Job ID = 1293318 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,684,729 reads read : 34,684,729 reads written : 34,684,729 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:48 34684729 reads; of these: 34684729 (100.00%) were unpaired; of these: 453030 (1.31%) aligned 0 times 27164352 (78.32%) aligned exactly 1 time 7067347 (20.38%) aligned >1 times 98.69% overall alignment rate Time searching: 00:16:49 Overall time: 00:16:49 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] 14728412 / 34231699 = 0.4303 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 @ Sun, 02 Jun 2019 23:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.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 @ Sun, 02 Jun 2019 23:46:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:46:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.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 @ Sun, 02 Jun 2019 23:46:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:46:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.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 @ Sun, 02 Jun 2019 23:46:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:46:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:46:41: 1000000 INFO @ Sun, 02 Jun 2019 23:46:44: 1000000 INFO @ Sun, 02 Jun 2019 23:46:45: 1000000 INFO @ Sun, 02 Jun 2019 23:46:50: 2000000 INFO @ Sun, 02 Jun 2019 23:46:55: 2000000 INFO @ Sun, 02 Jun 2019 23:46:56: 2000000 INFO @ Sun, 02 Jun 2019 23:46:59: 3000000 INFO @ Sun, 02 Jun 2019 23:47:06: 3000000 INFO @ Sun, 02 Jun 2019 23:47:07: 3000000 INFO @ Sun, 02 Jun 2019 23:47:08: 4000000 INFO @ Sun, 02 Jun 2019 23:47:16: 5000000 INFO @ Sun, 02 Jun 2019 23:47:17: 4000000 INFO @ Sun, 02 Jun 2019 23:47:19: 4000000 INFO @ Sun, 02 Jun 2019 23:47:25: 6000000 INFO @ Sun, 02 Jun 2019 23:47:28: 5000000 INFO @ Sun, 02 Jun 2019 23:47:30: 5000000 INFO @ Sun, 02 Jun 2019 23:47:33: 7000000 INFO @ Sun, 02 Jun 2019 23:47:39: 6000000 INFO @ Sun, 02 Jun 2019 23:47:41: 6000000 INFO @ Sun, 02 Jun 2019 23:47:42: 8000000 INFO @ Sun, 02 Jun 2019 23:47:50: 9000000 INFO @ Sun, 02 Jun 2019 23:47:50: 7000000 INFO @ Sun, 02 Jun 2019 23:47:53: 7000000 INFO @ Sun, 02 Jun 2019 23:47:58: 10000000 INFO @ Sun, 02 Jun 2019 23:48:01: 8000000 INFO @ Sun, 02 Jun 2019 23:48:05: 8000000 INFO @ Sun, 02 Jun 2019 23:48:06: 11000000 INFO @ Sun, 02 Jun 2019 23:48:11: 9000000 INFO @ Sun, 02 Jun 2019 23:48:15: 12000000 INFO @ Sun, 02 Jun 2019 23:48:16: 9000000 INFO @ Sun, 02 Jun 2019 23:48:22: 10000000 INFO @ Sun, 02 Jun 2019 23:48:23: 13000000 INFO @ Sun, 02 Jun 2019 23:48:27: 10000000 INFO @ Sun, 02 Jun 2019 23:48:31: 14000000 INFO @ Sun, 02 Jun 2019 23:48:33: 11000000 INFO @ Sun, 02 Jun 2019 23:48:38: 11000000 INFO @ Sun, 02 Jun 2019 23:48:40: 15000000 INFO @ Sun, 02 Jun 2019 23:48:43: 12000000 INFO @ Sun, 02 Jun 2019 23:48:48: 16000000 INFO @ Sun, 02 Jun 2019 23:48:49: 12000000 INFO @ Sun, 02 Jun 2019 23:48:54: 13000000 INFO @ Sun, 02 Jun 2019 23:48:56: 17000000 INFO @ Sun, 02 Jun 2019 23:49:00: 13000000 INFO @ Sun, 02 Jun 2019 23:49:04: 18000000 INFO @ Sun, 02 Jun 2019 23:49:05: 14000000 INFO @ Sun, 02 Jun 2019 23:49:10: 14000000 INFO @ Sun, 02 Jun 2019 23:49:13: 19000000 INFO @ Sun, 02 Jun 2019 23:49:16: 15000000 INFO @ Sun, 02 Jun 2019 23:49:17: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 23:49:17: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 23:49:17: #1 total tags in treatment: 19503287 INFO @ Sun, 02 Jun 2019 23:49:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:49:17: #1 tags after filtering in treatment: 19503287 INFO @ Sun, 02 Jun 2019 23:49:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:49:17: #1 finished! INFO @ Sun, 02 Jun 2019 23:49:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:49:20: #2 number of paired peaks: 5508 INFO @ Sun, 02 Jun 2019 23:49:20: start model_add_line... INFO @ Sun, 02 Jun 2019 23:49:20: start X-correlation... INFO @ Sun, 02 Jun 2019 23:49:20: end of X-cor INFO @ Sun, 02 Jun 2019 23:49:20: #2 finished! INFO @ Sun, 02 Jun 2019 23:49:20: #2 predicted fragment length is 147 bps INFO @ Sun, 02 Jun 2019 23:49:20: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 02 Jun 2019 23:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.10_model.r WARNING @ Sun, 02 Jun 2019 23:49:20: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:49:20: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 02 Jun 2019 23:49:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:49:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:49:22: 15000000 INFO @ Sun, 02 Jun 2019 23:49:26: 16000000 INFO @ Sun, 02 Jun 2019 23:49:33: 16000000 INFO @ Sun, 02 Jun 2019 23:49:37: 17000000 INFO @ Sun, 02 Jun 2019 23:49:44: 17000000 INFO @ Sun, 02 Jun 2019 23:49:47: 18000000 INFO @ Sun, 02 Jun 2019 23:49:55: 18000000 INFO @ Sun, 02 Jun 2019 23:49:57: 19000000 INFO @ Sun, 02 Jun 2019 23:50:03: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 23:50:03: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 23:50:03: #1 total tags in treatment: 19503287 INFO @ Sun, 02 Jun 2019 23:50:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:50:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:50:03: #1 tags after filtering in treatment: 19503287 INFO @ Sun, 02 Jun 2019 23:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:50:03: #1 finished! INFO @ Sun, 02 Jun 2019 23:50:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:50:05: 19000000 INFO @ Sun, 02 Jun 2019 23:50:05: #2 number of paired peaks: 5508 INFO @ Sun, 02 Jun 2019 23:50:05: start model_add_line... INFO @ Sun, 02 Jun 2019 23:50:06: start X-correlation... INFO @ Sun, 02 Jun 2019 23:50:06: end of X-cor INFO @ Sun, 02 Jun 2019 23:50:06: #2 finished! INFO @ Sun, 02 Jun 2019 23:50:06: #2 predicted fragment length is 147 bps INFO @ Sun, 02 Jun 2019 23:50:06: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 02 Jun 2019 23:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.05_model.r WARNING @ Sun, 02 Jun 2019 23:50:06: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:50:06: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 02 Jun 2019 23:50:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:50:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:50:10: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 23:50:10: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 23:50:10: #1 total tags in treatment: 19503287 INFO @ Sun, 02 Jun 2019 23:50:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:50:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:50:11: #1 tags after filtering in treatment: 19503287 INFO @ Sun, 02 Jun 2019 23:50:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:50:11: #1 finished! INFO @ Sun, 02 Jun 2019 23:50:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:50:13: #2 number of paired peaks: 5508 INFO @ Sun, 02 Jun 2019 23:50:13: start model_add_line... INFO @ Sun, 02 Jun 2019 23:50:14: start X-correlation... INFO @ Sun, 02 Jun 2019 23:50:14: end of X-cor INFO @ Sun, 02 Jun 2019 23:50:14: #2 finished! INFO @ Sun, 02 Jun 2019 23:50:14: #2 predicted fragment length is 147 bps INFO @ Sun, 02 Jun 2019 23:50:14: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 02 Jun 2019 23:50:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.20_model.r WARNING @ Sun, 02 Jun 2019 23:50:14: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:50:14: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 02 Jun 2019 23:50:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:50:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:50:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:50:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:50:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:50:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:50:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.10_summits.bed INFO @ Sun, 02 Jun 2019 23:50:49: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (11600 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:51:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:51:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.05_summits.bed INFO @ Sun, 02 Jun 2019 23:51:35: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (15066 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 23:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX102369/ERX102369.20_summits.bed INFO @ Sun, 02 Jun 2019 23:51:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8394 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。