Job ID = 1293190 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,790,196 reads read : 36,790,196 reads written : 36,790,196 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: 00:10:04 36790196 reads; of these: 36790196 (100.00%) were unpaired; of these: 10094691 (27.44%) aligned 0 times 15502682 (42.14%) aligned exactly 1 time 11192823 (30.42%) aligned >1 times 72.56% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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_sort_core] merging from 12 files... [bam_rmdupse_core] 10237700 / 26695505 = 0.3835 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 22:45:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.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 22:45:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:45:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:45:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.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 22:45:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:45:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:45:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.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 22:45:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:45:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:45:53: 1000000 INFO @ Sun, 02 Jun 2019 22:45:55: 1000000 INFO @ Sun, 02 Jun 2019 22:45:55: 1000000 INFO @ Sun, 02 Jun 2019 22:46:00: 2000000 INFO @ Sun, 02 Jun 2019 22:46:04: 2000000 INFO @ Sun, 02 Jun 2019 22:46:04: 2000000 INFO @ Sun, 02 Jun 2019 22:46:07: 3000000 INFO @ Sun, 02 Jun 2019 22:46:13: 3000000 INFO @ Sun, 02 Jun 2019 22:46:13: 3000000 INFO @ Sun, 02 Jun 2019 22:46:14: 4000000 INFO @ Sun, 02 Jun 2019 22:46:21: 5000000 INFO @ Sun, 02 Jun 2019 22:46:22: 4000000 INFO @ Sun, 02 Jun 2019 22:46:22: 4000000 INFO @ Sun, 02 Jun 2019 22:46:28: 6000000 INFO @ Sun, 02 Jun 2019 22:46:31: 5000000 INFO @ Sun, 02 Jun 2019 22:46:32: 5000000 INFO @ Sun, 02 Jun 2019 22:46:35: 7000000 INFO @ Sun, 02 Jun 2019 22:46:40: 6000000 INFO @ Sun, 02 Jun 2019 22:46:42: 6000000 INFO @ Sun, 02 Jun 2019 22:46:42: 8000000 INFO @ Sun, 02 Jun 2019 22:46:49: 7000000 INFO @ Sun, 02 Jun 2019 22:46:49: 9000000 INFO @ Sun, 02 Jun 2019 22:46:50: 7000000 INFO @ Sun, 02 Jun 2019 22:46:57: 10000000 INFO @ Sun, 02 Jun 2019 22:46:58: 8000000 INFO @ Sun, 02 Jun 2019 22:46:59: 8000000 INFO @ Sun, 02 Jun 2019 22:47:04: 11000000 INFO @ Sun, 02 Jun 2019 22:47:07: 9000000 INFO @ Sun, 02 Jun 2019 22:47:08: 9000000 INFO @ Sun, 02 Jun 2019 22:47:12: 12000000 INFO @ Sun, 02 Jun 2019 22:47:16: 10000000 INFO @ Sun, 02 Jun 2019 22:47:17: 10000000 INFO @ Sun, 02 Jun 2019 22:47:19: 13000000 INFO @ Sun, 02 Jun 2019 22:47:24: 11000000 INFO @ Sun, 02 Jun 2019 22:47:26: 11000000 INFO @ Sun, 02 Jun 2019 22:47:26: 14000000 INFO @ Sun, 02 Jun 2019 22:47:33: 12000000 INFO @ Sun, 02 Jun 2019 22:47:33: 15000000 INFO @ Sun, 02 Jun 2019 22:47:34: 12000000 INFO @ Sun, 02 Jun 2019 22:47:40: 16000000 INFO @ Sun, 02 Jun 2019 22:47:42: 13000000 INFO @ Sun, 02 Jun 2019 22:47:43: 13000000 INFO @ Sun, 02 Jun 2019 22:47:43: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:47:43: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:47:43: #1 total tags in treatment: 16457805 INFO @ Sun, 02 Jun 2019 22:47:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:47:43: #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 22:47:43: #1 tags after filtering in treatment: 16457805 INFO @ Sun, 02 Jun 2019 22:47:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:47:43: #1 finished! INFO @ Sun, 02 Jun 2019 22:47:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:47:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:47:45: #2 number of paired peaks: 1867 INFO @ Sun, 02 Jun 2019 22:47:45: start model_add_line... INFO @ Sun, 02 Jun 2019 22:47:45: start X-correlation... INFO @ Sun, 02 Jun 2019 22:47:45: end of X-cor INFO @ Sun, 02 Jun 2019 22:47:45: #2 finished! INFO @ Sun, 02 Jun 2019 22:47:45: #2 predicted fragment length is 76 bps INFO @ Sun, 02 Jun 2019 22:47:45: #2 alternative fragment length(s) may be 4,76 bps INFO @ Sun, 02 Jun 2019 22:47:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.20_model.r WARNING @ Sun, 02 Jun 2019 22:47:45: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:47:45: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Sun, 02 Jun 2019 22:47:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:47:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:47:50: 14000000 INFO @ Sun, 02 Jun 2019 22:47:51: 14000000 INFO @ Sun, 02 Jun 2019 22:47:59: 15000000 INFO @ Sun, 02 Jun 2019 22:48:00: 15000000 INFO @ Sun, 02 Jun 2019 22:48:07: 16000000 INFO @ Sun, 02 Jun 2019 22:48:08: 16000000 INFO @ Sun, 02 Jun 2019 22:48:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:48:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:48:11: #1 total tags in treatment: 16457805 INFO @ Sun, 02 Jun 2019 22:48:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:48:11: #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 22:48:12: #1 tags after filtering in treatment: 16457805 INFO @ Sun, 02 Jun 2019 22:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:48:12: #1 finished! INFO @ Sun, 02 Jun 2019 22:48:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:48:12: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:48:12: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:48:12: #1 total tags in treatment: 16457805 INFO @ Sun, 02 Jun 2019 22:48:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:48:12: #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 22:48:12: #1 tags after filtering in treatment: 16457805 INFO @ Sun, 02 Jun 2019 22:48:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:48:12: #1 finished! INFO @ Sun, 02 Jun 2019 22:48:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:48:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:48:13: #2 number of paired peaks: 1867 INFO @ Sun, 02 Jun 2019 22:48:13: start model_add_line... INFO @ Sun, 02 Jun 2019 22:48:13: start X-correlation... INFO @ Sun, 02 Jun 2019 22:48:13: end of X-cor INFO @ Sun, 02 Jun 2019 22:48:13: #2 finished! INFO @ Sun, 02 Jun 2019 22:48:13: #2 predicted fragment length is 76 bps INFO @ Sun, 02 Jun 2019 22:48:13: #2 alternative fragment length(s) may be 4,76 bps INFO @ Sun, 02 Jun 2019 22:48:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.05_model.r WARNING @ Sun, 02 Jun 2019 22:48:14: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:48:14: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Sun, 02 Jun 2019 22:48:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:48:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:48:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:48:14: #2 number of paired peaks: 1867 INFO @ Sun, 02 Jun 2019 22:48:14: start model_add_line... INFO @ Sun, 02 Jun 2019 22:48:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:48:14: end of X-cor INFO @ Sun, 02 Jun 2019 22:48:14: #2 finished! INFO @ Sun, 02 Jun 2019 22:48:14: #2 predicted fragment length is 76 bps INFO @ Sun, 02 Jun 2019 22:48:14: #2 alternative fragment length(s) may be 4,76 bps INFO @ Sun, 02 Jun 2019 22:48:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.10_model.r WARNING @ Sun, 02 Jun 2019 22:48:14: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:48:14: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Sun, 02 Jun 2019 22:48:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:48:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:48:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:48:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:48:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:48:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:48:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.20_summits.bed INFO @ Sun, 02 Jun 2019 22:48:49: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2894 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:48:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:48:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:49:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:49:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:49:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.05_summits.bed INFO @ Sun, 02 Jun 2019 22:49:18: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (10317 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:49:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:49:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:49:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402748/SRX5402748.10_summits.bed INFO @ Sun, 02 Jun 2019 22:49:19: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6489 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。