Job ID = 1294162 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,000,294 reads read : 37,000,294 reads written : 37,000,294 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: 00:17:06 37000294 reads; of these: 37000294 (100.00%) were unpaired; of these: 1243262 (3.36%) aligned 0 times 23196059 (62.69%) aligned exactly 1 time 12560973 (33.95%) aligned >1 times 96.64% overall alignment rate Time searching: 00:17:06 Overall time: 00:17:06 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] 6888352 / 35757032 = 0.1926 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 05:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.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 05:40:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:40:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.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 05:40:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:40:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.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 05:40:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:40:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:40:48: 1000000 INFO @ Mon, 03 Jun 2019 05:40:49: 1000000 INFO @ Mon, 03 Jun 2019 05:40:49: 1000000 INFO @ Mon, 03 Jun 2019 05:40:57: 2000000 INFO @ Mon, 03 Jun 2019 05:40:57: 2000000 INFO @ Mon, 03 Jun 2019 05:40:58: 2000000 INFO @ Mon, 03 Jun 2019 05:41:04: 3000000 INFO @ Mon, 03 Jun 2019 05:41:05: 3000000 INFO @ Mon, 03 Jun 2019 05:41:06: 3000000 INFO @ Mon, 03 Jun 2019 05:41:12: 4000000 INFO @ Mon, 03 Jun 2019 05:41:12: 4000000 INFO @ Mon, 03 Jun 2019 05:41:15: 4000000 INFO @ Mon, 03 Jun 2019 05:41:19: 5000000 INFO @ Mon, 03 Jun 2019 05:41:20: 5000000 INFO @ Mon, 03 Jun 2019 05:41:23: 5000000 INFO @ Mon, 03 Jun 2019 05:41:26: 6000000 INFO @ Mon, 03 Jun 2019 05:41:27: 6000000 INFO @ Mon, 03 Jun 2019 05:41:31: 6000000 INFO @ Mon, 03 Jun 2019 05:41:33: 7000000 INFO @ Mon, 03 Jun 2019 05:41:34: 7000000 INFO @ Mon, 03 Jun 2019 05:41:39: 7000000 INFO @ Mon, 03 Jun 2019 05:41:40: 8000000 INFO @ Mon, 03 Jun 2019 05:41:41: 8000000 INFO @ Mon, 03 Jun 2019 05:41:47: 9000000 INFO @ Mon, 03 Jun 2019 05:41:48: 8000000 INFO @ Mon, 03 Jun 2019 05:41:48: 9000000 INFO @ Mon, 03 Jun 2019 05:41:54: 10000000 INFO @ Mon, 03 Jun 2019 05:41:55: 10000000 INFO @ Mon, 03 Jun 2019 05:41:56: 9000000 INFO @ Mon, 03 Jun 2019 05:42:02: 11000000 INFO @ Mon, 03 Jun 2019 05:42:03: 11000000 INFO @ Mon, 03 Jun 2019 05:42:05: 10000000 INFO @ Mon, 03 Jun 2019 05:42:09: 12000000 INFO @ Mon, 03 Jun 2019 05:42:10: 12000000 INFO @ Mon, 03 Jun 2019 05:42:13: 11000000 INFO @ Mon, 03 Jun 2019 05:42:16: 13000000 INFO @ Mon, 03 Jun 2019 05:42:17: 13000000 INFO @ Mon, 03 Jun 2019 05:42:22: 12000000 INFO @ Mon, 03 Jun 2019 05:42:23: 14000000 INFO @ Mon, 03 Jun 2019 05:42:24: 14000000 INFO @ Mon, 03 Jun 2019 05:42:30: 15000000 INFO @ Mon, 03 Jun 2019 05:42:31: 13000000 INFO @ Mon, 03 Jun 2019 05:42:31: 15000000 INFO @ Mon, 03 Jun 2019 05:42:38: 16000000 INFO @ Mon, 03 Jun 2019 05:42:38: 16000000 INFO @ Mon, 03 Jun 2019 05:42:40: 14000000 INFO @ Mon, 03 Jun 2019 05:42:45: 17000000 INFO @ Mon, 03 Jun 2019 05:42:47: 17000000 INFO @ Mon, 03 Jun 2019 05:42:48: 15000000 INFO @ Mon, 03 Jun 2019 05:42:52: 18000000 INFO @ Mon, 03 Jun 2019 05:42:54: 18000000 INFO @ Mon, 03 Jun 2019 05:42:57: 16000000 INFO @ Mon, 03 Jun 2019 05:42:59: 19000000 INFO @ Mon, 03 Jun 2019 05:43:01: 19000000 INFO @ Mon, 03 Jun 2019 05:43:05: 17000000 INFO @ Mon, 03 Jun 2019 05:43:06: 20000000 INFO @ Mon, 03 Jun 2019 05:43:08: 20000000 INFO @ Mon, 03 Jun 2019 05:43:13: 21000000 INFO @ Mon, 03 Jun 2019 05:43:14: 18000000 INFO @ Mon, 03 Jun 2019 05:43:15: 21000000 INFO @ Mon, 03 Jun 2019 05:43:20: 22000000 INFO @ Mon, 03 Jun 2019 05:43:22: 19000000 INFO @ Mon, 03 Jun 2019 05:43:22: 22000000 INFO @ Mon, 03 Jun 2019 05:43:27: 23000000 INFO @ Mon, 03 Jun 2019 05:43:29: 23000000 INFO @ Mon, 03 Jun 2019 05:43:30: 20000000 INFO @ Mon, 03 Jun 2019 05:43:34: 24000000 INFO @ Mon, 03 Jun 2019 05:43:36: 24000000 INFO @ Mon, 03 Jun 2019 05:43:39: 21000000 INFO @ Mon, 03 Jun 2019 05:43:40: 25000000 INFO @ Mon, 03 Jun 2019 05:43:43: 25000000 INFO @ Mon, 03 Jun 2019 05:43:47: 22000000 INFO @ Mon, 03 Jun 2019 05:43:47: 26000000 INFO @ Mon, 03 Jun 2019 05:43:50: 26000000 INFO @ Mon, 03 Jun 2019 05:43:54: 27000000 INFO @ Mon, 03 Jun 2019 05:43:56: 23000000 INFO @ Mon, 03 Jun 2019 05:43:57: 27000000 INFO @ Mon, 03 Jun 2019 05:44:01: 28000000 INFO @ Mon, 03 Jun 2019 05:44:04: 24000000 INFO @ Mon, 03 Jun 2019 05:44:04: 28000000 INFO @ Mon, 03 Jun 2019 05:44:08: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:44:08: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:44:08: #1 total tags in treatment: 28868680 INFO @ Mon, 03 Jun 2019 05:44:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:44:08: #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 05:44:08: #1 tags after filtering in treatment: 28868680 INFO @ Mon, 03 Jun 2019 05:44:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:44:08: #1 finished! INFO @ Mon, 03 Jun 2019 05:44:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:44:10: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:44:10: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:44:10: #1 total tags in treatment: 28868680 INFO @ Mon, 03 Jun 2019 05:44:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:44:10: #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 05:44:11: #2 number of paired peaks: 215 WARNING @ Mon, 03 Jun 2019 05:44:11: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Mon, 03 Jun 2019 05:44:11: start model_add_line... INFO @ Mon, 03 Jun 2019 05:44:11: start X-correlation... INFO @ Mon, 03 Jun 2019 05:44:11: end of X-cor INFO @ Mon, 03 Jun 2019 05:44:11: #2 finished! INFO @ Mon, 03 Jun 2019 05:44:11: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 05:44:11: #2 alternative fragment length(s) may be 2,38,529 bps INFO @ Mon, 03 Jun 2019 05:44:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.05_model.r WARNING @ Mon, 03 Jun 2019 05:44:11: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:44:11: #2 You may need to consider one of the other alternative d(s): 2,38,529 WARNING @ Mon, 03 Jun 2019 05:44:11: #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 05:44:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:44:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:44:11: #1 tags after filtering in treatment: 28868680 INFO @ Mon, 03 Jun 2019 05:44:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:44:11: #1 finished! INFO @ Mon, 03 Jun 2019 05:44:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:44:12: 25000000 INFO @ Mon, 03 Jun 2019 05:44:14: #2 number of paired peaks: 215 WARNING @ Mon, 03 Jun 2019 05:44:14: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Mon, 03 Jun 2019 05:44:14: start model_add_line... INFO @ Mon, 03 Jun 2019 05:44:14: start X-correlation... INFO @ Mon, 03 Jun 2019 05:44:14: end of X-cor INFO @ Mon, 03 Jun 2019 05:44:14: #2 finished! INFO @ Mon, 03 Jun 2019 05:44:14: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 05:44:14: #2 alternative fragment length(s) may be 2,38,529 bps INFO @ Mon, 03 Jun 2019 05:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.10_model.r WARNING @ Mon, 03 Jun 2019 05:44:14: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:44:14: #2 You may need to consider one of the other alternative d(s): 2,38,529 WARNING @ Mon, 03 Jun 2019 05:44:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:44:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:44:20: 26000000 INFO @ Mon, 03 Jun 2019 05:44:29: 27000000 INFO @ Mon, 03 Jun 2019 05:44:37: 28000000 INFO @ Mon, 03 Jun 2019 05:44:44: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:44:44: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:44:44: #1 total tags in treatment: 28868680 INFO @ Mon, 03 Jun 2019 05:44:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:44:44: #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 05:44:45: #1 tags after filtering in treatment: 28868680 INFO @ Mon, 03 Jun 2019 05:44:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:44:45: #1 finished! INFO @ Mon, 03 Jun 2019 05:44:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:44:47: #2 number of paired peaks: 215 WARNING @ Mon, 03 Jun 2019 05:44:47: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Mon, 03 Jun 2019 05:44:47: start model_add_line... INFO @ Mon, 03 Jun 2019 05:44:47: start X-correlation... INFO @ Mon, 03 Jun 2019 05:44:48: end of X-cor INFO @ Mon, 03 Jun 2019 05:44:48: #2 finished! INFO @ Mon, 03 Jun 2019 05:44:48: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 05:44:48: #2 alternative fragment length(s) may be 2,38,529 bps INFO @ Mon, 03 Jun 2019 05:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.20_model.r WARNING @ Mon, 03 Jun 2019 05:44:48: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:44:48: #2 You may need to consider one of the other alternative d(s): 2,38,529 WARNING @ Mon, 03 Jun 2019 05:44:48: #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 05:44:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:45:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:45:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:45:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:45:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.05_summits.bed INFO @ Mon, 03 Jun 2019 05:45:42: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.10_summits.bed INFO @ Mon, 03 Jun 2019 05:45:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:45:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:46:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:46:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:46:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193338/SRX193338.20_summits.bed INFO @ Mon, 03 Jun 2019 05:46:19: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。