Job ID = 2590307 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,575,683 reads read : 21,575,683 reads written : 21,575,683 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: 00:08:36 21575683 reads; of these: 21575683 (100.00%) were unpaired; of these: 2893551 (13.41%) aligned 0 times 11812686 (54.75%) aligned exactly 1 time 6869446 (31.84%) aligned >1 times 86.59% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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 8 files... [bam_rmdupse_core] 2373015 / 18682132 = 0.1270 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 21:00:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.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 @ Mon, 12 Aug 2019 21:00:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:00:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.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 @ Mon, 12 Aug 2019 21:00:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:00:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.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 @ Mon, 12 Aug 2019 21:00:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:00:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:00:21: 1000000 INFO @ Mon, 12 Aug 2019 21:00:21: 1000000 INFO @ Mon, 12 Aug 2019 21:00:21: 1000000 INFO @ Mon, 12 Aug 2019 21:00:28: 2000000 INFO @ Mon, 12 Aug 2019 21:00:28: 2000000 INFO @ Mon, 12 Aug 2019 21:00:30: 2000000 INFO @ Mon, 12 Aug 2019 21:00:36: 3000000 INFO @ Mon, 12 Aug 2019 21:00:36: 3000000 INFO @ Mon, 12 Aug 2019 21:00:38: 3000000 INFO @ Mon, 12 Aug 2019 21:00:42: 4000000 INFO @ Mon, 12 Aug 2019 21:00:43: 4000000 INFO @ Mon, 12 Aug 2019 21:00:46: 4000000 INFO @ Mon, 12 Aug 2019 21:00:49: 5000000 INFO @ Mon, 12 Aug 2019 21:00:50: 5000000 INFO @ Mon, 12 Aug 2019 21:00:54: 5000000 INFO @ Mon, 12 Aug 2019 21:00:56: 6000000 INFO @ Mon, 12 Aug 2019 21:00:57: 6000000 INFO @ Mon, 12 Aug 2019 21:01:03: 6000000 INFO @ Mon, 12 Aug 2019 21:01:03: 7000000 INFO @ Mon, 12 Aug 2019 21:01:05: 7000000 INFO @ Mon, 12 Aug 2019 21:01:10: 8000000 INFO @ Mon, 12 Aug 2019 21:01:12: 7000000 INFO @ Mon, 12 Aug 2019 21:01:12: 8000000 INFO @ Mon, 12 Aug 2019 21:01:17: 9000000 INFO @ Mon, 12 Aug 2019 21:01:20: 9000000 INFO @ Mon, 12 Aug 2019 21:01:20: 8000000 INFO @ Mon, 12 Aug 2019 21:01:24: 10000000 INFO @ Mon, 12 Aug 2019 21:01:27: 10000000 INFO @ Mon, 12 Aug 2019 21:01:29: 9000000 INFO @ Mon, 12 Aug 2019 21:01:30: 11000000 INFO @ Mon, 12 Aug 2019 21:01:34: 11000000 INFO @ Mon, 12 Aug 2019 21:01:37: 12000000 INFO @ Mon, 12 Aug 2019 21:01:37: 10000000 INFO @ Mon, 12 Aug 2019 21:01:41: 12000000 INFO @ Mon, 12 Aug 2019 21:01:44: 13000000 INFO @ Mon, 12 Aug 2019 21:01:46: 11000000 INFO @ Mon, 12 Aug 2019 21:01:49: 13000000 INFO @ Mon, 12 Aug 2019 21:01:50: 14000000 INFO @ Mon, 12 Aug 2019 21:01:54: 12000000 INFO @ Mon, 12 Aug 2019 21:01:56: 14000000 INFO @ Mon, 12 Aug 2019 21:01:57: 15000000 INFO @ Mon, 12 Aug 2019 21:02:02: 13000000 INFO @ Mon, 12 Aug 2019 21:02:03: 15000000 INFO @ Mon, 12 Aug 2019 21:02:04: 16000000 INFO @ Mon, 12 Aug 2019 21:02:06: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:02:06: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:02:06: #1 total tags in treatment: 16309117 INFO @ Mon, 12 Aug 2019 21:02:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:02:06: #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 21:02:06: #1 tags after filtering in treatment: 16309117 INFO @ Mon, 12 Aug 2019 21:02:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:02:06: #1 finished! INFO @ Mon, 12 Aug 2019 21:02:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:02:08: #2 number of paired peaks: 419 WARNING @ Mon, 12 Aug 2019 21:02:08: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Mon, 12 Aug 2019 21:02:08: start model_add_line... INFO @ Mon, 12 Aug 2019 21:02:08: start X-correlation... INFO @ Mon, 12 Aug 2019 21:02:08: end of X-cor INFO @ Mon, 12 Aug 2019 21:02:08: #2 finished! INFO @ Mon, 12 Aug 2019 21:02:08: #2 predicted fragment length is 56 bps INFO @ Mon, 12 Aug 2019 21:02:08: #2 alternative fragment length(s) may be 2,56,546 bps INFO @ Mon, 12 Aug 2019 21:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.20_model.r WARNING @ Mon, 12 Aug 2019 21:02:08: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:02:08: #2 You may need to consider one of the other alternative d(s): 2,56,546 WARNING @ Mon, 12 Aug 2019 21:02:08: #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 21:02:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:02:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:02:10: 16000000 INFO @ Mon, 12 Aug 2019 21:02:10: 14000000 INFO @ Mon, 12 Aug 2019 21:02:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:02:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:02:12: #1 total tags in treatment: 16309117 INFO @ Mon, 12 Aug 2019 21:02:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:02:12: #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 21:02:13: #1 tags after filtering in treatment: 16309117 INFO @ Mon, 12 Aug 2019 21:02:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:02:13: #1 finished! INFO @ Mon, 12 Aug 2019 21:02:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:02:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:02:14: #2 number of paired peaks: 419 WARNING @ Mon, 12 Aug 2019 21:02:14: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Mon, 12 Aug 2019 21:02:14: start model_add_line... INFO @ Mon, 12 Aug 2019 21:02:14: start X-correlation... INFO @ Mon, 12 Aug 2019 21:02:14: end of X-cor INFO @ Mon, 12 Aug 2019 21:02:14: #2 finished! INFO @ Mon, 12 Aug 2019 21:02:14: #2 predicted fragment length is 56 bps INFO @ Mon, 12 Aug 2019 21:02:14: #2 alternative fragment length(s) may be 2,56,546 bps INFO @ Mon, 12 Aug 2019 21:02:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.10_model.r WARNING @ Mon, 12 Aug 2019 21:02:14: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:02:14: #2 You may need to consider one of the other alternative d(s): 2,56,546 WARNING @ Mon, 12 Aug 2019 21:02:14: #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 21:02:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:02:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:02:18: 15000000 INFO @ Mon, 12 Aug 2019 21:02:27: 16000000 INFO @ Mon, 12 Aug 2019 21:02:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:02:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:02:30: #1 total tags in treatment: 16309117 INFO @ Mon, 12 Aug 2019 21:02:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:02:30: #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 21:02:30: #1 tags after filtering in treatment: 16309117 INFO @ Mon, 12 Aug 2019 21:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:02:30: #1 finished! INFO @ Mon, 12 Aug 2019 21:02:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:02:31: #2 number of paired peaks: 419 WARNING @ Mon, 12 Aug 2019 21:02:31: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Mon, 12 Aug 2019 21:02:31: start model_add_line... INFO @ Mon, 12 Aug 2019 21:02:32: start X-correlation... INFO @ Mon, 12 Aug 2019 21:02:32: end of X-cor INFO @ Mon, 12 Aug 2019 21:02:32: #2 finished! INFO @ Mon, 12 Aug 2019 21:02:32: #2 predicted fragment length is 56 bps INFO @ Mon, 12 Aug 2019 21:02:32: #2 alternative fragment length(s) may be 2,56,546 bps INFO @ Mon, 12 Aug 2019 21:02:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.05_model.r WARNING @ Mon, 12 Aug 2019 21:02:32: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:02:32: #2 You may need to consider one of the other alternative d(s): 2,56,546 WARNING @ Mon, 12 Aug 2019 21:02:32: #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 21:02:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:02:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:02:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:02:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.20_summits.bed INFO @ Mon, 12 Aug 2019 21:03:12: Done! pass1 - making usageList (10 chroms): 3 millis pass2 - checking and writing primary data (477 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:03:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:03:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:03:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:03:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.10_summits.bed INFO @ Mon, 12 Aug 2019 21:03:19: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1374 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:03:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:03:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:03:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331413/SRX331413.05_summits.bed INFO @ Mon, 12 Aug 2019 21:03:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2548 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。