Job ID = 2590229 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,106,398 reads read : 56,212,796 reads written : 28,106,398 reads 0-length : 28,106,398 rm: cannot remove ‘[DSE]RR*’: 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: 00:06:41 28106398 reads; of these: 28106398 (100.00%) were unpaired; of these: 4925772 (17.53%) aligned 0 times 19324387 (68.75%) aligned exactly 1 time 3856239 (13.72%) aligned >1 times 82.47% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 9534513 / 23180626 = 0.4113 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 @ Mon, 12 Aug 2019 20:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.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 @ Mon, 12 Aug 2019 20:30:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:30:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:30:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.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 @ Mon, 12 Aug 2019 20:30:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:30:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.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 @ Mon, 12 Aug 2019 20:30:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:30:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:30:34: 1000000 INFO @ Mon, 12 Aug 2019 20:30:35: 1000000 INFO @ Mon, 12 Aug 2019 20:30:36: 1000000 INFO @ Mon, 12 Aug 2019 20:30:42: 2000000 INFO @ Mon, 12 Aug 2019 20:30:43: 2000000 INFO @ Mon, 12 Aug 2019 20:30:44: 2000000 INFO @ Mon, 12 Aug 2019 20:30:50: 3000000 INFO @ Mon, 12 Aug 2019 20:30:51: 3000000 INFO @ Mon, 12 Aug 2019 20:30:52: 3000000 INFO @ Mon, 12 Aug 2019 20:30:58: 4000000 INFO @ Mon, 12 Aug 2019 20:30:58: 4000000 INFO @ Mon, 12 Aug 2019 20:31:00: 4000000 INFO @ Mon, 12 Aug 2019 20:31:06: 5000000 INFO @ Mon, 12 Aug 2019 20:31:06: 5000000 INFO @ Mon, 12 Aug 2019 20:31:08: 5000000 INFO @ Mon, 12 Aug 2019 20:31:14: 6000000 INFO @ Mon, 12 Aug 2019 20:31:14: 6000000 INFO @ Mon, 12 Aug 2019 20:31:17: 6000000 INFO @ Mon, 12 Aug 2019 20:31:21: 7000000 INFO @ Mon, 12 Aug 2019 20:31:22: 7000000 INFO @ Mon, 12 Aug 2019 20:31:25: 7000000 INFO @ Mon, 12 Aug 2019 20:31:29: 8000000 INFO @ Mon, 12 Aug 2019 20:31:30: 8000000 INFO @ Mon, 12 Aug 2019 20:31:33: 8000000 INFO @ Mon, 12 Aug 2019 20:31:38: 9000000 INFO @ Mon, 12 Aug 2019 20:31:39: 9000000 INFO @ Mon, 12 Aug 2019 20:31:40: 9000000 INFO @ Mon, 12 Aug 2019 20:31:47: 10000000 INFO @ Mon, 12 Aug 2019 20:31:48: 10000000 INFO @ Mon, 12 Aug 2019 20:31:49: 10000000 INFO @ Mon, 12 Aug 2019 20:31:55: 11000000 INFO @ Mon, 12 Aug 2019 20:31:56: 11000000 INFO @ Mon, 12 Aug 2019 20:31:58: 11000000 INFO @ Mon, 12 Aug 2019 20:32:03: 12000000 INFO @ Mon, 12 Aug 2019 20:32:05: 12000000 INFO @ Mon, 12 Aug 2019 20:32:07: 12000000 INFO @ Mon, 12 Aug 2019 20:32:10: 13000000 INFO @ Mon, 12 Aug 2019 20:32:13: 13000000 INFO @ Mon, 12 Aug 2019 20:32:15: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:32:15: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:32:15: #1 total tags in treatment: 13646113 INFO @ Mon, 12 Aug 2019 20:32:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:32:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:32:15: #1 tags after filtering in treatment: 13646113 INFO @ Mon, 12 Aug 2019 20:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:32:15: #1 finished! INFO @ Mon, 12 Aug 2019 20:32:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:32:16: 13000000 INFO @ Mon, 12 Aug 2019 20:32:17: #2 number of paired peaks: 408 WARNING @ Mon, 12 Aug 2019 20:32:17: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Mon, 12 Aug 2019 20:32:17: start model_add_line... INFO @ Mon, 12 Aug 2019 20:32:17: start X-correlation... INFO @ Mon, 12 Aug 2019 20:32:17: end of X-cor INFO @ Mon, 12 Aug 2019 20:32:17: #2 finished! INFO @ Mon, 12 Aug 2019 20:32:17: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 20:32:17: #2 alternative fragment length(s) may be 2,45,561 bps INFO @ Mon, 12 Aug 2019 20:32:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.10_model.r WARNING @ Mon, 12 Aug 2019 20:32:17: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:32:17: #2 You may need to consider one of the other alternative d(s): 2,45,561 WARNING @ Mon, 12 Aug 2019 20:32:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:32:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:32:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:32:19: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:32:19: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:32:19: #1 total tags in treatment: 13646113 INFO @ Mon, 12 Aug 2019 20:32:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:32:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:32:19: #1 tags after filtering in treatment: 13646113 INFO @ Mon, 12 Aug 2019 20:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:32:19: #1 finished! INFO @ Mon, 12 Aug 2019 20:32:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:32:20: #2 number of paired peaks: 408 WARNING @ Mon, 12 Aug 2019 20:32:20: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Mon, 12 Aug 2019 20:32:20: start model_add_line... INFO @ Mon, 12 Aug 2019 20:32:20: start X-correlation... INFO @ Mon, 12 Aug 2019 20:32:20: end of X-cor INFO @ Mon, 12 Aug 2019 20:32:20: #2 finished! INFO @ Mon, 12 Aug 2019 20:32:20: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 20:32:20: #2 alternative fragment length(s) may be 2,45,561 bps INFO @ Mon, 12 Aug 2019 20:32:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.20_model.r WARNING @ Mon, 12 Aug 2019 20:32:20: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:32:20: #2 You may need to consider one of the other alternative d(s): 2,45,561 WARNING @ Mon, 12 Aug 2019 20:32:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:32:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:32:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:32:21: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:32:21: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:32:21: #1 total tags in treatment: 13646113 INFO @ Mon, 12 Aug 2019 20:32:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:32:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:32:21: #1 tags after filtering in treatment: 13646113 INFO @ Mon, 12 Aug 2019 20:32:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:32:21: #1 finished! INFO @ Mon, 12 Aug 2019 20:32:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:32:23: #2 number of paired peaks: 408 WARNING @ Mon, 12 Aug 2019 20:32:23: Fewer paired peaks (408) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 408 pairs to build model! INFO @ Mon, 12 Aug 2019 20:32:23: start model_add_line... INFO @ Mon, 12 Aug 2019 20:32:23: start X-correlation... INFO @ Mon, 12 Aug 2019 20:32:23: end of X-cor INFO @ Mon, 12 Aug 2019 20:32:23: #2 finished! INFO @ Mon, 12 Aug 2019 20:32:23: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 20:32:23: #2 alternative fragment length(s) may be 2,45,561 bps INFO @ Mon, 12 Aug 2019 20:32:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.05_model.r WARNING @ Mon, 12 Aug 2019 20:32:23: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:32:23: #2 You may need to consider one of the other alternative d(s): 2,45,561 WARNING @ Mon, 12 Aug 2019 20:32:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:32:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:32:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:32:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:32:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:32:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:33:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:33:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.10_summits.bed INFO @ Mon, 12 Aug 2019 20:33:07: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (531 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:33:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:33:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:33:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.20_summits.bed INFO @ Mon, 12 Aug 2019 20:33:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5709770/SRX5709770.05_summits.bed INFO @ Mon, 12 Aug 2019 20:33:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (802 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。