Job ID = 2002534 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,209,632 reads read : 29,209,632 reads written : 29,209,632 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR572272.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: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:15:58 29209632 reads; of these: 29209632 (100.00%) were unpaired; of these: 2052117 (7.03%) aligned 0 times 23448271 (80.28%) aligned exactly 1 time 3709244 (12.70%) aligned >1 times 92.97% overall alignment rate Time searching: 00:16:03 Overall time: 00:16:03 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] 8379506 / 27157515 = 0.3086 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 12:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.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 12:14:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:14:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:14:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.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 12:14:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:14:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:14:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.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 12:14:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:14:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:14:46: 1000000 INFO @ Fri, 05 Jul 2019 12:14:48: 1000000 INFO @ Fri, 05 Jul 2019 12:14:50: 1000000 INFO @ Fri, 05 Jul 2019 12:14:58: 2000000 INFO @ Fri, 05 Jul 2019 12:14:59: 2000000 INFO @ Fri, 05 Jul 2019 12:15:04: 2000000 INFO @ Fri, 05 Jul 2019 12:15:08: 3000000 INFO @ Fri, 05 Jul 2019 12:15:09: 3000000 INFO @ Fri, 05 Jul 2019 12:15:17: 3000000 INFO @ Fri, 05 Jul 2019 12:15:20: 4000000 INFO @ Fri, 05 Jul 2019 12:15:20: 4000000 INFO @ Fri, 05 Jul 2019 12:15:31: 5000000 INFO @ Fri, 05 Jul 2019 12:15:31: 4000000 INFO @ Fri, 05 Jul 2019 12:15:31: 5000000 INFO @ Fri, 05 Jul 2019 12:15:40: 6000000 INFO @ Fri, 05 Jul 2019 12:15:41: 6000000 INFO @ Fri, 05 Jul 2019 12:15:44: 5000000 INFO @ Fri, 05 Jul 2019 12:15:50: 7000000 INFO @ Fri, 05 Jul 2019 12:15:52: 7000000 INFO @ Fri, 05 Jul 2019 12:15:55: 6000000 INFO @ Fri, 05 Jul 2019 12:16:02: 8000000 INFO @ Fri, 05 Jul 2019 12:16:02: 8000000 INFO @ Fri, 05 Jul 2019 12:16:04: 7000000 INFO @ Fri, 05 Jul 2019 12:16:12: 9000000 INFO @ Fri, 05 Jul 2019 12:16:13: 9000000 INFO @ Fri, 05 Jul 2019 12:16:15: 8000000 INFO @ Fri, 05 Jul 2019 12:16:22: 10000000 INFO @ Fri, 05 Jul 2019 12:16:24: 10000000 INFO @ Fri, 05 Jul 2019 12:16:26: 9000000 INFO @ Fri, 05 Jul 2019 12:16:32: 11000000 INFO @ Fri, 05 Jul 2019 12:16:34: 11000000 INFO @ Fri, 05 Jul 2019 12:16:35: 10000000 INFO @ Fri, 05 Jul 2019 12:16:45: 12000000 INFO @ Fri, 05 Jul 2019 12:16:46: 12000000 INFO @ Fri, 05 Jul 2019 12:16:46: 11000000 INFO @ Fri, 05 Jul 2019 12:16:55: 13000000 INFO @ Fri, 05 Jul 2019 12:16:56: 12000000 INFO @ Fri, 05 Jul 2019 12:16:57: 13000000 INFO @ Fri, 05 Jul 2019 12:17:06: 14000000 INFO @ Fri, 05 Jul 2019 12:17:06: 13000000 INFO @ Fri, 05 Jul 2019 12:17:07: 14000000 INFO @ Fri, 05 Jul 2019 12:17:16: 15000000 INFO @ Fri, 05 Jul 2019 12:17:16: 14000000 INFO @ Fri, 05 Jul 2019 12:17:17: 15000000 INFO @ Fri, 05 Jul 2019 12:17:25: 15000000 INFO @ Fri, 05 Jul 2019 12:17:26: 16000000 INFO @ Fri, 05 Jul 2019 12:17:27: 16000000 INFO @ Fri, 05 Jul 2019 12:17:34: 16000000 INFO @ Fri, 05 Jul 2019 12:17:35: 17000000 INFO @ Fri, 05 Jul 2019 12:17:37: 17000000 INFO @ Fri, 05 Jul 2019 12:17:45: 18000000 INFO @ Fri, 05 Jul 2019 12:17:45: 17000000 INFO @ Fri, 05 Jul 2019 12:17:48: 18000000 INFO @ Fri, 05 Jul 2019 12:17:53: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:17:53: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:17:53: #1 total tags in treatment: 18778009 INFO @ Fri, 05 Jul 2019 12:17:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:17:53: #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 12:17:54: #1 tags after filtering in treatment: 18777791 INFO @ Fri, 05 Jul 2019 12:17:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:17:54: #1 finished! INFO @ Fri, 05 Jul 2019 12:17:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:17:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:17:56: 18000000 INFO @ Fri, 05 Jul 2019 12:17:57: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:17:57: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:17:57: #1 total tags in treatment: 18778009 INFO @ Fri, 05 Jul 2019 12:17:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:17:57: #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 12:17:57: #1 tags after filtering in treatment: 18777791 INFO @ Fri, 05 Jul 2019 12:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:17:57: #1 finished! INFO @ Fri, 05 Jul 2019 12:17:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:17:57: #2 number of paired peaks: 27046 INFO @ Fri, 05 Jul 2019 12:17:57: start model_add_line... INFO @ Fri, 05 Jul 2019 12:17:58: start X-correlation... INFO @ Fri, 05 Jul 2019 12:17:58: end of X-cor INFO @ Fri, 05 Jul 2019 12:17:58: #2 finished! INFO @ Fri, 05 Jul 2019 12:17:58: #2 predicted fragment length is 244 bps INFO @ Fri, 05 Jul 2019 12:17:58: #2 alternative fragment length(s) may be 244 bps INFO @ Fri, 05 Jul 2019 12:17:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.05_model.r INFO @ Fri, 05 Jul 2019 12:17:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:17:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:18:01: #2 number of paired peaks: 27046 INFO @ Fri, 05 Jul 2019 12:18:01: start model_add_line... INFO @ Fri, 05 Jul 2019 12:18:02: start X-correlation... INFO @ Fri, 05 Jul 2019 12:18:02: end of X-cor INFO @ Fri, 05 Jul 2019 12:18:02: #2 finished! INFO @ Fri, 05 Jul 2019 12:18:02: #2 predicted fragment length is 244 bps INFO @ Fri, 05 Jul 2019 12:18:02: #2 alternative fragment length(s) may be 244 bps INFO @ Fri, 05 Jul 2019 12:18:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.20_model.r INFO @ Fri, 05 Jul 2019 12:18:04: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:18:04: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:18:04: #1 total tags in treatment: 18778009 INFO @ Fri, 05 Jul 2019 12:18:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:18:04: #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 12:18:05: #1 tags after filtering in treatment: 18777791 INFO @ Fri, 05 Jul 2019 12:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:18:05: #1 finished! INFO @ Fri, 05 Jul 2019 12:18:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:18:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:18:09: #2 number of paired peaks: 27046 INFO @ Fri, 05 Jul 2019 12:18:09: start model_add_line... INFO @ Fri, 05 Jul 2019 12:18:10: start X-correlation... INFO @ Fri, 05 Jul 2019 12:18:10: end of X-cor INFO @ Fri, 05 Jul 2019 12:18:10: #2 finished! INFO @ Fri, 05 Jul 2019 12:18:10: #2 predicted fragment length is 244 bps INFO @ Fri, 05 Jul 2019 12:18:10: #2 alternative fragment length(s) may be 244 bps INFO @ Fri, 05 Jul 2019 12:18:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.10_model.r INFO @ Fri, 05 Jul 2019 12:18:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:19:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:19:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:19:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:20:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.05_summits.bed INFO @ Fri, 05 Jul 2019 12:20:02: Done! pass1 - making usageList (139 chroms): 6 millis pass2 - checking and writing primary data (20500 records, 4 fields): 70 millis INFO @ Fri, 05 Jul 2019 12:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:20:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:20:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.20_summits.bed INFO @ Fri, 05 Jul 2019 12:20:10: Done! pass1 - making usageList (91 chroms): 4 millis pass2 - checking and writing primary data (16190 records, 4 fields): 43 millis INFO @ Fri, 05 Jul 2019 12:20:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:20:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:20:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530991/ERX530991.10_summits.bed INFO @ Fri, 05 Jul 2019 12:20:13: Done! CompletedMACS2peakCalling pass1 - making usageList (113 chroms): 13 millis pass2 - checking and writing primary data (18479 records, 4 fields): 76 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。