Job ID = 1292787 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,255,371 reads read : 12,255,371 reads written : 12,255,371 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: 00:03:39 12255371 reads; of these: 12255371 (100.00%) were unpaired; of these: 2103070 (17.16%) aligned 0 times 8163790 (66.61%) aligned exactly 1 time 1988511 (16.23%) aligned >1 times 82.84% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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] 2432232 / 10152301 = 0.2396 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 20:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.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 20:38:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:38:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.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 20:38:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:38:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.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 20:38:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:38:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:39:08: 1000000 INFO @ Sun, 02 Jun 2019 20:39:08: 1000000 INFO @ Sun, 02 Jun 2019 20:39:08: 1000000 INFO @ Sun, 02 Jun 2019 20:39:23: 2000000 INFO @ Sun, 02 Jun 2019 20:39:24: 2000000 INFO @ Sun, 02 Jun 2019 20:39:25: 2000000 INFO @ Sun, 02 Jun 2019 20:39:38: 3000000 INFO @ Sun, 02 Jun 2019 20:39:39: 3000000 INFO @ Sun, 02 Jun 2019 20:39:41: 3000000 INFO @ Sun, 02 Jun 2019 20:39:53: 4000000 INFO @ Sun, 02 Jun 2019 20:39:54: 4000000 INFO @ Sun, 02 Jun 2019 20:39:57: 4000000 INFO @ Sun, 02 Jun 2019 20:40:08: 5000000 INFO @ Sun, 02 Jun 2019 20:40:08: 5000000 INFO @ Sun, 02 Jun 2019 20:40:12: 5000000 INFO @ Sun, 02 Jun 2019 20:40:23: 6000000 INFO @ Sun, 02 Jun 2019 20:40:24: 6000000 INFO @ Sun, 02 Jun 2019 20:40:28: 6000000 INFO @ Sun, 02 Jun 2019 20:40:38: 7000000 INFO @ Sun, 02 Jun 2019 20:40:39: 7000000 INFO @ Sun, 02 Jun 2019 20:40:44: 7000000 INFO @ Sun, 02 Jun 2019 20:40:48: #1 tag size is determined as 37 bps INFO @ Sun, 02 Jun 2019 20:40:48: #1 tag size = 37 INFO @ Sun, 02 Jun 2019 20:40:48: #1 total tags in treatment: 7720069 INFO @ Sun, 02 Jun 2019 20:40:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:40:48: #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 20:40:49: #1 tags after filtering in treatment: 7720069 INFO @ Sun, 02 Jun 2019 20:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:40:49: #1 finished! INFO @ Sun, 02 Jun 2019 20:40:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:40:49: #1 tag size is determined as 37 bps INFO @ Sun, 02 Jun 2019 20:40:49: #1 tag size = 37 INFO @ Sun, 02 Jun 2019 20:40:49: #1 total tags in treatment: 7720069 INFO @ Sun, 02 Jun 2019 20:40:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:40:49: #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 20:40:49: #1 tags after filtering in treatment: 7720069 INFO @ Sun, 02 Jun 2019 20:40:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:40:49: #1 finished! INFO @ Sun, 02 Jun 2019 20:40:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:40:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:40:50: #2 number of paired peaks: 566 WARNING @ Sun, 02 Jun 2019 20:40:50: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Sun, 02 Jun 2019 20:40:50: start model_add_line... INFO @ Sun, 02 Jun 2019 20:40:50: start X-correlation... INFO @ Sun, 02 Jun 2019 20:40:50: end of X-cor INFO @ Sun, 02 Jun 2019 20:40:50: #2 finished! INFO @ Sun, 02 Jun 2019 20:40:50: #2 predicted fragment length is 86 bps INFO @ Sun, 02 Jun 2019 20:40:50: #2 alternative fragment length(s) may be 86 bps INFO @ Sun, 02 Jun 2019 20:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.05_model.r INFO @ Sun, 02 Jun 2019 20:40:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:40:50: #2 number of paired peaks: 566 WARNING @ Sun, 02 Jun 2019 20:40:50: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Sun, 02 Jun 2019 20:40:50: start model_add_line... INFO @ Sun, 02 Jun 2019 20:40:50: start X-correlation... INFO @ Sun, 02 Jun 2019 20:40:50: end of X-cor INFO @ Sun, 02 Jun 2019 20:40:50: #2 finished! INFO @ Sun, 02 Jun 2019 20:40:50: #2 predicted fragment length is 86 bps INFO @ Sun, 02 Jun 2019 20:40:50: #2 alternative fragment length(s) may be 86 bps INFO @ Sun, 02 Jun 2019 20:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.20_model.r INFO @ Sun, 02 Jun 2019 20:40:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:40:54: #1 tag size is determined as 37 bps INFO @ Sun, 02 Jun 2019 20:40:54: #1 tag size = 37 INFO @ Sun, 02 Jun 2019 20:40:54: #1 total tags in treatment: 7720069 INFO @ Sun, 02 Jun 2019 20:40:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:40:54: #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 20:40:54: #1 tags after filtering in treatment: 7720069 INFO @ Sun, 02 Jun 2019 20:40:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:40:54: #1 finished! INFO @ Sun, 02 Jun 2019 20:40:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:40:55: #2 number of paired peaks: 566 WARNING @ Sun, 02 Jun 2019 20:40:55: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Sun, 02 Jun 2019 20:40:55: start model_add_line... INFO @ Sun, 02 Jun 2019 20:40:55: start X-correlation... INFO @ Sun, 02 Jun 2019 20:40:55: end of X-cor INFO @ Sun, 02 Jun 2019 20:40:55: #2 finished! INFO @ Sun, 02 Jun 2019 20:40:55: #2 predicted fragment length is 86 bps INFO @ Sun, 02 Jun 2019 20:40:55: #2 alternative fragment length(s) may be 86 bps INFO @ Sun, 02 Jun 2019 20:40:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.10_model.r INFO @ Sun, 02 Jun 2019 20:40:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:40:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:41:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:41:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:41:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:41:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:41:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:41:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.05_summits.bed INFO @ Sun, 02 Jun 2019 20:41:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1413 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:41:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:41:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:41:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.20_summits.bed INFO @ Sun, 02 Jun 2019 20:41:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (430 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495036/SRX495036.10_summits.bed INFO @ Sun, 02 Jun 2019 20:41:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (795 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。