Job ID = 1294206 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,593,052 reads read : 32,593,052 reads written : 32,593,052 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:37:25 32593052 reads; of these: 32593052 (100.00%) were unpaired; of these: 814527 (2.50%) aligned 0 times 10193519 (31.28%) aligned exactly 1 time 21585006 (66.23%) aligned >1 times 97.50% overall alignment rate Time searching: 00:37:25 Overall time: 00:37:25 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 16 files... [bam_rmdupse_core] 9811321 / 31778525 = 0.3087 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, 03 Jun 2019 06:24:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.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, 03 Jun 2019 06:24:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:24:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:24:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.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, 03 Jun 2019 06:24:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:24:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:24:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.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, 03 Jun 2019 06:24:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:24:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:25:06: 1000000 INFO @ Mon, 03 Jun 2019 06:25:07: 1000000 INFO @ Mon, 03 Jun 2019 06:25:08: 1000000 INFO @ Mon, 03 Jun 2019 06:25:15: 2000000 INFO @ Mon, 03 Jun 2019 06:25:18: 2000000 INFO @ Mon, 03 Jun 2019 06:25:20: 2000000 INFO @ Mon, 03 Jun 2019 06:25:25: 3000000 INFO @ Mon, 03 Jun 2019 06:25:28: 3000000 INFO @ Mon, 03 Jun 2019 06:25:32: 3000000 INFO @ Mon, 03 Jun 2019 06:25:34: 4000000 INFO @ Mon, 03 Jun 2019 06:25:39: 4000000 INFO @ Mon, 03 Jun 2019 06:25:44: 4000000 INFO @ Mon, 03 Jun 2019 06:25:45: 5000000 INFO @ Mon, 03 Jun 2019 06:25:50: 5000000 INFO @ Mon, 03 Jun 2019 06:25:55: 6000000 INFO @ Mon, 03 Jun 2019 06:25:56: 5000000 INFO @ Mon, 03 Jun 2019 06:26:01: 6000000 INFO @ Mon, 03 Jun 2019 06:26:04: 7000000 INFO @ Mon, 03 Jun 2019 06:26:08: 6000000 INFO @ Mon, 03 Jun 2019 06:26:11: 7000000 INFO @ Mon, 03 Jun 2019 06:26:14: 8000000 INFO @ Mon, 03 Jun 2019 06:26:19: 7000000 INFO @ Mon, 03 Jun 2019 06:26:22: 8000000 INFO @ Mon, 03 Jun 2019 06:26:23: 9000000 INFO @ Mon, 03 Jun 2019 06:26:31: 8000000 INFO @ Mon, 03 Jun 2019 06:26:32: 9000000 INFO @ Mon, 03 Jun 2019 06:26:32: 10000000 INFO @ Mon, 03 Jun 2019 06:26:42: 11000000 INFO @ Mon, 03 Jun 2019 06:26:42: 9000000 INFO @ Mon, 03 Jun 2019 06:26:42: 10000000 INFO @ Mon, 03 Jun 2019 06:26:51: 12000000 INFO @ Mon, 03 Jun 2019 06:26:53: 11000000 INFO @ Mon, 03 Jun 2019 06:26:54: 10000000 INFO @ Mon, 03 Jun 2019 06:27:01: 13000000 INFO @ Mon, 03 Jun 2019 06:27:03: 12000000 INFO @ Mon, 03 Jun 2019 06:27:05: 11000000 INFO @ Mon, 03 Jun 2019 06:27:10: 14000000 INFO @ Mon, 03 Jun 2019 06:27:13: 13000000 INFO @ Mon, 03 Jun 2019 06:27:16: 12000000 INFO @ Mon, 03 Jun 2019 06:27:20: 15000000 INFO @ Mon, 03 Jun 2019 06:27:23: 14000000 INFO @ Mon, 03 Jun 2019 06:27:27: 13000000 INFO @ Mon, 03 Jun 2019 06:27:29: 16000000 INFO @ Mon, 03 Jun 2019 06:27:33: 15000000 INFO @ Mon, 03 Jun 2019 06:27:38: 14000000 INFO @ Mon, 03 Jun 2019 06:27:39: 17000000 INFO @ Mon, 03 Jun 2019 06:27:44: 16000000 INFO @ Mon, 03 Jun 2019 06:27:48: 18000000 INFO @ Mon, 03 Jun 2019 06:27:49: 15000000 INFO @ Mon, 03 Jun 2019 06:27:54: 17000000 INFO @ Mon, 03 Jun 2019 06:27:58: 19000000 INFO @ Mon, 03 Jun 2019 06:28:01: 16000000 INFO @ Mon, 03 Jun 2019 06:28:04: 18000000 INFO @ Mon, 03 Jun 2019 06:28:07: 20000000 INFO @ Mon, 03 Jun 2019 06:28:12: 17000000 INFO @ Mon, 03 Jun 2019 06:28:14: 19000000 INFO @ Mon, 03 Jun 2019 06:28:17: 21000000 INFO @ Mon, 03 Jun 2019 06:28:23: 18000000 INFO @ Mon, 03 Jun 2019 06:28:24: 20000000 INFO @ Mon, 03 Jun 2019 06:28:26: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 06:28:26: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 06:28:26: #1 total tags in treatment: 21967204 INFO @ Mon, 03 Jun 2019 06:28:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:28:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:28:27: #1 tags after filtering in treatment: 21967204 INFO @ Mon, 03 Jun 2019 06:28:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:28:27: #1 finished! INFO @ Mon, 03 Jun 2019 06:28:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:28:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:28:30: #2 number of paired peaks: 3012 INFO @ Mon, 03 Jun 2019 06:28:30: start model_add_line... INFO @ Mon, 03 Jun 2019 06:28:30: start X-correlation... INFO @ Mon, 03 Jun 2019 06:28:30: end of X-cor INFO @ Mon, 03 Jun 2019 06:28:30: #2 finished! INFO @ Mon, 03 Jun 2019 06:28:30: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 06:28:30: #2 alternative fragment length(s) may be 4,86 bps INFO @ Mon, 03 Jun 2019 06:28:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.05_model.r WARNING @ Mon, 03 Jun 2019 06:28:30: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:28:30: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Mon, 03 Jun 2019 06:28:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:28:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:28:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:28:35: 21000000 INFO @ Mon, 03 Jun 2019 06:28:35: 19000000 INFO @ Mon, 03 Jun 2019 06:28:45: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 06:28:45: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 06:28:45: #1 total tags in treatment: 21967204 INFO @ Mon, 03 Jun 2019 06:28:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:28:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:28:45: #1 tags after filtering in treatment: 21967204 INFO @ Mon, 03 Jun 2019 06:28:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:28:45: #1 finished! INFO @ Mon, 03 Jun 2019 06:28:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:28:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:28:47: 20000000 INFO @ Mon, 03 Jun 2019 06:28:48: #2 number of paired peaks: 3012 INFO @ Mon, 03 Jun 2019 06:28:48: start model_add_line... INFO @ Mon, 03 Jun 2019 06:28:48: start X-correlation... INFO @ Mon, 03 Jun 2019 06:28:48: end of X-cor INFO @ Mon, 03 Jun 2019 06:28:48: #2 finished! INFO @ Mon, 03 Jun 2019 06:28:48: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 06:28:48: #2 alternative fragment length(s) may be 4,86 bps INFO @ Mon, 03 Jun 2019 06:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.10_model.r WARNING @ Mon, 03 Jun 2019 06:28:48: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:28:48: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Mon, 03 Jun 2019 06:28:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:28:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:28:58: 21000000 INFO @ Mon, 03 Jun 2019 06:29:09: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 06:29:09: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 06:29:09: #1 total tags in treatment: 21967204 INFO @ Mon, 03 Jun 2019 06:29:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:29:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 06:29:10: #1 tags after filtering in treatment: 21967204 INFO @ Mon, 03 Jun 2019 06:29:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:29:10: #1 finished! INFO @ Mon, 03 Jun 2019 06:29:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:29:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:29:12: #2 number of paired peaks: 3012 INFO @ Mon, 03 Jun 2019 06:29:12: start model_add_line... INFO @ Mon, 03 Jun 2019 06:29:12: start X-correlation... INFO @ Mon, 03 Jun 2019 06:29:13: end of X-cor INFO @ Mon, 03 Jun 2019 06:29:13: #2 finished! INFO @ Mon, 03 Jun 2019 06:29:13: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 06:29:13: #2 alternative fragment length(s) may be 4,86 bps INFO @ Mon, 03 Jun 2019 06:29:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.20_model.r WARNING @ Mon, 03 Jun 2019 06:29:13: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:29:13: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Mon, 03 Jun 2019 06:29:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 06:29:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:29:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:29:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:29:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:29:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.05_summits.bed INFO @ Mon, 03 Jun 2019 06:29:58: Done! pass1 - making usageList (14 chroms): 8 millis pass2 - checking and writing primary data (19730 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:30:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.10_summits.bed INFO @ Mon, 03 Jun 2019 06:30:15: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (13216 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201884/SRX201884.20_summits.bed INFO @ Mon, 03 Jun 2019 06:30:41: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (6655 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。