Job ID = 1291523 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,127,846 reads read : 12,127,846 reads written : 12,127,846 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:06 12127846 reads; of these: 12127846 (100.00%) were unpaired; of these: 553061 (4.56%) aligned 0 times 8297310 (68.42%) aligned exactly 1 time 3277475 (27.02%) aligned >1 times 95.44% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 4869000 / 11574785 = 0.4207 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 @ Sun, 02 Jun 2019 16:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.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 @ Sun, 02 Jun 2019 16:03:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.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 @ Sun, 02 Jun 2019 16:03:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.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 @ Sun, 02 Jun 2019 16:03:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:59: 1000000 INFO @ Sun, 02 Jun 2019 16:03:59: 1000000 INFO @ Sun, 02 Jun 2019 16:03:59: 1000000 INFO @ Sun, 02 Jun 2019 16:04:06: 2000000 INFO @ Sun, 02 Jun 2019 16:04:06: 2000000 INFO @ Sun, 02 Jun 2019 16:04:06: 2000000 INFO @ Sun, 02 Jun 2019 16:04:12: 3000000 INFO @ Sun, 02 Jun 2019 16:04:13: 3000000 INFO @ Sun, 02 Jun 2019 16:04:13: 3000000 INFO @ Sun, 02 Jun 2019 16:04:20: 4000000 INFO @ Sun, 02 Jun 2019 16:04:20: 4000000 INFO @ Sun, 02 Jun 2019 16:04:20: 4000000 INFO @ Sun, 02 Jun 2019 16:04:26: 5000000 INFO @ Sun, 02 Jun 2019 16:04:26: 5000000 INFO @ Sun, 02 Jun 2019 16:04:27: 5000000 INFO @ Sun, 02 Jun 2019 16:04:32: 6000000 INFO @ Sun, 02 Jun 2019 16:04:33: 6000000 INFO @ Sun, 02 Jun 2019 16:04:33: 6000000 INFO @ Sun, 02 Jun 2019 16:04:36: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:04:36: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:04:36: #1 total tags in treatment: 6705785 INFO @ Sun, 02 Jun 2019 16:04:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:04:36: #1 tags after filtering in treatment: 6705785 INFO @ Sun, 02 Jun 2019 16:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:36: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:37: #2 number of paired peaks: 2013 INFO @ Sun, 02 Jun 2019 16:04:37: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:37: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:37: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:37: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:37: #2 predicted fragment length is 147 bps INFO @ Sun, 02 Jun 2019 16:04:37: #2 alternative fragment length(s) may be 0,41,68,92,119,147 bps INFO @ Sun, 02 Jun 2019 16:04:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.20_model.r INFO @ Sun, 02 Jun 2019 16:04:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:38: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:04:38: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:04:38: #1 total tags in treatment: 6705785 INFO @ Sun, 02 Jun 2019 16:04:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:04:38: #1 tags after filtering in treatment: 6705785 INFO @ Sun, 02 Jun 2019 16:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:38: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:38: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:04:38: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:04:38: #1 total tags in treatment: 6705785 INFO @ Sun, 02 Jun 2019 16:04:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:04:38: #1 tags after filtering in treatment: 6705785 INFO @ Sun, 02 Jun 2019 16:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:38: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:39: #2 number of paired peaks: 2013 INFO @ Sun, 02 Jun 2019 16:04:39: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:39: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:39: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:39: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:39: #2 predicted fragment length is 147 bps INFO @ Sun, 02 Jun 2019 16:04:39: #2 alternative fragment length(s) may be 0,41,68,92,119,147 bps INFO @ Sun, 02 Jun 2019 16:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.05_model.r INFO @ Sun, 02 Jun 2019 16:04:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:39: #2 number of paired peaks: 2013 INFO @ Sun, 02 Jun 2019 16:04:39: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:39: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:39: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:39: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:39: #2 predicted fragment length is 147 bps INFO @ Sun, 02 Jun 2019 16:04:39: #2 alternative fragment length(s) may be 0,41,68,92,119,147 bps INFO @ Sun, 02 Jun 2019 16:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.10_model.r INFO @ Sun, 02 Jun 2019 16:04:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:04:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:04:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:05:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:05:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:05:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.20_summits.bed INFO @ Sun, 02 Jun 2019 16:05:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (68 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.05_summits.bed INFO @ Sun, 02 Jun 2019 16:05:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113601/SRX113601.10_summits.bed INFO @ Sun, 02 Jun 2019 16:05:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。