Job ID = 2589915 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,488,610 reads read : 6,488,610 reads written : 6,488,610 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947559.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:58 6488610 reads; of these: 6488610 (100.00%) were unpaired; of these: 1303612 (20.09%) aligned 0 times 4559625 (70.27%) aligned exactly 1 time 625373 (9.64%) aligned >1 times 79.91% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1407350 / 5184998 = 0.2714 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 @ Mon, 12 Aug 2019 18:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 18:46:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:46:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 18:46:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:46:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 18:46:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:46:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:52: 1000000 INFO @ Mon, 12 Aug 2019 18:46:54: 1000000 INFO @ Mon, 12 Aug 2019 18:46:54: 1000000 INFO @ Mon, 12 Aug 2019 18:46:58: 2000000 INFO @ Mon, 12 Aug 2019 18:47:00: 2000000 INFO @ Mon, 12 Aug 2019 18:47:01: 2000000 INFO @ Mon, 12 Aug 2019 18:47:04: 3000000 INFO @ Mon, 12 Aug 2019 18:47:07: 3000000 INFO @ Mon, 12 Aug 2019 18:47:08: 3000000 INFO @ Mon, 12 Aug 2019 18:47:09: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:47:09: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:47:09: #1 total tags in treatment: 3777648 INFO @ Mon, 12 Aug 2019 18:47:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:47:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:47:09: #1 tags after filtering in treatment: 3777648 INFO @ Mon, 12 Aug 2019 18:47:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:47:09: #1 finished! INFO @ Mon, 12 Aug 2019 18:47:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:47:09: #2 number of paired peaks: 2666 INFO @ Mon, 12 Aug 2019 18:47:09: start model_add_line... INFO @ Mon, 12 Aug 2019 18:47:09: start X-correlation... INFO @ Mon, 12 Aug 2019 18:47:09: end of X-cor INFO @ Mon, 12 Aug 2019 18:47:09: #2 finished! INFO @ Mon, 12 Aug 2019 18:47:09: #2 predicted fragment length is 162 bps INFO @ Mon, 12 Aug 2019 18:47:09: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 12 Aug 2019 18:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.05_model.r INFO @ Mon, 12 Aug 2019 18:47:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:47:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:47:11: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:47:11: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:47:11: #1 total tags in treatment: 3777648 INFO @ Mon, 12 Aug 2019 18:47:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:47:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:47:11: #1 tags after filtering in treatment: 3777648 INFO @ Mon, 12 Aug 2019 18:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:47:11: #1 finished! INFO @ Mon, 12 Aug 2019 18:47:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:47:12: #2 number of paired peaks: 2666 INFO @ Mon, 12 Aug 2019 18:47:12: start model_add_line... INFO @ Mon, 12 Aug 2019 18:47:12: start X-correlation... INFO @ Mon, 12 Aug 2019 18:47:12: end of X-cor INFO @ Mon, 12 Aug 2019 18:47:12: #2 finished! INFO @ Mon, 12 Aug 2019 18:47:12: #2 predicted fragment length is 162 bps INFO @ Mon, 12 Aug 2019 18:47:12: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 12 Aug 2019 18:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.20_model.r INFO @ Mon, 12 Aug 2019 18:47:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:47:13: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:47:13: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:47:13: #1 total tags in treatment: 3777648 INFO @ Mon, 12 Aug 2019 18:47:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:47:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:47:13: #1 tags after filtering in treatment: 3777648 INFO @ Mon, 12 Aug 2019 18:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:47:13: #1 finished! INFO @ Mon, 12 Aug 2019 18:47:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:47:14: #2 number of paired peaks: 2666 INFO @ Mon, 12 Aug 2019 18:47:14: start model_add_line... INFO @ Mon, 12 Aug 2019 18:47:14: start X-correlation... INFO @ Mon, 12 Aug 2019 18:47:14: end of X-cor INFO @ Mon, 12 Aug 2019 18:47:14: #2 finished! INFO @ Mon, 12 Aug 2019 18:47:14: #2 predicted fragment length is 162 bps INFO @ Mon, 12 Aug 2019 18:47:14: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 12 Aug 2019 18:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.10_model.r INFO @ Mon, 12 Aug 2019 18:47:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:47:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:47:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:47:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.05_summits.bed INFO @ Mon, 12 Aug 2019 18:47:28: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (7167 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:47:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.20_summits.bed INFO @ Mon, 12 Aug 2019 18:47:31: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2760 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331322/SRX331322.10_summits.bed INFO @ Mon, 12 Aug 2019 18:47:34: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4792 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。