Job ID = 4178538 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,052,425 reads read : 22,052,425 reads written : 22,052,425 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: 00:07:04 22052425 reads; of these: 22052425 (100.00%) were unpaired; of these: 415227 (1.88%) aligned 0 times 17163571 (77.83%) aligned exactly 1 time 4473627 (20.29%) aligned >1 times 98.12% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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] 6331442 / 21637198 = 0.2926 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.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 13:11:50: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:11:50: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:11:58: 1000000 INFO @ Thu, 05 Dec 2019 13:12:06: 2000000 INFO @ Thu, 05 Dec 2019 13:12:14: 3000000 INFO @ Thu, 05 Dec 2019 13:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.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 13:12:20: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:12:20: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:12:22: 4000000 INFO @ Thu, 05 Dec 2019 13:12:31: 5000000 INFO @ Thu, 05 Dec 2019 13:12:31: 1000000 INFO @ Thu, 05 Dec 2019 13:12:39: 6000000 INFO @ Thu, 05 Dec 2019 13:12:42: 2000000 INFO @ Thu, 05 Dec 2019 13:12:47: 7000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.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 13:12:52: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:12:52: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:12:53: 3000000 INFO @ Thu, 05 Dec 2019 13:12:56: 8000000 INFO @ Thu, 05 Dec 2019 13:13:04: 9000000 INFO @ Thu, 05 Dec 2019 13:13:05: 1000000 INFO @ Thu, 05 Dec 2019 13:13:05: 4000000 INFO @ Thu, 05 Dec 2019 13:13:12: 10000000 INFO @ Thu, 05 Dec 2019 13:13:16: 5000000 INFO @ Thu, 05 Dec 2019 13:13:17: 2000000 INFO @ Thu, 05 Dec 2019 13:13:20: 11000000 INFO @ Thu, 05 Dec 2019 13:13:27: 6000000 INFO @ Thu, 05 Dec 2019 13:13:27: 12000000 INFO @ Thu, 05 Dec 2019 13:13:29: 3000000 INFO @ Thu, 05 Dec 2019 13:13:35: 13000000 INFO @ Thu, 05 Dec 2019 13:13:37: 7000000 INFO @ Thu, 05 Dec 2019 13:13:41: 4000000 INFO @ Thu, 05 Dec 2019 13:13:43: 14000000 INFO @ Thu, 05 Dec 2019 13:13:48: 8000000 INFO @ Thu, 05 Dec 2019 13:13:50: 15000000 INFO @ Thu, 05 Dec 2019 13:13:52: 5000000 INFO @ Thu, 05 Dec 2019 13:13:53: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:13:53: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:13:53: #1 total tags in treatment: 15305756 INFO @ Thu, 05 Dec 2019 13:13:53: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:13:53: #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 13:13:53: #1 tags after filtering in treatment: 15305756 INFO @ Thu, 05 Dec 2019 13:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:13:53: #1 finished! INFO @ Thu, 05 Dec 2019 13:13:53: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:13:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:13:55: #2 number of paired peaks: 107 WARNING @ Thu, 05 Dec 2019 13:13:55: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Thu, 05 Dec 2019 13:13:55: start model_add_line... INFO @ Thu, 05 Dec 2019 13:13:55: start X-correlation... INFO @ Thu, 05 Dec 2019 13:13:55: end of X-cor INFO @ Thu, 05 Dec 2019 13:13:55: #2 finished! INFO @ Thu, 05 Dec 2019 13:13:55: #2 predicted fragment length is 78 bps INFO @ Thu, 05 Dec 2019 13:13:55: #2 alternative fragment length(s) may be 18,42,47,55,78,103,128,146,167,215,236,243,265,292,311,343,357,380,425,433,475,497,518,538,554,597 bps INFO @ Thu, 05 Dec 2019 13:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.05_model.r WARNING @ Thu, 05 Dec 2019 13:13:55: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:13:55: #2 You may need to consider one of the other alternative d(s): 18,42,47,55,78,103,128,146,167,215,236,243,265,292,311,343,357,380,425,433,475,497,518,538,554,597 WARNING @ Thu, 05 Dec 2019 13:13:55: #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 13:13:55: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:14:01: 9000000 INFO @ Thu, 05 Dec 2019 13:14:09: 6000000 INFO @ Thu, 05 Dec 2019 13:14:13: 10000000 INFO @ Thu, 05 Dec 2019 13:14:20: 7000000 INFO @ Thu, 05 Dec 2019 13:14:24: 11000000 INFO @ Thu, 05 Dec 2019 13:14:31: 8000000 INFO @ Thu, 05 Dec 2019 13:14:35: 12000000 INFO @ Thu, 05 Dec 2019 13:14:41: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:14:42: 9000000 INFO @ Thu, 05 Dec 2019 13:14:45: 13000000 INFO @ Thu, 05 Dec 2019 13:14:53: 10000000 INFO @ Thu, 05 Dec 2019 13:14:56: 14000000 INFO @ Thu, 05 Dec 2019 13:15:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:15:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.05_summits.bed INFO @ Thu, 05 Dec 2019 13:15:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1241 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:15:04: 11000000 INFO @ Thu, 05 Dec 2019 13:15:06: 15000000 INFO @ Thu, 05 Dec 2019 13:15:09: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:15:09: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:15:09: #1 total tags in treatment: 15305756 INFO @ Thu, 05 Dec 2019 13:15:09: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:15:09: #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 13:15:10: #1 tags after filtering in treatment: 15305756 INFO @ Thu, 05 Dec 2019 13:15:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:15:10: #1 finished! INFO @ Thu, 05 Dec 2019 13:15:10: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:15:11: #2 number of paired peaks: 107 WARNING @ Thu, 05 Dec 2019 13:15:11: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Thu, 05 Dec 2019 13:15:11: start model_add_line... INFO @ Thu, 05 Dec 2019 13:15:11: start X-correlation... INFO @ Thu, 05 Dec 2019 13:15:11: end of X-cor INFO @ Thu, 05 Dec 2019 13:15:11: #2 finished! INFO @ Thu, 05 Dec 2019 13:15:11: #2 predicted fragment length is 78 bps INFO @ Thu, 05 Dec 2019 13:15:11: #2 alternative fragment length(s) may be 18,42,47,55,78,103,128,146,167,215,236,243,265,292,311,343,357,380,425,433,475,497,518,538,554,597 bps INFO @ Thu, 05 Dec 2019 13:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.10_model.r WARNING @ Thu, 05 Dec 2019 13:15:11: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:15:11: #2 You may need to consider one of the other alternative d(s): 18,42,47,55,78,103,128,146,167,215,236,243,265,292,311,343,357,380,425,433,475,497,518,538,554,597 WARNING @ Thu, 05 Dec 2019 13:15:11: #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 13:15:11: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:15:16: 12000000 INFO @ Thu, 05 Dec 2019 13:15:27: 13000000 INFO @ Thu, 05 Dec 2019 13:15:39: 14000000 INFO @ Thu, 05 Dec 2019 13:15:50: 15000000 INFO @ Thu, 05 Dec 2019 13:15:53: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:15:53: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:15:53: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:15:53: #1 total tags in treatment: 15305756 INFO @ Thu, 05 Dec 2019 13:15:53: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:15:53: #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 13:15:54: #1 tags after filtering in treatment: 15305756 INFO @ Thu, 05 Dec 2019 13:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:15:54: #1 finished! INFO @ Thu, 05 Dec 2019 13:15:54: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:15:55: #2 number of paired peaks: 107 WARNING @ Thu, 05 Dec 2019 13:15:55: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Thu, 05 Dec 2019 13:15:55: start model_add_line... INFO @ Thu, 05 Dec 2019 13:15:55: start X-correlation... INFO @ Thu, 05 Dec 2019 13:15:55: end of X-cor INFO @ Thu, 05 Dec 2019 13:15:55: #2 finished! INFO @ Thu, 05 Dec 2019 13:15:55: #2 predicted fragment length is 78 bps INFO @ Thu, 05 Dec 2019 13:15:55: #2 alternative fragment length(s) may be 18,42,47,55,78,103,128,146,167,215,236,243,265,292,311,343,357,380,425,433,475,497,518,538,554,597 bps INFO @ Thu, 05 Dec 2019 13:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.20_model.r WARNING @ Thu, 05 Dec 2019 13:15:55: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:15:55: #2 You may need to consider one of the other alternative d(s): 18,42,47,55,78,103,128,146,167,215,236,243,265,292,311,343,357,380,425,433,475,497,518,538,554,597 WARNING @ Thu, 05 Dec 2019 13:15:55: #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 13:15:55: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:16:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:16:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:16:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.10_summits.bed INFO @ Thu, 05 Dec 2019 13:16:12: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (249 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:16:38: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736589/SRX5736589.20_summits.bed INFO @ Thu, 05 Dec 2019 13:17:01: Done! pass1 - making usageList (3 chroms): 3 millis pass2 - checking and writing primary data (69 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。