Job ID = 4178536 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,036,307 reads read : 29,036,307 reads written : 29,036,307 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: 00:10:24 29036307 reads; of these: 29036307 (100.00%) were unpaired; of these: 558564 (1.92%) aligned 0 times 22235707 (76.58%) aligned exactly 1 time 6242036 (21.50%) aligned >1 times 98.08% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 10350831 / 28477743 = 0.3635 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:21:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:21:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:21:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:22:12: 1000000 INFO @ Thu, 05 Dec 2019 13:22:22: 2000000 INFO @ Thu, 05 Dec 2019 13:22:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:22:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:22:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:22:33: 3000000 INFO @ Thu, 05 Dec 2019 13:22:38: 1000000 INFO @ Thu, 05 Dec 2019 13:22:43: 4000000 INFO @ Thu, 05 Dec 2019 13:22:49: 2000000 INFO @ Thu, 05 Dec 2019 13:22:54: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:22:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:22:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:23:00: 3000000 INFO @ Thu, 05 Dec 2019 13:23:05: 6000000 INFO @ Thu, 05 Dec 2019 13:23:08: 1000000 INFO @ Thu, 05 Dec 2019 13:23:10: 4000000 INFO @ Thu, 05 Dec 2019 13:23:15: 7000000 INFO @ Thu, 05 Dec 2019 13:23:19: 2000000 INFO @ Thu, 05 Dec 2019 13:23:20: 5000000 INFO @ Thu, 05 Dec 2019 13:23:26: 8000000 INFO @ Thu, 05 Dec 2019 13:23:33: 3000000 INFO @ Thu, 05 Dec 2019 13:23:36: 6000000 INFO @ Thu, 05 Dec 2019 13:23:42: 9000000 INFO @ Thu, 05 Dec 2019 13:23:47: 4000000 INFO @ Thu, 05 Dec 2019 13:23:49: 7000000 INFO @ Thu, 05 Dec 2019 13:23:52: 10000000 INFO @ Thu, 05 Dec 2019 13:23:59: 5000000 INFO @ Thu, 05 Dec 2019 13:24:00: 8000000 INFO @ Thu, 05 Dec 2019 13:24:02: 11000000 INFO @ Thu, 05 Dec 2019 13:24:10: 9000000 INFO @ Thu, 05 Dec 2019 13:24:11: 6000000 INFO @ Thu, 05 Dec 2019 13:24:13: 12000000 INFO @ Thu, 05 Dec 2019 13:24:21: 10000000 INFO @ Thu, 05 Dec 2019 13:24:24: 7000000 INFO @ Thu, 05 Dec 2019 13:24:27: 13000000 INFO @ Thu, 05 Dec 2019 13:24:35: 11000000 INFO @ Thu, 05 Dec 2019 13:24:38: 8000000 INFO @ Thu, 05 Dec 2019 13:24:40: 14000000 INFO @ Thu, 05 Dec 2019 13:24:47: 12000000 INFO @ Thu, 05 Dec 2019 13:24:52: 9000000 INFO @ Thu, 05 Dec 2019 13:24:55: 15000000 INFO @ Thu, 05 Dec 2019 13:24:58: 13000000 INFO @ Thu, 05 Dec 2019 13:25:01: 10000000 INFO @ Thu, 05 Dec 2019 13:25:05: 16000000 INFO @ Thu, 05 Dec 2019 13:25:08: 14000000 INFO @ Thu, 05 Dec 2019 13:25:11: 11000000 INFO @ Thu, 05 Dec 2019 13:25:15: 17000000 INFO @ Thu, 05 Dec 2019 13:25:19: 15000000 INFO @ Thu, 05 Dec 2019 13:25:21: 12000000 INFO @ Thu, 05 Dec 2019 13:25:26: 18000000 INFO @ Thu, 05 Dec 2019 13:25:27: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:25:27: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:25:27: #1 total tags in treatment: 18126912 INFO @ Thu, 05 Dec 2019 13:25:27: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:25:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:25:28: #1 tags after filtering in treatment: 18126912 INFO @ Thu, 05 Dec 2019 13:25:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:25:28: #1 finished! INFO @ Thu, 05 Dec 2019 13:25:28: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:25:30: #2 number of paired peaks: 169 WARNING @ Thu, 05 Dec 2019 13:25:30: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Thu, 05 Dec 2019 13:25:30: start model_add_line... INFO @ Thu, 05 Dec 2019 13:25:30: start X-correlation... INFO @ Thu, 05 Dec 2019 13:25:30: end of X-cor INFO @ Thu, 05 Dec 2019 13:25:30: #2 finished! INFO @ Thu, 05 Dec 2019 13:25:30: #2 predicted fragment length is 84 bps INFO @ Thu, 05 Dec 2019 13:25:30: #2 alternative fragment length(s) may be 16,43,64,84,102,125,148,172,194,236,247,283,298,320,342,359,385,410,430,453,478,511,537,561,586 bps INFO @ Thu, 05 Dec 2019 13:25:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.05_model.r WARNING @ Thu, 05 Dec 2019 13:25:30: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:25:30: #2 You may need to consider one of the other alternative d(s): 16,43,64,84,102,125,148,172,194,236,247,283,298,320,342,359,385,410,430,453,478,511,537,561,586 WARNING @ Thu, 05 Dec 2019 13:25:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:25:30: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:25:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:25:31: 16000000 INFO @ Thu, 05 Dec 2019 13:25:32: 13000000 INFO @ Thu, 05 Dec 2019 13:25:41: 14000000 INFO @ Thu, 05 Dec 2019 13:25:41: 17000000 INFO @ Thu, 05 Dec 2019 13:25:51: 15000000 INFO @ Thu, 05 Dec 2019 13:25:52: 18000000 INFO @ Thu, 05 Dec 2019 13:25:53: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:25:53: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:25:53: #1 total tags in treatment: 18126912 INFO @ Thu, 05 Dec 2019 13:25:53: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:25:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:25:53: #1 tags after filtering in treatment: 18126912 INFO @ Thu, 05 Dec 2019 13:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:25:53: #1 finished! INFO @ Thu, 05 Dec 2019 13:25:53: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:25:55: #2 number of paired peaks: 169 WARNING @ Thu, 05 Dec 2019 13:25:55: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Thu, 05 Dec 2019 13:25:55: start model_add_line... INFO @ Thu, 05 Dec 2019 13:25:55: start X-correlation... INFO @ Thu, 05 Dec 2019 13:25:55: end of X-cor INFO @ Thu, 05 Dec 2019 13:25:55: #2 finished! INFO @ Thu, 05 Dec 2019 13:25:55: #2 predicted fragment length is 84 bps INFO @ Thu, 05 Dec 2019 13:25:55: #2 alternative fragment length(s) may be 16,43,64,84,102,125,148,172,194,236,247,283,298,320,342,359,385,410,430,453,478,511,537,561,586 bps INFO @ Thu, 05 Dec 2019 13:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.10_model.r WARNING @ Thu, 05 Dec 2019 13:25:55: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:25:55: #2 You may need to consider one of the other alternative d(s): 16,43,64,84,102,125,148,172,194,236,247,283,298,320,342,359,385,410,430,453,478,511,537,561,586 WARNING @ Thu, 05 Dec 2019 13:25:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:25:55: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:26:01: 16000000 INFO @ Thu, 05 Dec 2019 13:26:11: 17000000 INFO @ Thu, 05 Dec 2019 13:26:18: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:26:21: 18000000 INFO @ Thu, 05 Dec 2019 13:26:22: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:26:22: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:26:22: #1 total tags in treatment: 18126912 INFO @ Thu, 05 Dec 2019 13:26:22: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:26:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:26:22: #1 tags after filtering in treatment: 18126912 INFO @ Thu, 05 Dec 2019 13:26:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:26:22: #1 finished! INFO @ Thu, 05 Dec 2019 13:26:22: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:26:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:26:24: #2 number of paired peaks: 169 WARNING @ Thu, 05 Dec 2019 13:26:24: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Thu, 05 Dec 2019 13:26:24: start model_add_line... INFO @ Thu, 05 Dec 2019 13:26:24: start X-correlation... INFO @ Thu, 05 Dec 2019 13:26:24: end of X-cor INFO @ Thu, 05 Dec 2019 13:26:24: #2 finished! INFO @ Thu, 05 Dec 2019 13:26:24: #2 predicted fragment length is 84 bps INFO @ Thu, 05 Dec 2019 13:26:24: #2 alternative fragment length(s) may be 16,43,64,84,102,125,148,172,194,236,247,283,298,320,342,359,385,410,430,453,478,511,537,561,586 bps INFO @ Thu, 05 Dec 2019 13:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.20_model.r WARNING @ Thu, 05 Dec 2019 13:26:24: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:26:24: #2 You may need to consider one of the other alternative d(s): 16,43,64,84,102,125,148,172,194,236,247,283,298,320,342,359,385,410,430,453,478,511,537,561,586 WARNING @ Thu, 05 Dec 2019 13:26:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:26:24: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:26:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:26:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:26:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.05_summits.bed INFO @ Thu, 05 Dec 2019 13:26:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2866 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:26:43: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.10_summits.bed INFO @ Thu, 05 Dec 2019 13:27:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:27:14: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736587/SRX5736587.20_summits.bed INFO @ Thu, 05 Dec 2019 13:27:43: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (95 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。