Job ID = 2003172 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 44,516,649 reads read : 44,516,649 reads written : 44,516,649 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR498445.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:52 44516649 reads; of these: 44516649 (100.00%) were unpaired; of these: 8783866 (19.73%) aligned 0 times 31740002 (71.30%) aligned exactly 1 time 3992781 (8.97%) aligned >1 times 80.27% overall alignment rate Time searching: 00:15:54 Overall time: 00:15:54 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] 15372336 / 35732783 = 0.4302 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 12:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.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 12:24:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:24:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:24:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.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 12:24:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:24:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:24:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.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 12:24:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:24:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:24:31: 1000000 INFO @ Fri, 05 Jul 2019 12:24:34: 1000000 INFO @ Fri, 05 Jul 2019 12:24:34: 1000000 INFO @ Fri, 05 Jul 2019 12:24:38: 2000000 INFO @ Fri, 05 Jul 2019 12:24:41: 2000000 INFO @ Fri, 05 Jul 2019 12:24:41: 2000000 INFO @ Fri, 05 Jul 2019 12:24:45: 3000000 INFO @ Fri, 05 Jul 2019 12:24:48: 3000000 INFO @ Fri, 05 Jul 2019 12:24:49: 3000000 INFO @ Fri, 05 Jul 2019 12:24:51: 4000000 INFO @ Fri, 05 Jul 2019 12:24:54: 4000000 INFO @ Fri, 05 Jul 2019 12:24:56: 4000000 INFO @ Fri, 05 Jul 2019 12:24:58: 5000000 INFO @ Fri, 05 Jul 2019 12:25:01: 5000000 INFO @ Fri, 05 Jul 2019 12:25:05: 5000000 INFO @ Fri, 05 Jul 2019 12:25:05: 6000000 INFO @ Fri, 05 Jul 2019 12:25:07: 6000000 INFO @ Fri, 05 Jul 2019 12:25:11: 7000000 INFO @ Fri, 05 Jul 2019 12:25:12: 6000000 INFO @ Fri, 05 Jul 2019 12:25:14: 7000000 INFO @ Fri, 05 Jul 2019 12:25:18: 8000000 INFO @ Fri, 05 Jul 2019 12:25:18: 7000000 INFO @ Fri, 05 Jul 2019 12:25:20: 8000000 INFO @ Fri, 05 Jul 2019 12:25:24: 9000000 INFO @ Fri, 05 Jul 2019 12:25:25: 8000000 INFO @ Fri, 05 Jul 2019 12:25:27: 9000000 INFO @ Fri, 05 Jul 2019 12:25:31: 10000000 INFO @ Fri, 05 Jul 2019 12:25:32: 9000000 INFO @ Fri, 05 Jul 2019 12:25:33: 10000000 INFO @ Fri, 05 Jul 2019 12:25:37: 11000000 INFO @ Fri, 05 Jul 2019 12:25:40: 10000000 INFO @ Fri, 05 Jul 2019 12:25:41: 11000000 INFO @ Fri, 05 Jul 2019 12:25:44: 12000000 INFO @ Fri, 05 Jul 2019 12:25:47: 11000000 INFO @ Fri, 05 Jul 2019 12:25:48: 12000000 INFO @ Fri, 05 Jul 2019 12:25:51: 13000000 INFO @ Fri, 05 Jul 2019 12:25:54: 12000000 INFO @ Fri, 05 Jul 2019 12:25:55: 13000000 INFO @ Fri, 05 Jul 2019 12:25:58: 14000000 INFO @ Fri, 05 Jul 2019 12:26:01: 13000000 INFO @ Fri, 05 Jul 2019 12:26:02: 14000000 INFO @ Fri, 05 Jul 2019 12:26:05: 15000000 INFO @ Fri, 05 Jul 2019 12:26:08: 14000000 INFO @ Fri, 05 Jul 2019 12:26:09: 15000000 INFO @ Fri, 05 Jul 2019 12:26:13: 16000000 INFO @ Fri, 05 Jul 2019 12:26:16: 15000000 INFO @ Fri, 05 Jul 2019 12:26:16: 16000000 INFO @ Fri, 05 Jul 2019 12:26:20: 17000000 INFO @ Fri, 05 Jul 2019 12:26:23: 16000000 INFO @ Fri, 05 Jul 2019 12:26:24: 17000000 INFO @ Fri, 05 Jul 2019 12:26:27: 18000000 INFO @ Fri, 05 Jul 2019 12:26:31: 18000000 INFO @ Fri, 05 Jul 2019 12:26:31: 17000000 INFO @ Fri, 05 Jul 2019 12:26:34: 19000000 INFO @ Fri, 05 Jul 2019 12:26:38: 18000000 INFO @ Fri, 05 Jul 2019 12:26:38: 19000000 INFO @ Fri, 05 Jul 2019 12:26:41: 20000000 INFO @ Fri, 05 Jul 2019 12:26:44: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:26:44: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:26:44: #1 total tags in treatment: 20360447 INFO @ Fri, 05 Jul 2019 12:26:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:26:44: #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 12:26:44: #1 tags after filtering in treatment: 20360195 INFO @ Fri, 05 Jul 2019 12:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:26:44: #1 finished! INFO @ Fri, 05 Jul 2019 12:26:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:26:46: 20000000 INFO @ Fri, 05 Jul 2019 12:26:47: 19000000 INFO @ Fri, 05 Jul 2019 12:26:48: #2 number of paired peaks: 29732 INFO @ Fri, 05 Jul 2019 12:26:48: start model_add_line... INFO @ Fri, 05 Jul 2019 12:26:48: start X-correlation... INFO @ Fri, 05 Jul 2019 12:26:48: end of X-cor INFO @ Fri, 05 Jul 2019 12:26:48: #2 finished! INFO @ Fri, 05 Jul 2019 12:26:48: #2 predicted fragment length is 217 bps INFO @ Fri, 05 Jul 2019 12:26:48: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 05 Jul 2019 12:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.05_model.r INFO @ Fri, 05 Jul 2019 12:26:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:26:49: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:26:49: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:26:49: #1 total tags in treatment: 20360447 INFO @ Fri, 05 Jul 2019 12:26:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:26:49: #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 12:26:50: #1 tags after filtering in treatment: 20360195 INFO @ Fri, 05 Jul 2019 12:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:26:50: #1 finished! INFO @ Fri, 05 Jul 2019 12:26:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:26:53: #2 number of paired peaks: 29732 INFO @ Fri, 05 Jul 2019 12:26:53: start model_add_line... INFO @ Fri, 05 Jul 2019 12:26:54: start X-correlation... INFO @ Fri, 05 Jul 2019 12:26:54: end of X-cor INFO @ Fri, 05 Jul 2019 12:26:54: #2 finished! INFO @ Fri, 05 Jul 2019 12:26:54: #2 predicted fragment length is 217 bps INFO @ Fri, 05 Jul 2019 12:26:54: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 05 Jul 2019 12:26:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.10_model.r INFO @ Fri, 05 Jul 2019 12:26:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:26:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:26:54: 20000000 INFO @ Fri, 05 Jul 2019 12:26:57: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:26:57: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:26:57: #1 total tags in treatment: 20360447 INFO @ Fri, 05 Jul 2019 12:26:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:26:57: #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 12:26:58: #1 tags after filtering in treatment: 20360195 INFO @ Fri, 05 Jul 2019 12:26:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:26:58: #1 finished! INFO @ Fri, 05 Jul 2019 12:26:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:27:01: #2 number of paired peaks: 29732 INFO @ Fri, 05 Jul 2019 12:27:01: start model_add_line... INFO @ Fri, 05 Jul 2019 12:27:02: start X-correlation... INFO @ Fri, 05 Jul 2019 12:27:02: end of X-cor INFO @ Fri, 05 Jul 2019 12:27:02: #2 finished! INFO @ Fri, 05 Jul 2019 12:27:02: #2 predicted fragment length is 217 bps INFO @ Fri, 05 Jul 2019 12:27:02: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 05 Jul 2019 12:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.20_model.r INFO @ Fri, 05 Jul 2019 12:27:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:27:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:27:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:28:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:28:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:28:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:28:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.05_summits.bed INFO @ Fri, 05 Jul 2019 12:28:26: Done! pass1 - making usageList (125 chroms): 6 millis pass2 - checking and writing primary data (25840 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:28:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:28:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:28:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.10_summits.bed INFO @ Fri, 05 Jul 2019 12:28:31: Done! pass1 - making usageList (115 chroms): 5 millis pass2 - checking and writing primary data (22673 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:28:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:28:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:28:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148691/SRX148691.20_summits.bed INFO @ Fri, 05 Jul 2019 12:28:42: Done! pass1 - making usageList (105 chroms): 8 millis pass2 - checking and writing primary data (19851 records, 4 fields): 32 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。