Job ID = 2002162 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,257,639 reads read : 26,257,639 reads written : 26,257,639 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR458086.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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:25 26257639 reads; of these: 26257639 (100.00%) were unpaired; of these: 908625 (3.46%) aligned 0 times 18476695 (70.37%) aligned exactly 1 time 6872319 (26.17%) aligned >1 times 96.54% overall alignment rate Time searching: 00:09:28 Overall time: 00:09:28 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 8 files... [bam_rmdupse_core] 2340048 / 25349014 = 0.0923 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 10:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.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 10:59:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:59:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.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 10:59:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:59:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:59:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.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 10:59:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:59:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:59:10: 1000000 INFO @ Fri, 05 Jul 2019 10:59:11: 1000000 INFO @ Fri, 05 Jul 2019 10:59:12: 1000000 INFO @ Fri, 05 Jul 2019 10:59:18: 2000000 INFO @ Fri, 05 Jul 2019 10:59:19: 2000000 INFO @ Fri, 05 Jul 2019 10:59:20: 2000000 INFO @ Fri, 05 Jul 2019 10:59:27: 3000000 INFO @ Fri, 05 Jul 2019 10:59:27: 3000000 INFO @ Fri, 05 Jul 2019 10:59:30: 3000000 INFO @ Fri, 05 Jul 2019 10:59:35: 4000000 INFO @ Fri, 05 Jul 2019 10:59:36: 4000000 INFO @ Fri, 05 Jul 2019 10:59:39: 4000000 INFO @ Fri, 05 Jul 2019 10:59:44: 5000000 INFO @ Fri, 05 Jul 2019 10:59:44: 5000000 INFO @ Fri, 05 Jul 2019 10:59:49: 5000000 INFO @ Fri, 05 Jul 2019 10:59:52: 6000000 INFO @ Fri, 05 Jul 2019 10:59:53: 6000000 INFO @ Fri, 05 Jul 2019 10:59:58: 6000000 INFO @ Fri, 05 Jul 2019 11:00:00: 7000000 INFO @ Fri, 05 Jul 2019 11:00:01: 7000000 INFO @ Fri, 05 Jul 2019 11:00:07: 7000000 INFO @ Fri, 05 Jul 2019 11:00:08: 8000000 INFO @ Fri, 05 Jul 2019 11:00:09: 8000000 INFO @ Fri, 05 Jul 2019 11:00:16: 8000000 INFO @ Fri, 05 Jul 2019 11:00:17: 9000000 INFO @ Fri, 05 Jul 2019 11:00:17: 9000000 INFO @ Fri, 05 Jul 2019 11:00:24: 10000000 INFO @ Fri, 05 Jul 2019 11:00:25: 10000000 INFO @ Fri, 05 Jul 2019 11:00:26: 9000000 INFO @ Fri, 05 Jul 2019 11:00:32: 11000000 INFO @ Fri, 05 Jul 2019 11:00:33: 11000000 INFO @ Fri, 05 Jul 2019 11:00:33: 10000000 INFO @ Fri, 05 Jul 2019 11:00:40: 12000000 INFO @ Fri, 05 Jul 2019 11:00:41: 12000000 INFO @ Fri, 05 Jul 2019 11:00:42: 11000000 INFO @ Fri, 05 Jul 2019 11:00:48: 13000000 INFO @ Fri, 05 Jul 2019 11:00:49: 13000000 INFO @ Fri, 05 Jul 2019 11:00:51: 12000000 INFO @ Fri, 05 Jul 2019 11:00:56: 14000000 INFO @ Fri, 05 Jul 2019 11:00:57: 14000000 INFO @ Fri, 05 Jul 2019 11:00:59: 13000000 INFO @ Fri, 05 Jul 2019 11:01:04: 15000000 INFO @ Fri, 05 Jul 2019 11:01:05: 15000000 INFO @ Fri, 05 Jul 2019 11:01:06: 14000000 INFO @ Fri, 05 Jul 2019 11:01:12: 16000000 INFO @ Fri, 05 Jul 2019 11:01:13: 16000000 INFO @ Fri, 05 Jul 2019 11:01:13: 15000000 INFO @ Fri, 05 Jul 2019 11:01:19: 16000000 INFO @ Fri, 05 Jul 2019 11:01:20: 17000000 INFO @ Fri, 05 Jul 2019 11:01:21: 17000000 INFO @ Fri, 05 Jul 2019 11:01:26: 17000000 INFO @ Fri, 05 Jul 2019 11:01:28: 18000000 INFO @ Fri, 05 Jul 2019 11:01:28: 18000000 INFO @ Fri, 05 Jul 2019 11:01:33: 18000000 INFO @ Fri, 05 Jul 2019 11:01:36: 19000000 INFO @ Fri, 05 Jul 2019 11:01:36: 19000000 INFO @ Fri, 05 Jul 2019 11:01:39: 19000000 INFO @ Fri, 05 Jul 2019 11:01:43: 20000000 INFO @ Fri, 05 Jul 2019 11:01:44: 20000000 INFO @ Fri, 05 Jul 2019 11:01:46: 20000000 INFO @ Fri, 05 Jul 2019 11:01:51: 21000000 INFO @ Fri, 05 Jul 2019 11:01:52: 21000000 INFO @ Fri, 05 Jul 2019 11:01:52: 21000000 INFO @ Fri, 05 Jul 2019 11:01:59: 22000000 INFO @ Fri, 05 Jul 2019 11:02:00: 22000000 INFO @ Fri, 05 Jul 2019 11:02:00: 22000000 INFO @ Fri, 05 Jul 2019 11:02:06: 23000000 INFO @ Fri, 05 Jul 2019 11:02:06: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:02:06: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:02:06: #1 total tags in treatment: 23008966 INFO @ Fri, 05 Jul 2019 11:02:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:02:06: #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 11:02:07: #1 tags after filtering in treatment: 23008855 INFO @ Fri, 05 Jul 2019 11:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:02:07: #1 finished! INFO @ Fri, 05 Jul 2019 11:02:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:02:08: 23000000 INFO @ Fri, 05 Jul 2019 11:02:08: 23000000 INFO @ Fri, 05 Jul 2019 11:02:08: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:02:08: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:02:08: #1 total tags in treatment: 23008966 INFO @ Fri, 05 Jul 2019 11:02:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:02:08: #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 11:02:08: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:02:08: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:02:08: #1 total tags in treatment: 23008966 INFO @ Fri, 05 Jul 2019 11:02:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:02:08: #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 11:02:09: #1 tags after filtering in treatment: 23008855 INFO @ Fri, 05 Jul 2019 11:02:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:02:09: #1 finished! INFO @ Fri, 05 Jul 2019 11:02:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:02:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:02:09: #1 tags after filtering in treatment: 23008855 INFO @ Fri, 05 Jul 2019 11:02:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:02:09: #1 finished! INFO @ Fri, 05 Jul 2019 11:02:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:02:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:02:10: #2 number of paired peaks: 31444 INFO @ Fri, 05 Jul 2019 11:02:10: start model_add_line... INFO @ Fri, 05 Jul 2019 11:02:11: start X-correlation... INFO @ Fri, 05 Jul 2019 11:02:11: end of X-cor INFO @ Fri, 05 Jul 2019 11:02:11: #2 finished! INFO @ Fri, 05 Jul 2019 11:02:11: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 11:02:11: #2 alternative fragment length(s) may be 134 bps INFO @ Fri, 05 Jul 2019 11:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.05_model.r INFO @ Fri, 05 Jul 2019 11:02:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:02:12: #2 number of paired peaks: 31444 INFO @ Fri, 05 Jul 2019 11:02:12: start model_add_line... INFO @ Fri, 05 Jul 2019 11:02:13: start X-correlation... INFO @ Fri, 05 Jul 2019 11:02:13: #2 number of paired peaks: 31444 INFO @ Fri, 05 Jul 2019 11:02:13: start model_add_line... INFO @ Fri, 05 Jul 2019 11:02:13: end of X-cor INFO @ Fri, 05 Jul 2019 11:02:13: #2 finished! INFO @ Fri, 05 Jul 2019 11:02:13: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 11:02:13: #2 alternative fragment length(s) may be 134 bps INFO @ Fri, 05 Jul 2019 11:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.10_model.r INFO @ Fri, 05 Jul 2019 11:02:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:02:13: start X-correlation... INFO @ Fri, 05 Jul 2019 11:02:13: end of X-cor INFO @ Fri, 05 Jul 2019 11:02:13: #2 finished! INFO @ Fri, 05 Jul 2019 11:02:13: #2 predicted fragment length is 134 bps INFO @ Fri, 05 Jul 2019 11:02:13: #2 alternative fragment length(s) may be 134 bps INFO @ Fri, 05 Jul 2019 11:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.20_model.r INFO @ Fri, 05 Jul 2019 11:02:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:03:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:03:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:03:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:04:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:04:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:04:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.05_summits.bed INFO @ Fri, 05 Jul 2019 11:04:02: Done! pass1 - making usageList (112 chroms): 11 millis pass2 - checking and writing primary data (28941 records, 4 fields): 42 millis INFO @ Fri, 05 Jul 2019 11:04:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:04:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.10_summits.bed INFO @ Fri, 05 Jul 2019 11:04:05: Done! INFO @ Fri, 05 Jul 2019 11:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190366/ERX190366.20_summits.bed INFO @ Fri, 05 Jul 2019 11:04:05: Done! pass1 - making usageList (89 chroms): 10 millis pass2 - checking and writing primary data (19550 records, 4 fields): 28 millis pass1 - making usageList (60 chroms): 2 millis pass2 - checking and writing primary data (11485 records, 4 fields): 198 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。