Job ID = 1291867 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,440,500 reads read : 16,440,500 reads written : 16,440,500 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: 00:04:13 16440500 reads; of these: 16440500 (100.00%) were unpaired; of these: 138374 (0.84%) aligned 0 times 13512969 (82.19%) aligned exactly 1 time 2789157 (16.97%) aligned >1 times 99.16% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 1797617 / 16302126 = 0.1103 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 17:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.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 17:01:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:01:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.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 17:01:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:01:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.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 17:01:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:01:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:01:57: 1000000 INFO @ Sun, 02 Jun 2019 17:01:58: 1000000 INFO @ Sun, 02 Jun 2019 17:01:58: 1000000 INFO @ Sun, 02 Jun 2019 17:02:04: 2000000 INFO @ Sun, 02 Jun 2019 17:02:05: 2000000 INFO @ Sun, 02 Jun 2019 17:02:06: 2000000 INFO @ Sun, 02 Jun 2019 17:02:11: 3000000 INFO @ Sun, 02 Jun 2019 17:02:13: 3000000 INFO @ Sun, 02 Jun 2019 17:02:13: 3000000 INFO @ Sun, 02 Jun 2019 17:02:18: 4000000 INFO @ Sun, 02 Jun 2019 17:02:22: 4000000 INFO @ Sun, 02 Jun 2019 17:02:22: 4000000 INFO @ Sun, 02 Jun 2019 17:02:25: 5000000 INFO @ Sun, 02 Jun 2019 17:02:29: 5000000 INFO @ Sun, 02 Jun 2019 17:02:31: 5000000 INFO @ Sun, 02 Jun 2019 17:02:32: 6000000 INFO @ Sun, 02 Jun 2019 17:02:37: 6000000 INFO @ Sun, 02 Jun 2019 17:02:39: 6000000 INFO @ Sun, 02 Jun 2019 17:02:39: 7000000 INFO @ Sun, 02 Jun 2019 17:02:44: 7000000 INFO @ Sun, 02 Jun 2019 17:02:46: 8000000 INFO @ Sun, 02 Jun 2019 17:02:47: 7000000 INFO @ Sun, 02 Jun 2019 17:02:52: 8000000 INFO @ Sun, 02 Jun 2019 17:02:53: 9000000 INFO @ Sun, 02 Jun 2019 17:02:55: 8000000 INFO @ Sun, 02 Jun 2019 17:03:00: 9000000 INFO @ Sun, 02 Jun 2019 17:03:00: 10000000 INFO @ Sun, 02 Jun 2019 17:03:03: 9000000 INFO @ Sun, 02 Jun 2019 17:03:07: 11000000 INFO @ Sun, 02 Jun 2019 17:03:07: 10000000 INFO @ Sun, 02 Jun 2019 17:03:12: 10000000 INFO @ Sun, 02 Jun 2019 17:03:14: 12000000 INFO @ Sun, 02 Jun 2019 17:03:15: 11000000 INFO @ Sun, 02 Jun 2019 17:03:20: 11000000 INFO @ Sun, 02 Jun 2019 17:03:21: 13000000 INFO @ Sun, 02 Jun 2019 17:03:22: 12000000 INFO @ Sun, 02 Jun 2019 17:03:28: 12000000 INFO @ Sun, 02 Jun 2019 17:03:28: 14000000 INFO @ Sun, 02 Jun 2019 17:03:30: 13000000 INFO @ Sun, 02 Jun 2019 17:03:33: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:03:33: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:03:33: #1 total tags in treatment: 14504509 INFO @ Sun, 02 Jun 2019 17:03:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:03:33: #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 17:03:33: #1 tags after filtering in treatment: 14504509 INFO @ Sun, 02 Jun 2019 17:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:03:33: #1 finished! INFO @ Sun, 02 Jun 2019 17:03:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:03:34: #2 number of paired peaks: 332 WARNING @ Sun, 02 Jun 2019 17:03:34: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Sun, 02 Jun 2019 17:03:34: start model_add_line... INFO @ Sun, 02 Jun 2019 17:03:34: start X-correlation... INFO @ Sun, 02 Jun 2019 17:03:34: end of X-cor INFO @ Sun, 02 Jun 2019 17:03:34: #2 finished! INFO @ Sun, 02 Jun 2019 17:03:34: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 17:03:34: #2 alternative fragment length(s) may be 2,48,538 bps INFO @ Sun, 02 Jun 2019 17:03:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.10_model.r WARNING @ Sun, 02 Jun 2019 17:03:34: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:03:34: #2 You may need to consider one of the other alternative d(s): 2,48,538 WARNING @ Sun, 02 Jun 2019 17:03:34: #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 17:03:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:03:36: 13000000 INFO @ Sun, 02 Jun 2019 17:03:37: 14000000 INFO @ Sun, 02 Jun 2019 17:03:42: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:03:42: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:03:42: #1 total tags in treatment: 14504509 INFO @ Sun, 02 Jun 2019 17:03:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:03:42: #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 17:03:42: #1 tags after filtering in treatment: 14504509 INFO @ Sun, 02 Jun 2019 17:03:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:03:42: #1 finished! INFO @ Sun, 02 Jun 2019 17:03:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:03:44: #2 number of paired peaks: 332 WARNING @ Sun, 02 Jun 2019 17:03:44: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Sun, 02 Jun 2019 17:03:44: start model_add_line... INFO @ Sun, 02 Jun 2019 17:03:44: start X-correlation... INFO @ Sun, 02 Jun 2019 17:03:44: end of X-cor INFO @ Sun, 02 Jun 2019 17:03:44: #2 finished! INFO @ Sun, 02 Jun 2019 17:03:44: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 17:03:44: #2 alternative fragment length(s) may be 2,48,538 bps INFO @ Sun, 02 Jun 2019 17:03:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.20_model.r WARNING @ Sun, 02 Jun 2019 17:03:44: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:03:44: #2 You may need to consider one of the other alternative d(s): 2,48,538 WARNING @ Sun, 02 Jun 2019 17:03:44: #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 17:03:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:03:44: 14000000 INFO @ Sun, 02 Jun 2019 17:03:48: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:03:48: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:03:48: #1 total tags in treatment: 14504509 INFO @ Sun, 02 Jun 2019 17:03:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:03:48: #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 17:03:48: #1 tags after filtering in treatment: 14504509 INFO @ Sun, 02 Jun 2019 17:03:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:03:48: #1 finished! INFO @ Sun, 02 Jun 2019 17:03:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:03:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:03:50: #2 number of paired peaks: 332 WARNING @ Sun, 02 Jun 2019 17:03:50: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Sun, 02 Jun 2019 17:03:50: start model_add_line... INFO @ Sun, 02 Jun 2019 17:03:50: start X-correlation... INFO @ Sun, 02 Jun 2019 17:03:50: end of X-cor INFO @ Sun, 02 Jun 2019 17:03:50: #2 finished! INFO @ Sun, 02 Jun 2019 17:03:50: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 17:03:50: #2 alternative fragment length(s) may be 2,48,538 bps INFO @ Sun, 02 Jun 2019 17:03:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.05_model.r WARNING @ Sun, 02 Jun 2019 17:03:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:03:50: #2 You may need to consider one of the other alternative d(s): 2,48,538 WARNING @ Sun, 02 Jun 2019 17:03:50: #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 17:03:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:03:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:04:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:04:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:04:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.10_summits.bed INFO @ Sun, 02 Jun 2019 17:04:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (496 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:04:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:04:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:04:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.20_summits.bed INFO @ Sun, 02 Jun 2019 17:04:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:04:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:04:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257702/SRX257702.05_summits.bed INFO @ Sun, 02 Jun 2019 17:04:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。