Job ID = 1292785 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,634,552 reads read : 22,634,552 reads written : 22,634,552 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: 00:04:47 22634552 reads; of these: 22634552 (100.00%) were unpaired; of these: 3509016 (15.50%) aligned 0 times 16087791 (71.08%) aligned exactly 1 time 3037745 (13.42%) aligned >1 times 84.50% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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 8 files... [bam_rmdupse_core] 3757908 / 19125536 = 0.1965 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 20:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.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 20:51:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:51:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.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 20:51:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:51:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.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 20:51:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:51:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:51:51: 1000000 INFO @ Sun, 02 Jun 2019 20:51:52: 1000000 INFO @ Sun, 02 Jun 2019 20:51:53: 1000000 INFO @ Sun, 02 Jun 2019 20:51:59: 2000000 INFO @ Sun, 02 Jun 2019 20:52:00: 2000000 INFO @ Sun, 02 Jun 2019 20:52:03: 2000000 INFO @ Sun, 02 Jun 2019 20:52:07: 3000000 INFO @ Sun, 02 Jun 2019 20:52:09: 3000000 INFO @ Sun, 02 Jun 2019 20:52:13: 3000000 INFO @ Sun, 02 Jun 2019 20:52:15: 4000000 INFO @ Sun, 02 Jun 2019 20:52:17: 4000000 INFO @ Sun, 02 Jun 2019 20:52:23: 4000000 INFO @ Sun, 02 Jun 2019 20:52:23: 5000000 INFO @ Sun, 02 Jun 2019 20:52:26: 5000000 INFO @ Sun, 02 Jun 2019 20:52:31: 6000000 INFO @ Sun, 02 Jun 2019 20:52:32: 5000000 INFO @ Sun, 02 Jun 2019 20:52:34: 6000000 INFO @ Sun, 02 Jun 2019 20:52:39: 7000000 INFO @ Sun, 02 Jun 2019 20:52:42: 6000000 INFO @ Sun, 02 Jun 2019 20:52:42: 7000000 INFO @ Sun, 02 Jun 2019 20:52:47: 8000000 INFO @ Sun, 02 Jun 2019 20:52:51: 8000000 INFO @ Sun, 02 Jun 2019 20:52:51: 7000000 INFO @ Sun, 02 Jun 2019 20:52:55: 9000000 INFO @ Sun, 02 Jun 2019 20:53:00: 9000000 INFO @ Sun, 02 Jun 2019 20:53:01: 8000000 INFO @ Sun, 02 Jun 2019 20:53:03: 10000000 INFO @ Sun, 02 Jun 2019 20:53:08: 10000000 INFO @ Sun, 02 Jun 2019 20:53:11: 9000000 INFO @ Sun, 02 Jun 2019 20:53:11: 11000000 INFO @ Sun, 02 Jun 2019 20:53:16: 11000000 INFO @ Sun, 02 Jun 2019 20:53:19: 12000000 INFO @ Sun, 02 Jun 2019 20:53:20: 10000000 INFO @ Sun, 02 Jun 2019 20:53:24: 12000000 INFO @ Sun, 02 Jun 2019 20:53:27: 13000000 INFO @ Sun, 02 Jun 2019 20:53:30: 11000000 INFO @ Sun, 02 Jun 2019 20:53:32: 13000000 INFO @ Sun, 02 Jun 2019 20:53:34: 14000000 INFO @ Sun, 02 Jun 2019 20:53:40: 12000000 INFO @ Sun, 02 Jun 2019 20:53:40: 14000000 INFO @ Sun, 02 Jun 2019 20:53:42: 15000000 INFO @ Sun, 02 Jun 2019 20:53:46: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:53:46: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:53:46: #1 total tags in treatment: 15367628 INFO @ Sun, 02 Jun 2019 20:53:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:53:46: #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 20:53:46: #1 tags after filtering in treatment: 15367628 INFO @ Sun, 02 Jun 2019 20:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:53:46: #1 finished! INFO @ Sun, 02 Jun 2019 20:53:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:53:47: #2 number of paired peaks: 265 WARNING @ Sun, 02 Jun 2019 20:53:47: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sun, 02 Jun 2019 20:53:47: start model_add_line... INFO @ Sun, 02 Jun 2019 20:53:47: start X-correlation... INFO @ Sun, 02 Jun 2019 20:53:47: end of X-cor INFO @ Sun, 02 Jun 2019 20:53:47: #2 finished! INFO @ Sun, 02 Jun 2019 20:53:47: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 20:53:47: #2 alternative fragment length(s) may be 2,41,595,597 bps INFO @ Sun, 02 Jun 2019 20:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.10_model.r WARNING @ Sun, 02 Jun 2019 20:53:47: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:53:47: #2 You may need to consider one of the other alternative d(s): 2,41,595,597 WARNING @ Sun, 02 Jun 2019 20:53:47: #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 20:53:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:53:47: 15000000 INFO @ Sun, 02 Jun 2019 20:53:49: 13000000 INFO @ Sun, 02 Jun 2019 20:53:50: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:53:51: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:53:51: #1 total tags in treatment: 15367628 INFO @ Sun, 02 Jun 2019 20:53:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:53:51: #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 20:53:51: #1 tags after filtering in treatment: 15367628 INFO @ Sun, 02 Jun 2019 20:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:53:51: #1 finished! INFO @ Sun, 02 Jun 2019 20:53:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:53:52: #2 number of paired peaks: 265 WARNING @ Sun, 02 Jun 2019 20:53:52: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sun, 02 Jun 2019 20:53:52: start model_add_line... INFO @ Sun, 02 Jun 2019 20:53:52: start X-correlation... INFO @ Sun, 02 Jun 2019 20:53:52: end of X-cor INFO @ Sun, 02 Jun 2019 20:53:52: #2 finished! INFO @ Sun, 02 Jun 2019 20:53:52: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 20:53:52: #2 alternative fragment length(s) may be 2,41,595,597 bps INFO @ Sun, 02 Jun 2019 20:53:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.05_model.r WARNING @ Sun, 02 Jun 2019 20:53:52: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:53:52: #2 You may need to consider one of the other alternative d(s): 2,41,595,597 WARNING @ Sun, 02 Jun 2019 20:53:52: #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 20:53:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:53:58: 14000000 INFO @ Sun, 02 Jun 2019 20:54:08: 15000000 INFO @ Sun, 02 Jun 2019 20:54:12: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:54:12: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:54:12: #1 total tags in treatment: 15367628 INFO @ Sun, 02 Jun 2019 20:54:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:54:12: #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 20:54:12: #1 tags after filtering in treatment: 15367628 INFO @ Sun, 02 Jun 2019 20:54:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:54:12: #1 finished! INFO @ Sun, 02 Jun 2019 20:54:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:54:13: #2 number of paired peaks: 265 WARNING @ Sun, 02 Jun 2019 20:54:13: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sun, 02 Jun 2019 20:54:13: start model_add_line... INFO @ Sun, 02 Jun 2019 20:54:13: start X-correlation... INFO @ Sun, 02 Jun 2019 20:54:13: end of X-cor INFO @ Sun, 02 Jun 2019 20:54:13: #2 finished! INFO @ Sun, 02 Jun 2019 20:54:13: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 20:54:13: #2 alternative fragment length(s) may be 2,41,595,597 bps INFO @ Sun, 02 Jun 2019 20:54:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.20_model.r WARNING @ Sun, 02 Jun 2019 20:54:13: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:54:13: #2 You may need to consider one of the other alternative d(s): 2,41,595,597 WARNING @ Sun, 02 Jun 2019 20:54:13: #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 20:54:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:54:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:54:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:54:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.10_summits.bed INFO @ Sun, 02 Jun 2019 20:54:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:54:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.05_summits.bed INFO @ Sun, 02 Jun 2019 20:54:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (716 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:54:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:55:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:55:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495034/SRX495034.20_summits.bed INFO @ Sun, 02 Jun 2019 20:55:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (121 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。