Job ID = 4178643 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 46,504,024 reads read : 93,008,048 reads written : 46,504,024 reads 0-length : 46,504,024 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:44 46504024 reads; of these: 46504024 (100.00%) were unpaired; of these: 1385436 (2.98%) aligned 0 times 40573097 (87.25%) aligned exactly 1 time 4545491 (9.77%) aligned >1 times 97.02% overall alignment rate Time searching: 00:18:45 Overall time: 00:18:45 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 20 files... [bam_rmdupse_core] 21496735 / 45118588 = 0.4764 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 14:17:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.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 14:17:10: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:17:10: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:17:21: 1000000 INFO @ Thu, 05 Dec 2019 14:17:32: 2000000 INFO @ Thu, 05 Dec 2019 14:17:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.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 14:17:39: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:17:39: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:17:43: 3000000 INFO @ Thu, 05 Dec 2019 14:17:53: 1000000 INFO @ Thu, 05 Dec 2019 14:17:56: 4000000 INFO @ Thu, 05 Dec 2019 14:18:05: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 14:18:08: 5000000 INFO @ Thu, 05 Dec 2019 14:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.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 14:18:09: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:18:09: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:18:18: 3000000 INFO @ Thu, 05 Dec 2019 14:18:19: 1000000 INFO @ Thu, 05 Dec 2019 14:18:21: 6000000 INFO @ Thu, 05 Dec 2019 14:18:29: 2000000 INFO @ Thu, 05 Dec 2019 14:18:30: 4000000 INFO @ Thu, 05 Dec 2019 14:18:34: 7000000 INFO @ Thu, 05 Dec 2019 14:18:40: 3000000 INFO @ Thu, 05 Dec 2019 14:18:43: 5000000 INFO @ Thu, 05 Dec 2019 14:18:46: 8000000 INFO @ Thu, 05 Dec 2019 14:18:50: 4000000 INFO @ Thu, 05 Dec 2019 14:18:56: 6000000 INFO @ Thu, 05 Dec 2019 14:19:00: 9000000 INFO @ Thu, 05 Dec 2019 14:19:00: 5000000 INFO @ Thu, 05 Dec 2019 14:19:10: 7000000 INFO @ Thu, 05 Dec 2019 14:19:10: 6000000 INFO @ Thu, 05 Dec 2019 14:19:12: 10000000 INFO @ Thu, 05 Dec 2019 14:19:20: 7000000 INFO @ Thu, 05 Dec 2019 14:19:23: 8000000 INFO @ Thu, 05 Dec 2019 14:19:25: 11000000 INFO @ Thu, 05 Dec 2019 14:19:30: 8000000 INFO @ Thu, 05 Dec 2019 14:19:36: 9000000 INFO @ Thu, 05 Dec 2019 14:19:38: 12000000 INFO @ Thu, 05 Dec 2019 14:19:40: 9000000 INFO @ Thu, 05 Dec 2019 14:19:49: 10000000 INFO @ Thu, 05 Dec 2019 14:19:51: 10000000 INFO @ Thu, 05 Dec 2019 14:19:51: 13000000 INFO @ Thu, 05 Dec 2019 14:20:02: 11000000 INFO @ Thu, 05 Dec 2019 14:20:03: 11000000 INFO @ Thu, 05 Dec 2019 14:20:03: 14000000 INFO @ Thu, 05 Dec 2019 14:20:12: 12000000 INFO @ Thu, 05 Dec 2019 14:20:16: 15000000 INFO @ Thu, 05 Dec 2019 14:20:16: 12000000 INFO @ Thu, 05 Dec 2019 14:20:21: 13000000 INFO @ Thu, 05 Dec 2019 14:20:28: 16000000 INFO @ Thu, 05 Dec 2019 14:20:30: 13000000 INFO @ Thu, 05 Dec 2019 14:20:30: 14000000 INFO @ Thu, 05 Dec 2019 14:20:40: 15000000 INFO @ Thu, 05 Dec 2019 14:20:42: 17000000 INFO @ Thu, 05 Dec 2019 14:20:44: 14000000 INFO @ Thu, 05 Dec 2019 14:20:49: 16000000 INFO @ Thu, 05 Dec 2019 14:20:56: 18000000 INFO @ Thu, 05 Dec 2019 14:20:57: 15000000 INFO @ Thu, 05 Dec 2019 14:20:59: 17000000 INFO @ Thu, 05 Dec 2019 14:21:09: 18000000 INFO @ Thu, 05 Dec 2019 14:21:09: 19000000 INFO @ Thu, 05 Dec 2019 14:21:10: 16000000 INFO @ Thu, 05 Dec 2019 14:21:19: 19000000 INFO @ Thu, 05 Dec 2019 14:21:23: 20000000 INFO @ Thu, 05 Dec 2019 14:21:23: 17000000 INFO @ Thu, 05 Dec 2019 14:21:29: 20000000 INFO @ Thu, 05 Dec 2019 14:21:34: 21000000 INFO @ Thu, 05 Dec 2019 14:21:36: 18000000 INFO @ Thu, 05 Dec 2019 14:21:38: 21000000 INFO @ Thu, 05 Dec 2019 14:21:47: 22000000 INFO @ Thu, 05 Dec 2019 14:21:48: 22000000 INFO @ Thu, 05 Dec 2019 14:21:48: 19000000 INFO @ Thu, 05 Dec 2019 14:21:59: 23000000 INFO @ Thu, 05 Dec 2019 14:22:00: 23000000 INFO @ Thu, 05 Dec 2019 14:22:01: 20000000 INFO @ Thu, 05 Dec 2019 14:22:05: #1 tag size is determined as 75 bps INFO @ Thu, 05 Dec 2019 14:22:05: #1 tag size = 75 INFO @ Thu, 05 Dec 2019 14:22:05: #1 total tags in treatment: 23621853 INFO @ Thu, 05 Dec 2019 14:22:05: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:22:05: #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 14:22:05: #1 tags after filtering in treatment: 23621853 INFO @ Thu, 05 Dec 2019 14:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 14:22:05: #1 finished! INFO @ Thu, 05 Dec 2019 14:22:05: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:22:07: #1 tag size is determined as 75 bps INFO @ Thu, 05 Dec 2019 14:22:07: #1 tag size = 75 INFO @ Thu, 05 Dec 2019 14:22:07: #1 total tags in treatment: 23621853 INFO @ Thu, 05 Dec 2019 14:22:07: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:22:07: #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 14:22:07: #2 number of paired peaks: 275 WARNING @ Thu, 05 Dec 2019 14:22:07: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Thu, 05 Dec 2019 14:22:07: start model_add_line... INFO @ Thu, 05 Dec 2019 14:22:07: #1 tags after filtering in treatment: 23621853 INFO @ Thu, 05 Dec 2019 14:22:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 14:22:07: #1 finished! INFO @ Thu, 05 Dec 2019 14:22:07: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:22:08: start X-correlation... INFO @ Thu, 05 Dec 2019 14:22:08: end of X-cor INFO @ Thu, 05 Dec 2019 14:22:08: #2 finished! INFO @ Thu, 05 Dec 2019 14:22:08: #2 predicted fragment length is 80 bps INFO @ Thu, 05 Dec 2019 14:22:08: #2 alternative fragment length(s) may be 3,80,101,115 bps INFO @ Thu, 05 Dec 2019 14:22:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.20_model.r WARNING @ Thu, 05 Dec 2019 14:22:08: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 14:22:08: #2 You may need to consider one of the other alternative d(s): 3,80,101,115 WARNING @ Thu, 05 Dec 2019 14:22:08: #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 14:22:08: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:22:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:22:09: #2 number of paired peaks: 275 WARNING @ Thu, 05 Dec 2019 14:22:09: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Thu, 05 Dec 2019 14:22:09: start model_add_line... INFO @ Thu, 05 Dec 2019 14:22:10: start X-correlation... INFO @ Thu, 05 Dec 2019 14:22:10: end of X-cor INFO @ Thu, 05 Dec 2019 14:22:10: #2 finished! INFO @ Thu, 05 Dec 2019 14:22:10: #2 predicted fragment length is 80 bps INFO @ Thu, 05 Dec 2019 14:22:10: #2 alternative fragment length(s) may be 3,80,101,115 bps INFO @ Thu, 05 Dec 2019 14:22:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.05_model.r WARNING @ Thu, 05 Dec 2019 14:22:10: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 14:22:10: #2 You may need to consider one of the other alternative d(s): 3,80,101,115 WARNING @ Thu, 05 Dec 2019 14:22:10: #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 14:22:10: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:22:13: 21000000 INFO @ Thu, 05 Dec 2019 14:22:24: 22000000 INFO @ Thu, 05 Dec 2019 14:22:35: 23000000 INFO @ Thu, 05 Dec 2019 14:22:42: #1 tag size is determined as 75 bps INFO @ Thu, 05 Dec 2019 14:22:42: #1 tag size = 75 INFO @ Thu, 05 Dec 2019 14:22:42: #1 total tags in treatment: 23621853 INFO @ Thu, 05 Dec 2019 14:22:42: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:22:42: #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 14:22:42: #1 tags after filtering in treatment: 23621853 INFO @ Thu, 05 Dec 2019 14:22:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 14:22:42: #1 finished! INFO @ Thu, 05 Dec 2019 14:22:42: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:22:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:22:44: #2 number of paired peaks: 275 WARNING @ Thu, 05 Dec 2019 14:22:44: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Thu, 05 Dec 2019 14:22:44: start model_add_line... INFO @ Thu, 05 Dec 2019 14:22:44: start X-correlation... INFO @ Thu, 05 Dec 2019 14:22:44: end of X-cor INFO @ Thu, 05 Dec 2019 14:22:44: #2 finished! INFO @ Thu, 05 Dec 2019 14:22:44: #2 predicted fragment length is 80 bps INFO @ Thu, 05 Dec 2019 14:22:44: #2 alternative fragment length(s) may be 3,80,101,115 bps INFO @ Thu, 05 Dec 2019 14:22:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.10_model.r WARNING @ Thu, 05 Dec 2019 14:22:44: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 14:22:44: #2 You may need to consider one of the other alternative d(s): 3,80,101,115 WARNING @ Thu, 05 Dec 2019 14:22:44: #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 14:22:44: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:22:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:23:06: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:23:09: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:23:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.05_peaks.xls INFO @ Thu, 05 Dec 2019 14:23:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:23:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.05_summits.bed INFO @ Thu, 05 Dec 2019 14:23:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5348 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:23:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.20_peaks.xls INFO @ Thu, 05 Dec 2019 14:23:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:23:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.20_summits.bed INFO @ Thu, 05 Dec 2019 14:23:38: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:23:41: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.10_peaks.xls INFO @ Thu, 05 Dec 2019 14:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7158301/SRX7158301.10_summits.bed INFO @ Thu, 05 Dec 2019 14:24:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1566 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。