 number of paired peaks: 115198 INFO @ Fri, 05 Jul 2019 12:23:34: start model_add_line... INFO @ Fri, 05 Jul 2019 12:23:35: start X-correlation... INFO @ Fri, 05 Jul 2019 12:23:35: end of X-cor INFO @ Fri, 05 Jul 2019 12:23:35: #2 finished! INFO @ Fri, 05 Jul 2019 12:23:35: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 12:23:35: #2 alternative fragment length(s) may be 226 bps INFO @ Fri, 05 Jul 2019 12:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.10_model.r INFO @ Fri, 05 Jul 2019 12:23:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:23:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:24:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:25:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:25:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:25:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:26:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:26:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:26:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.20_summits.bed INFO @ Fri, 05 Jul 2019 12:26:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:26:05: Done! INFO @ Fri, 05 Jul 2019 12:26:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:26:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.10_summits.bed INFO @ Fri, 05 Jul 2019 12:26:05: Done! pass1 - making usageList (59 chroms): 10 millis pass2 - checking and writing primary data (10321 records, 4 fields): 22 millis pass1 - making usageList (89 chroms): 9 millis pass2 - checking and writing primary data (21232 records, 4 fields): 37 millis INFO @ Fri, 05 Jul 2019 12:26:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530988/ERX530988.05_summits.bed INFO @ Fri, 05 Jul 2019 12:26:06: Done! pass1 - making usageList (113 chroms): 11 millis pass2 - checking and writing primary data (34418 records, 4 fields): 54 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。