Job ID = 1294142 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,520,236 reads read : 36,520,236 reads written : 36,520,236 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: 00:12:09 36520236 reads; of these: 36520236 (100.00%) were unpaired; of these: 1367783 (3.75%) aligned 0 times 26157014 (71.62%) aligned exactly 1 time 8995439 (24.63%) aligned >1 times 96.25% overall alignment rate Time searching: 00:12:09 Overall time: 00:12:09 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] 5479277 / 35152453 = 0.1559 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 05:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.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 05:27:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:27:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.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 05:27:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:27:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.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 05:27:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:27:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:27:47: 1000000 INFO @ Mon, 03 Jun 2019 05:27:47: 1000000 INFO @ Mon, 03 Jun 2019 05:27:48: 1000000 INFO @ Mon, 03 Jun 2019 05:27:55: 2000000 INFO @ Mon, 03 Jun 2019 05:27:55: 2000000 INFO @ Mon, 03 Jun 2019 05:27:56: 2000000 INFO @ Mon, 03 Jun 2019 05:28:02: 3000000 INFO @ Mon, 03 Jun 2019 05:28:02: 3000000 INFO @ Mon, 03 Jun 2019 05:28:03: 3000000 INFO @ Mon, 03 Jun 2019 05:28:09: 4000000 INFO @ Mon, 03 Jun 2019 05:28:09: 4000000 INFO @ Mon, 03 Jun 2019 05:28:11: 4000000 INFO @ Mon, 03 Jun 2019 05:28:17: 5000000 INFO @ Mon, 03 Jun 2019 05:28:17: 5000000 INFO @ Mon, 03 Jun 2019 05:28:19: 5000000 INFO @ Mon, 03 Jun 2019 05:28:24: 6000000 INFO @ Mon, 03 Jun 2019 05:28:24: 6000000 INFO @ Mon, 03 Jun 2019 05:28:27: 6000000 INFO @ Mon, 03 Jun 2019 05:28:31: 7000000 INFO @ Mon, 03 Jun 2019 05:28:31: 7000000 INFO @ Mon, 03 Jun 2019 05:28:35: 7000000 INFO @ Mon, 03 Jun 2019 05:28:39: 8000000 INFO @ Mon, 03 Jun 2019 05:28:39: 8000000 INFO @ Mon, 03 Jun 2019 05:28:42: 8000000 INFO @ Mon, 03 Jun 2019 05:28:46: 9000000 INFO @ Mon, 03 Jun 2019 05:28:46: 9000000 INFO @ Mon, 03 Jun 2019 05:28:50: 9000000 INFO @ Mon, 03 Jun 2019 05:28:53: 10000000 INFO @ Mon, 03 Jun 2019 05:28:53: 10000000 INFO @ Mon, 03 Jun 2019 05:28:58: 10000000 INFO @ Mon, 03 Jun 2019 05:29:01: 11000000 INFO @ Mon, 03 Jun 2019 05:29:01: 11000000 INFO @ Mon, 03 Jun 2019 05:29:06: 11000000 INFO @ Mon, 03 Jun 2019 05:29:08: 12000000 INFO @ Mon, 03 Jun 2019 05:29:08: 12000000 INFO @ Mon, 03 Jun 2019 05:29:15: 13000000 INFO @ Mon, 03 Jun 2019 05:29:16: 13000000 INFO @ Mon, 03 Jun 2019 05:29:16: 12000000 INFO @ Mon, 03 Jun 2019 05:29:23: 14000000 INFO @ Mon, 03 Jun 2019 05:29:23: 14000000 INFO @ Mon, 03 Jun 2019 05:29:24: 13000000 INFO @ Mon, 03 Jun 2019 05:29:30: 15000000 INFO @ Mon, 03 Jun 2019 05:29:30: 15000000 INFO @ Mon, 03 Jun 2019 05:29:32: 14000000 INFO @ Mon, 03 Jun 2019 05:29:37: 16000000 INFO @ Mon, 03 Jun 2019 05:29:37: 16000000 INFO @ Mon, 03 Jun 2019 05:29:39: 15000000 INFO @ Mon, 03 Jun 2019 05:29:44: 17000000 INFO @ Mon, 03 Jun 2019 05:29:45: 17000000 INFO @ Mon, 03 Jun 2019 05:29:47: 16000000 INFO @ Mon, 03 Jun 2019 05:29:51: 18000000 INFO @ Mon, 03 Jun 2019 05:29:53: 18000000 INFO @ Mon, 03 Jun 2019 05:29:55: 17000000 INFO @ Mon, 03 Jun 2019 05:29:59: 19000000 INFO @ Mon, 03 Jun 2019 05:30:03: 18000000 INFO @ Mon, 03 Jun 2019 05:30:03: 19000000 INFO @ Mon, 03 Jun 2019 05:30:06: 20000000 INFO @ Mon, 03 Jun 2019 05:30:11: 19000000 INFO @ Mon, 03 Jun 2019 05:30:13: 20000000 INFO @ Mon, 03 Jun 2019 05:30:13: 21000000 INFO @ Mon, 03 Jun 2019 05:30:19: 20000000 INFO @ Mon, 03 Jun 2019 05:30:20: 22000000 INFO @ Mon, 03 Jun 2019 05:30:22: 21000000 INFO @ Mon, 03 Jun 2019 05:30:27: 21000000 INFO @ Mon, 03 Jun 2019 05:30:27: 23000000 INFO @ Mon, 03 Jun 2019 05:30:32: 22000000 INFO @ Mon, 03 Jun 2019 05:30:34: 24000000 INFO @ Mon, 03 Jun 2019 05:30:35: 22000000 INFO @ Mon, 03 Jun 2019 05:30:41: 23000000 INFO @ Mon, 03 Jun 2019 05:30:42: 25000000 INFO @ Mon, 03 Jun 2019 05:30:43: 23000000 INFO @ Mon, 03 Jun 2019 05:30:49: 26000000 INFO @ Mon, 03 Jun 2019 05:30:51: 24000000 INFO @ Mon, 03 Jun 2019 05:30:51: 24000000 INFO @ Mon, 03 Jun 2019 05:30:56: 27000000 INFO @ Mon, 03 Jun 2019 05:31:00: 25000000 INFO @ Mon, 03 Jun 2019 05:31:02: 25000000 INFO @ Mon, 03 Jun 2019 05:31:04: 28000000 INFO @ Mon, 03 Jun 2019 05:31:08: 26000000 INFO @ Mon, 03 Jun 2019 05:31:11: 29000000 INFO @ Mon, 03 Jun 2019 05:31:12: 26000000 INFO @ Mon, 03 Jun 2019 05:31:16: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:31:16: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:31:16: #1 total tags in treatment: 29673176 INFO @ Mon, 03 Jun 2019 05:31:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:31:16: #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 05:31:16: 27000000 INFO @ Mon, 03 Jun 2019 05:31:17: #1 tags after filtering in treatment: 29673176 INFO @ Mon, 03 Jun 2019 05:31:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:31:17: #1 finished! INFO @ Mon, 03 Jun 2019 05:31:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:31:19: #2 number of paired peaks: 155 WARNING @ Mon, 03 Jun 2019 05:31:19: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Mon, 03 Jun 2019 05:31:19: start model_add_line... INFO @ Mon, 03 Jun 2019 05:31:20: start X-correlation... INFO @ Mon, 03 Jun 2019 05:31:20: end of X-cor INFO @ Mon, 03 Jun 2019 05:31:20: #2 finished! INFO @ Mon, 03 Jun 2019 05:31:20: #2 predicted fragment length is 29 bps INFO @ Mon, 03 Jun 2019 05:31:20: #2 alternative fragment length(s) may be 3,29 bps INFO @ Mon, 03 Jun 2019 05:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.10_model.r WARNING @ Mon, 03 Jun 2019 05:31:20: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:31:20: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Mon, 03 Jun 2019 05:31:20: #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 05:31:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:31:22: 27000000 INFO @ Mon, 03 Jun 2019 05:31:25: 28000000 INFO @ Mon, 03 Jun 2019 05:31:32: 28000000 INFO @ Mon, 03 Jun 2019 05:31:33: 29000000 INFO @ Mon, 03 Jun 2019 05:31:39: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:31:39: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:31:39: #1 total tags in treatment: 29673176 INFO @ Mon, 03 Jun 2019 05:31:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:31:39: #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 05:31:40: #1 tags after filtering in treatment: 29673176 INFO @ Mon, 03 Jun 2019 05:31:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:31:40: #1 finished! INFO @ Mon, 03 Jun 2019 05:31:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:31:42: #2 number of paired peaks: 155 WARNING @ Mon, 03 Jun 2019 05:31:42: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Mon, 03 Jun 2019 05:31:42: start model_add_line... INFO @ Mon, 03 Jun 2019 05:31:43: start X-correlation... INFO @ Mon, 03 Jun 2019 05:31:43: end of X-cor INFO @ Mon, 03 Jun 2019 05:31:43: #2 finished! INFO @ Mon, 03 Jun 2019 05:31:43: #2 predicted fragment length is 29 bps INFO @ Mon, 03 Jun 2019 05:31:43: #2 alternative fragment length(s) may be 3,29 bps INFO @ Mon, 03 Jun 2019 05:31:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.05_model.r WARNING @ Mon, 03 Jun 2019 05:31:43: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:31:43: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Mon, 03 Jun 2019 05:31:43: #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 05:31:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:31:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:31:43: 29000000 INFO @ Mon, 03 Jun 2019 05:31:50: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:31:50: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:31:50: #1 total tags in treatment: 29673176 INFO @ Mon, 03 Jun 2019 05:31:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:31:50: #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 05:31:50: #1 tags after filtering in treatment: 29673176 INFO @ Mon, 03 Jun 2019 05:31:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:31:50: #1 finished! INFO @ Mon, 03 Jun 2019 05:31:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:31:53: #2 number of paired peaks: 155 WARNING @ Mon, 03 Jun 2019 05:31:53: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Mon, 03 Jun 2019 05:31:53: start model_add_line... INFO @ Mon, 03 Jun 2019 05:31:53: start X-correlation... INFO @ Mon, 03 Jun 2019 05:31:53: end of X-cor INFO @ Mon, 03 Jun 2019 05:31:53: #2 finished! INFO @ Mon, 03 Jun 2019 05:31:53: #2 predicted fragment length is 29 bps INFO @ Mon, 03 Jun 2019 05:31:53: #2 alternative fragment length(s) may be 3,29 bps INFO @ Mon, 03 Jun 2019 05:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.20_model.r WARNING @ Mon, 03 Jun 2019 05:31:53: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:31:53: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Mon, 03 Jun 2019 05:31:53: #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 05:31:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:32:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:32:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:32:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:32:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:32:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.10_summits.bed INFO @ Mon, 03 Jun 2019 05:32:55: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (718 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:32:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.05_summits.bed INFO @ Mon, 03 Jun 2019 05:33:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2598 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:33:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:33:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:33:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193320/SRX193320.20_summits.bed INFO @ Mon, 03 Jun 2019 05:33:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。