Job ID = 10194728 sra ファイルのダウンロード中... Completed: 1193589K bytes transferred in 16 seconds (582419K bits/sec), in 1 file. Completed: 1771188K bytes transferred in 22 seconds (631902K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 20474398 spots for /home/okishinya/chipatlas/results/rn6/SRX1056324/SRR2060189.sra Written 20474398 spots total Written 29881261 spots for /home/okishinya/chipatlas/results/rn6/SRX1056324/SRR2060190.sra Written 29881261 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 03:04:47 50355659 reads; of these: 50355659 (100.00%) were unpaired; of these: 6178777 (12.27%) aligned 0 times 32713837 (64.97%) aligned exactly 1 time 11463045 (22.76%) aligned >1 times 87.73% overall alignment rate Time searching: 03:04:51 Overall time: 03:04:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 5120781 / 44176882 = 0.1159 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 @ Fri, 10 Nov 2017 23:01:28: # Command line: callpeak -t SRX1056324.bam -f BAM -g 2.15e9 -n SRX1056324.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056324.05 # format = BAM # ChIP-seq file = ['SRX1056324.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 23:01:28: # Command line: callpeak -t SRX1056324.bam -f BAM -g 2.15e9 -n SRX1056324.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056324.10 # format = BAM # ChIP-seq file = ['SRX1056324.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 23:01:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:01:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:01:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:01:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:01:28: # Command line: callpeak -t SRX1056324.bam -f BAM -g 2.15e9 -n SRX1056324.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056324.20 # format = BAM # ChIP-seq file = ['SRX1056324.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 10 Nov 2017 23:01:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:01:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:01:45: 1000000 INFO @ Fri, 10 Nov 2017 23:01:53: 1000000 INFO @ Fri, 10 Nov 2017 23:02:01: 2000000 INFO @ Fri, 10 Nov 2017 23:02:01: 1000000 INFO @ Fri, 10 Nov 2017 23:02:23: 3000000 INFO @ Fri, 10 Nov 2017 23:02:23: 2000000 INFO @ Fri, 10 Nov 2017 23:02:36: 2000000 INFO @ Fri, 10 Nov 2017 23:02:53: 3000000 INFO @ Fri, 10 Nov 2017 23:03:02: 4000000 INFO @ Fri, 10 Nov 2017 23:03:11: 3000000 INFO @ Fri, 10 Nov 2017 23:03:23: 4000000 INFO @ Fri, 10 Nov 2017 23:03:41: 5000000 INFO @ Fri, 10 Nov 2017 23:03:42: 4000000 INFO @ Fri, 10 Nov 2017 23:03:55: 5000000 INFO @ Fri, 10 Nov 2017 23:04:14: 5000000 INFO @ Fri, 10 Nov 2017 23:04:22: 6000000 INFO @ Fri, 10 Nov 2017 23:04:25: 6000000 INFO @ Fri, 10 Nov 2017 23:04:47: 6000000 INFO @ Fri, 10 Nov 2017 23:04:57: 7000000 INFO @ Fri, 10 Nov 2017 23:05:00: 7000000 INFO @ Fri, 10 Nov 2017 23:05:20: 7000000 INFO @ Fri, 10 Nov 2017 23:05:31: 8000000 INFO @ Fri, 10 Nov 2017 23:05:38: 8000000 INFO @ Fri, 10 Nov 2017 23:05:51: 8000000 INFO @ Fri, 10 Nov 2017 23:06:05: 9000000 INFO @ Fri, 10 Nov 2017 23:06:16: 9000000 INFO @ Fri, 10 Nov 2017 23:06:21: 9000000 INFO @ Fri, 10 Nov 2017 23:06:40: 10000000 INFO @ Fri, 10 Nov 2017 23:06:51: 10000000 INFO @ Fri, 10 Nov 2017 23:06:55: 10000000 INFO @ Fri, 10 Nov 2017 23:07:14: 11000000 INFO @ Fri, 10 Nov 2017 23:07:20: 11000000 INFO @ Fri, 10 Nov 2017 23:07:33: 11000000 INFO @ Fri, 10 Nov 2017 23:07:49: 12000000 INFO @ Fri, 10 Nov 2017 23:07:50: 12000000 INFO @ Fri, 10 Nov 2017 23:08:13: 12000000 INFO @ Fri, 10 Nov 2017 23:08:22: 13000000 INFO @ Fri, 10 Nov 2017 23:08:23: 13000000 INFO @ Fri, 10 Nov 2017 23:08:53: 14000000 INFO @ Fri, 10 Nov 2017 23:08:54: 13000000 INFO @ Fri, 10 Nov 2017 23:08:56: 14000000 INFO @ Fri, 10 Nov 2017 23:09:23: 15000000 INFO @ Fri, 10 Nov 2017 23:09:29: 15000000 INFO @ Fri, 10 Nov 2017 23:09:35: 14000000 INFO @ Fri, 10 Nov 2017 23:09:54: 16000000 INFO @ Fri, 10 Nov 2017 23:09:59: 16000000 INFO @ Fri, 10 Nov 2017 23:10:15: 15000000 INFO @ Fri, 10 Nov 2017 23:10:25: 17000000 INFO @ Fri, 10 Nov 2017 23:10:31: 17000000 INFO @ Fri, 10 Nov 2017 23:10:53: 16000000 INFO @ Fri, 10 Nov 2017 23:10:55: 18000000 INFO @ Fri, 10 Nov 2017 23:11:01: 18000000 INFO @ Fri, 10 Nov 2017 23:11:26: 19000000 INFO @ Fri, 10 Nov 2017 23:11:29: 17000000 INFO @ Fri, 10 Nov 2017 23:11:30: 19000000 INFO @ Fri, 10 Nov 2017 23:11:53: 20000000 INFO @ Fri, 10 Nov 2017 23:12:00: 20000000 INFO @ Fri, 10 Nov 2017 23:12:04: 18000000 INFO @ Fri, 10 Nov 2017 23:12:14: 21000000 INFO @ Fri, 10 Nov 2017 23:12:28: 21000000 INFO @ Fri, 10 Nov 2017 23:12:33: 22000000 INFO @ Fri, 10 Nov 2017 23:12:39: 19000000 INFO @ Fri, 10 Nov 2017 23:12:54: 23000000 INFO @ Fri, 10 Nov 2017 23:12:57: 22000000 INFO @ Fri, 10 Nov 2017 23:13:13: 20000000 INFO @ Fri, 10 Nov 2017 23:13:19: 24000000 INFO @ Fri, 10 Nov 2017 23:13:26: 23000000 INFO @ Fri, 10 Nov 2017 23:13:48: 21000000 INFO @ Fri, 10 Nov 2017 23:13:51: 25000000 INFO @ Fri, 10 Nov 2017 23:13:55: 24000000 INFO @ Fri, 10 Nov 2017 23:14:10: 26000000 INFO @ Fri, 10 Nov 2017 23:14:22: 25000000 INFO @ Fri, 10 Nov 2017 23:14:23: 22000000 INFO @ Fri, 10 Nov 2017 23:14:38: 27000000 INFO @ Fri, 10 Nov 2017 23:14:47: 26000000 INFO @ Fri, 10 Nov 2017 23:14:58: 28000000 INFO @ Fri, 10 Nov 2017 23:14:58: 23000000 INFO @ Fri, 10 Nov 2017 23:15:14: 27000000 INFO @ Fri, 10 Nov 2017 23:15:17: 29000000 INFO @ Fri, 10 Nov 2017 23:15:32: 24000000 INFO @ Fri, 10 Nov 2017 23:15:40: 30000000 INFO @ Fri, 10 Nov 2017 23:15:43: 28000000 INFO @ Fri, 10 Nov 2017 23:15:59: 31000000 INFO @ Fri, 10 Nov 2017 23:16:07: 25000000 INFO @ Fri, 10 Nov 2017 23:16:13: 29000000 INFO @ Fri, 10 Nov 2017 23:16:17: 32000000 INFO @ Fri, 10 Nov 2017 23:16:38: 33000000 INFO @ Fri, 10 Nov 2017 23:16:41: 26000000 INFO @ Fri, 10 Nov 2017 23:16:43: 30000000 INFO @ Fri, 10 Nov 2017 23:16:58: 34000000 INFO @ Fri, 10 Nov 2017 23:17:13: 27000000 INFO @ Fri, 10 Nov 2017 23:17:14: 31000000 INFO @ Fri, 10 Nov 2017 23:17:15: 35000000 INFO @ Fri, 10 Nov 2017 23:17:39: 36000000 INFO @ Fri, 10 Nov 2017 23:17:44: 32000000 INFO @ Fri, 10 Nov 2017 23:17:47: 28000000 INFO @ Fri, 10 Nov 2017 23:18:04: 37000000 INFO @ Fri, 10 Nov 2017 23:18:14: 33000000 INFO @ Fri, 10 Nov 2017 23:18:20: 29000000 INFO @ Fri, 10 Nov 2017 23:18:21: 38000000 INFO @ Fri, 10 Nov 2017 23:18:37: 39000000 INFO @ Fri, 10 Nov 2017 23:18:39: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:18:39: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:18:39: #1 total tags in treatment: 39056101 INFO @ Fri, 10 Nov 2017 23:18:39: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:18:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:18:41: #1 tags after filtering in treatment: 39056019 INFO @ Fri, 10 Nov 2017 23:18:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:18:41: #1 finished! INFO @ Fri, 10 Nov 2017 23:18:41: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:18:43: 34000000 INFO @ Fri, 10 Nov 2017 23:18:45: #2 number of paired peaks: 6000 INFO @ Fri, 10 Nov 2017 23:18:45: start model_add_line... INFO @ Fri, 10 Nov 2017 23:18:46: start X-correlation... INFO @ Fri, 10 Nov 2017 23:18:46: end of X-cor INFO @ Fri, 10 Nov 2017 23:18:46: #2 finished! INFO @ Fri, 10 Nov 2017 23:18:46: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Nov 2017 23:18:46: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Nov 2017 23:18:46: #2.2 Generate R script for model : SRX1056324.05_model.r WARNING @ Fri, 10 Nov 2017 23:18:46: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:18:46: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 10 Nov 2017 23:18:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:18:46: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:18:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:18:52: 30000000 INFO @ Fri, 10 Nov 2017 23:19:11: 35000000 INFO @ Fri, 10 Nov 2017 23:19:25: 31000000 INFO @ Fri, 10 Nov 2017 23:19:38: 36000000 INFO @ Fri, 10 Nov 2017 23:19:59: 32000000 INFO @ Fri, 10 Nov 2017 23:20:03: 37000000 INFO @ Fri, 10 Nov 2017 23:20:28: 38000000 INFO @ Fri, 10 Nov 2017 23:20:34: 33000000 INFO @ Fri, 10 Nov 2017 23:20:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:20:54: 39000000 INFO @ Fri, 10 Nov 2017 23:20:56: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:20:56: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:20:56: #1 total tags in treatment: 39056101 INFO @ Fri, 10 Nov 2017 23:20:56: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:20:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:20:57: #1 tags after filtering in treatment: 39056019 INFO @ Fri, 10 Nov 2017 23:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:20:57: #1 finished! INFO @ Fri, 10 Nov 2017 23:20:57: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:21:02: #2 number of paired peaks: 6000 INFO @ Fri, 10 Nov 2017 23:21:02: start model_add_line... INFO @ Fri, 10 Nov 2017 23:21:02: start X-correlation... INFO @ Fri, 10 Nov 2017 23:21:02: end of X-cor INFO @ Fri, 10 Nov 2017 23:21:02: #2 finished! INFO @ Fri, 10 Nov 2017 23:21:02: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Nov 2017 23:21:02: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Nov 2017 23:21:02: #2.2 Generate R script for model : SRX1056324.20_model.r WARNING @ Fri, 10 Nov 2017 23:21:02: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:21:02: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 10 Nov 2017 23:21:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:21:02: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:21:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:21:06: 34000000 INFO @ Fri, 10 Nov 2017 23:21:34: 35000000 INFO @ Fri, 10 Nov 2017 23:22:05: 36000000 INFO @ Fri, 10 Nov 2017 23:22:09: #4 Write output xls file... SRX1056324.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:22:09: #4 Write peak in narrowPeak format file... SRX1056324.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:22:09: #4 Write summits bed file... SRX1056324.05_summits.bed INFO @ Fri, 10 Nov 2017 23:22:09: Done! pass1 - making usageList (70 chroms): 2 millis pass2 - checking and writing primary data (2388 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:22:33: 37000000 INFO @ Fri, 10 Nov 2017 23:22:58: 38000000 INFO @ Fri, 10 Nov 2017 23:23:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:23:25: 39000000 INFO @ Fri, 10 Nov 2017 23:23:26: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:23:26: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:23:26: #1 total tags in treatment: 39056101 INFO @ Fri, 10 Nov 2017 23:23:26: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:23:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:23:28: #1 tags after filtering in treatment: 39056019 INFO @ Fri, 10 Nov 2017 23:23:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:23:28: #1 finished! INFO @ Fri, 10 Nov 2017 23:23:28: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:23:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:23:33: #2 number of paired peaks: 6000 INFO @ Fri, 10 Nov 2017 23:23:33: start model_add_line... INFO @ Fri, 10 Nov 2017 23:23:33: start X-correlation... INFO @ Fri, 10 Nov 2017 23:23:33: end of X-cor INFO @ Fri, 10 Nov 2017 23:23:33: #2 finished! INFO @ Fri, 10 Nov 2017 23:23:33: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Nov 2017 23:23:33: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Nov 2017 23:23:33: #2.2 Generate R script for model : SRX1056324.10_model.r WARNING @ Fri, 10 Nov 2017 23:23:33: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:23:33: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 10 Nov 2017 23:23:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:23:33: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:24:15: #4 Write output xls file... SRX1056324.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:24:15: #4 Write peak in narrowPeak format file... SRX1056324.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:24:15: #4 Write summits bed file... SRX1056324.20_summits.bed INFO @ Fri, 10 Nov 2017 23:24:15: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (635 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:25:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:26:46: #4 Write output xls file... SRX1056324.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:26:46: #4 Write peak in narrowPeak format file... SRX1056324.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:26:46: #4 Write summits bed file... SRX1056324.10_summits.bed INFO @ Fri, 10 Nov 2017 23:26:46: Done! pass1 - making usageList (53 chroms): 3 millis pass2 - checking and writing primary data (1246 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。