Job ID = 2003173 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 42,948,747 reads read : 42,948,747 reads written : 42,948,747 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR498446.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: 00:00:00 Multiseed full-index search: 00:25:13 42948747 reads; of these: 42948747 (100.00%) were unpaired; of these: 5864391 (13.65%) aligned 0 times 27234387 (63.41%) aligned exactly 1 time 9849969 (22.93%) aligned >1 times 86.35% overall alignment rate Time searching: 00:25:16 Overall time: 00:25:16 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] 13747566 / 37084356 = 0.3707 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 12:38:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.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 12:38:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.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 12:38:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.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 12:38:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:58: 1000000 INFO @ Fri, 05 Jul 2019 12:39:00: 1000000 INFO @ Fri, 05 Jul 2019 12:39:00: 1000000 INFO @ Fri, 05 Jul 2019 12:39:08: 2000000 INFO @ Fri, 05 Jul 2019 12:39:08: 2000000 INFO @ Fri, 05 Jul 2019 12:39:09: 2000000 INFO @ Fri, 05 Jul 2019 12:39:18: 3000000 INFO @ Fri, 05 Jul 2019 12:39:18: 3000000 INFO @ Fri, 05 Jul 2019 12:39:19: 3000000 INFO @ Fri, 05 Jul 2019 12:39:27: 4000000 INFO @ Fri, 05 Jul 2019 12:39:29: 4000000 INFO @ Fri, 05 Jul 2019 12:39:31: 4000000 INFO @ Fri, 05 Jul 2019 12:39:36: 5000000 INFO @ Fri, 05 Jul 2019 12:39:37: 5000000 INFO @ Fri, 05 Jul 2019 12:39:40: 5000000 INFO @ Fri, 05 Jul 2019 12:39:45: 6000000 INFO @ Fri, 05 Jul 2019 12:39:45: 6000000 INFO @ Fri, 05 Jul 2019 12:39:49: 6000000 INFO @ Fri, 05 Jul 2019 12:39:53: 7000000 INFO @ Fri, 05 Jul 2019 12:39:54: 7000000 INFO @ Fri, 05 Jul 2019 12:39:58: 7000000 INFO @ Fri, 05 Jul 2019 12:40:01: 8000000 INFO @ Fri, 05 Jul 2019 12:40:03: 8000000 INFO @ Fri, 05 Jul 2019 12:40:06: 8000000 INFO @ Fri, 05 Jul 2019 12:40:09: 9000000 INFO @ Fri, 05 Jul 2019 12:40:12: 9000000 INFO @ Fri, 05 Jul 2019 12:40:15: 9000000 INFO @ Fri, 05 Jul 2019 12:40:17: 10000000 INFO @ Fri, 05 Jul 2019 12:40:20: 10000000 INFO @ Fri, 05 Jul 2019 12:40:24: 10000000 INFO @ Fri, 05 Jul 2019 12:40:25: 11000000 INFO @ Fri, 05 Jul 2019 12:40:29: 11000000 INFO @ Fri, 05 Jul 2019 12:40:32: 11000000 INFO @ Fri, 05 Jul 2019 12:40:32: 12000000 INFO @ Fri, 05 Jul 2019 12:40:40: 13000000 INFO @ Fri, 05 Jul 2019 12:40:40: 12000000 INFO @ Fri, 05 Jul 2019 12:40:41: 12000000 INFO @ Fri, 05 Jul 2019 12:40:47: 14000000 INFO @ Fri, 05 Jul 2019 12:40:50: 13000000 INFO @ Fri, 05 Jul 2019 12:40:50: 13000000 INFO @ Fri, 05 Jul 2019 12:40:55: 15000000 INFO @ Fri, 05 Jul 2019 12:40:59: 14000000 INFO @ Fri, 05 Jul 2019 12:41:00: 14000000 INFO @ Fri, 05 Jul 2019 12:41:02: 16000000 INFO @ Fri, 05 Jul 2019 12:41:10: 17000000 INFO @ Fri, 05 Jul 2019 12:41:11: 15000000 INFO @ Fri, 05 Jul 2019 12:41:11: 15000000 INFO @ Fri, 05 Jul 2019 12:41:18: 18000000 INFO @ Fri, 05 Jul 2019 12:41:21: 16000000 INFO @ Fri, 05 Jul 2019 12:41:21: 16000000 INFO @ Fri, 05 Jul 2019 12:41:25: 19000000 INFO @ Fri, 05 Jul 2019 12:41:29: 17000000 INFO @ Fri, 05 Jul 2019 12:41:29: 17000000 INFO @ Fri, 05 Jul 2019 12:41:32: 20000000 INFO @ Fri, 05 Jul 2019 12:41:38: 18000000 INFO @ Fri, 05 Jul 2019 12:41:38: 18000000 INFO @ Fri, 05 Jul 2019 12:41:40: 21000000 INFO @ Fri, 05 Jul 2019 12:41:47: 19000000 INFO @ Fri, 05 Jul 2019 12:41:47: 19000000 INFO @ Fri, 05 Jul 2019 12:41:47: 22000000 INFO @ Fri, 05 Jul 2019 12:41:55: 23000000 INFO @ Fri, 05 Jul 2019 12:41:56: 20000000 INFO @ Fri, 05 Jul 2019 12:41:56: 20000000 INFO @ Fri, 05 Jul 2019 12:41:57: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:41:57: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:41:57: #1 total tags in treatment: 23336790 INFO @ Fri, 05 Jul 2019 12:41:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:41:57: #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 12:41:58: #1 tags after filtering in treatment: 23336669 INFO @ Fri, 05 Jul 2019 12:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:41:58: #1 finished! INFO @ Fri, 05 Jul 2019 12:41:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:42:02: #2 number of paired peaks: 17298 INFO @ Fri, 05 Jul 2019 12:42:02: start model_add_line... INFO @ Fri, 05 Jul 2019 12:42:02: start X-correlation... INFO @ Fri, 05 Jul 2019 12:42:02: end of X-cor INFO @ Fri, 05 Jul 2019 12:42:02: #2 finished! INFO @ Fri, 05 Jul 2019 12:42:02: #2 predicted fragment length is 229 bps INFO @ Fri, 05 Jul 2019 12:42:02: #2 alternative fragment length(s) may be 44,229 bps INFO @ Fri, 05 Jul 2019 12:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.20_model.r INFO @ Fri, 05 Jul 2019 12:42:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:42:04: 21000000 INFO @ Fri, 05 Jul 2019 12:42:04: 21000000 INFO @ Fri, 05 Jul 2019 12:42:12: 22000000 INFO @ Fri, 05 Jul 2019 12:42:12: 22000000 INFO @ Fri, 05 Jul 2019 12:42:20: 23000000 INFO @ Fri, 05 Jul 2019 12:42:21: 23000000 INFO @ Fri, 05 Jul 2019 12:42:23: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:42:23: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:42:23: #1 total tags in treatment: 23336790 INFO @ Fri, 05 Jul 2019 12:42:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:42:23: #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 12:42:24: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:42:24: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:42:24: #1 total tags in treatment: 23336790 INFO @ Fri, 05 Jul 2019 12:42:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:42:24: #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 12:42:24: #1 tags after filtering in treatment: 23336669 INFO @ Fri, 05 Jul 2019 12:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:42:24: #1 finished! INFO @ Fri, 05 Jul 2019 12:42:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:42:24: #1 tags after filtering in treatment: 23336669 INFO @ Fri, 05 Jul 2019 12:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:42:24: #1 finished! INFO @ Fri, 05 Jul 2019 12:42:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:42:28: #2 number of paired peaks: 17298 INFO @ Fri, 05 Jul 2019 12:42:28: start model_add_line... INFO @ Fri, 05 Jul 2019 12:42:28: #2 number of paired peaks: 17298 INFO @ Fri, 05 Jul 2019 12:42:28: start model_add_line... INFO @ Fri, 05 Jul 2019 12:42:28: start X-correlation... INFO @ Fri, 05 Jul 2019 12:42:28: end of X-cor INFO @ Fri, 05 Jul 2019 12:42:28: #2 finished! INFO @ Fri, 05 Jul 2019 12:42:28: #2 predicted fragment length is 229 bps INFO @ Fri, 05 Jul 2019 12:42:28: #2 alternative fragment length(s) may be 44,229 bps INFO @ Fri, 05 Jul 2019 12:42:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.05_model.r INFO @ Fri, 05 Jul 2019 12:42:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:42:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:42:28: start X-correlation... INFO @ Fri, 05 Jul 2019 12:42:28: end of X-cor INFO @ Fri, 05 Jul 2019 12:42:28: #2 finished! INFO @ Fri, 05 Jul 2019 12:42:28: #2 predicted fragment length is 229 bps INFO @ Fri, 05 Jul 2019 12:42:28: #2 alternative fragment length(s) may be 44,229 bps INFO @ Fri, 05 Jul 2019 12:42:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.10_model.r INFO @ Fri, 05 Jul 2019 12:42:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:42:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:43:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:43:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:43:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:43:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:43:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:43:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.20_summits.bed INFO @ Fri, 05 Jul 2019 12:43:59: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (452 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.05_summits.bed INFO @ Fri, 05 Jul 2019 12:44:23: Done! pass1 - making usageList (46 chroms): 3 millis pass2 - checking and writing primary data (2003 records, 4 fields): 17 millis INFO @ Fri, 05 Jul 2019 12:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148692/SRX148692.10_summits.bed INFO @ Fri, 05 Jul 2019 12:44:23: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (880 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。