Job ID = 11632719 sra ファイルのダウンロード中... Completed: 1594650K bytes transferred in 18 seconds (691555K 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... Read 60841336 spots for /home/okishinya/chipatlas/results/rn6/SRX3782478/SRR6826296.sra Written 60841336 spots for /home/okishinya/chipatlas/results/rn6/SRX3782478/SRR6826296.sra 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 rm: cannot remove `[DSE]RR*.fastq': 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: 00:00:00 Multiseed full-index search: 00:24:50 60841336 reads; of these: 60841336 (100.00%) were unpaired; of these: 4383838 (7.21%) aligned 0 times 43726595 (71.87%) aligned exactly 1 time 12730903 (20.92%) aligned >1 times 92.79% overall alignment rate Time searching: 00:24:52 Overall time: 00:24:52 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 16 files... [bam_rmdupse_core] 7105701 / 56457498 = 0.1259 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, 15 Feb 2019 07:18:39: # Command line: callpeak -t SRX3782478.bam -f BAM -g 2.15e9 -n SRX3782478.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782478.20 # format = BAM # ChIP-seq file = ['SRX3782478.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, 15 Feb 2019 07:18:39: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:18:39: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:18:39: # Command line: callpeak -t SRX3782478.bam -f BAM -g 2.15e9 -n SRX3782478.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782478.10 # format = BAM # ChIP-seq file = ['SRX3782478.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, 15 Feb 2019 07:18:39: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:18:39: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:18:39: # Command line: callpeak -t SRX3782478.bam -f BAM -g 2.15e9 -n SRX3782478.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782478.05 # format = BAM # ChIP-seq file = ['SRX3782478.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, 15 Feb 2019 07:18:39: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:18:39: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:18:45: 1000000 INFO @ Fri, 15 Feb 2019 07:18:45: 1000000 INFO @ Fri, 15 Feb 2019 07:18:45: 1000000 INFO @ Fri, 15 Feb 2019 07:18:52: 2000000 INFO @ Fri, 15 Feb 2019 07:18:52: 2000000 INFO @ Fri, 15 Feb 2019 07:18:52: 2000000 INFO @ Fri, 15 Feb 2019 07:18:58: 3000000 INFO @ Fri, 15 Feb 2019 07:18:58: 3000000 INFO @ Fri, 15 Feb 2019 07:18:59: 3000000 INFO @ Fri, 15 Feb 2019 07:19:05: 4000000 INFO @ Fri, 15 Feb 2019 07:19:05: 4000000 INFO @ Fri, 15 Feb 2019 07:19:06: 4000000 INFO @ Fri, 15 Feb 2019 07:19:11: 5000000 INFO @ Fri, 15 Feb 2019 07:19:11: 5000000 INFO @ Fri, 15 Feb 2019 07:19:12: 5000000 INFO @ Fri, 15 Feb 2019 07:19:18: 6000000 INFO @ Fri, 15 Feb 2019 07:19:18: 6000000 INFO @ Fri, 15 Feb 2019 07:19:19: 6000000 INFO @ Fri, 15 Feb 2019 07:19:24: 7000000 INFO @ Fri, 15 Feb 2019 07:19:25: 7000000 INFO @ Fri, 15 Feb 2019 07:19:26: 7000000 INFO @ Fri, 15 Feb 2019 07:19:31: 8000000 INFO @ Fri, 15 Feb 2019 07:19:31: 8000000 INFO @ Fri, 15 Feb 2019 07:19:33: 8000000 INFO @ Fri, 15 Feb 2019 07:19:38: 9000000 INFO @ Fri, 15 Feb 2019 07:19:38: 9000000 INFO @ Fri, 15 Feb 2019 07:19:40: 9000000 INFO @ Fri, 15 Feb 2019 07:19:44: 10000000 INFO @ Fri, 15 Feb 2019 07:19:45: 10000000 INFO @ Fri, 15 Feb 2019 07:19:47: 10000000 INFO @ Fri, 15 Feb 2019 07:19:51: 11000000 INFO @ Fri, 15 Feb 2019 07:19:52: 11000000 INFO @ Fri, 15 Feb 2019 07:19:54: 11000000 INFO @ Fri, 15 Feb 2019 07:19:57: 12000000 INFO @ Fri, 15 Feb 2019 07:19:58: 12000000 INFO @ Fri, 15 Feb 2019 07:20:01: 12000000 INFO @ Fri, 15 Feb 2019 07:20:04: 13000000 INFO @ Fri, 15 Feb 2019 07:20:05: 13000000 INFO @ Fri, 15 Feb 2019 07:20:08: 13000000 INFO @ Fri, 15 Feb 2019 07:20:10: 14000000 INFO @ Fri, 15 Feb 2019 07:20:12: 14000000 INFO @ Fri, 15 Feb 2019 07:20:15: 14000000 INFO @ Fri, 15 Feb 2019 07:20:17: 15000000 INFO @ Fri, 15 Feb 2019 07:20:18: 15000000 INFO @ Fri, 15 Feb 2019 07:20:22: 15000000 INFO @ Fri, 15 Feb 2019 07:20:23: 16000000 INFO @ Fri, 15 Feb 2019 07:20:25: 16000000 INFO @ Fri, 15 Feb 2019 07:20:29: 16000000 INFO @ Fri, 15 Feb 2019 07:20:30: 17000000 INFO @ Fri, 15 Feb 2019 07:20:32: 17000000 INFO @ Fri, 15 Feb 2019 07:20:36: 17000000 INFO @ Fri, 15 Feb 2019 07:20:37: 18000000 INFO @ Fri, 15 Feb 2019 07:20:39: 18000000 INFO @ Fri, 15 Feb 2019 07:20:43: 18000000 INFO @ Fri, 15 Feb 2019 07:20:43: 19000000 INFO @ Fri, 15 Feb 2019 07:20:45: 19000000 INFO @ Fri, 15 Feb 2019 07:20:50: 19000000 INFO @ Fri, 15 Feb 2019 07:20:50: 20000000 INFO @ Fri, 15 Feb 2019 07:20:52: 20000000 INFO @ Fri, 15 Feb 2019 07:20:56: 21000000 INFO @ Fri, 15 Feb 2019 07:20:57: 20000000 INFO @ Fri, 15 Feb 2019 07:20:59: 21000000 INFO @ Fri, 15 Feb 2019 07:21:03: 22000000 INFO @ Fri, 15 Feb 2019 07:21:04: 21000000 INFO @ Fri, 15 Feb 2019 07:21:06: 22000000 INFO @ Fri, 15 Feb 2019 07:21:09: 23000000 INFO @ Fri, 15 Feb 2019 07:21:11: 22000000 INFO @ Fri, 15 Feb 2019 07:21:12: 23000000 INFO @ Fri, 15 Feb 2019 07:21:16: 24000000 INFO @ Fri, 15 Feb 2019 07:21:17: 23000000 INFO @ Fri, 15 Feb 2019 07:21:19: 24000000 INFO @ Fri, 15 Feb 2019 07:21:23: 25000000 INFO @ Fri, 15 Feb 2019 07:21:24: 24000000 INFO @ Fri, 15 Feb 2019 07:21:26: 25000000 INFO @ Fri, 15 Feb 2019 07:21:29: 26000000 INFO @ Fri, 15 Feb 2019 07:21:31: 25000000 INFO @ Fri, 15 Feb 2019 07:21:33: 26000000 INFO @ Fri, 15 Feb 2019 07:21:36: 27000000 INFO @ Fri, 15 Feb 2019 07:21:38: 26000000 INFO @ Fri, 15 Feb 2019 07:21:39: 27000000 INFO @ Fri, 15 Feb 2019 07:21:42: 28000000 INFO @ Fri, 15 Feb 2019 07:21:45: 27000000 INFO @ Fri, 15 Feb 2019 07:21:46: 28000000 INFO @ Fri, 15 Feb 2019 07:21:49: 29000000 INFO @ Fri, 15 Feb 2019 07:21:52: 28000000 INFO @ Fri, 15 Feb 2019 07:21:53: 29000000 INFO @ Fri, 15 Feb 2019 07:21:55: 30000000 INFO @ Fri, 15 Feb 2019 07:21:59: 29000000 INFO @ Fri, 15 Feb 2019 07:22:00: 30000000 INFO @ Fri, 15 Feb 2019 07:22:02: 31000000 INFO @ Fri, 15 Feb 2019 07:22:06: 30000000 INFO @ Fri, 15 Feb 2019 07:22:06: 31000000 INFO @ Fri, 15 Feb 2019 07:22:09: 32000000 INFO @ Fri, 15 Feb 2019 07:22:13: 31000000 INFO @ Fri, 15 Feb 2019 07:22:13: 32000000 INFO @ Fri, 15 Feb 2019 07:22:15: 33000000 INFO @ Fri, 15 Feb 2019 07:22:20: 33000000 INFO @ Fri, 15 Feb 2019 07:22:20: 32000000 INFO @ Fri, 15 Feb 2019 07:22:22: 34000000 INFO @ Fri, 15 Feb 2019 07:22:27: 34000000 INFO @ Fri, 15 Feb 2019 07:22:27: 33000000 INFO @ Fri, 15 Feb 2019 07:22:28: 35000000 INFO @ Fri, 15 Feb 2019 07:22:33: 35000000 INFO @ Fri, 15 Feb 2019 07:22:34: 34000000 INFO @ Fri, 15 Feb 2019 07:22:35: 36000000 INFO @ Fri, 15 Feb 2019 07:22:40: 36000000 INFO @ Fri, 15 Feb 2019 07:22:41: 35000000 INFO @ Fri, 15 Feb 2019 07:22:41: 37000000 INFO @ Fri, 15 Feb 2019 07:22:47: 37000000 INFO @ Fri, 15 Feb 2019 07:22:48: 36000000 INFO @ Fri, 15 Feb 2019 07:22:48: 38000000 INFO @ Fri, 15 Feb 2019 07:22:54: 38000000 INFO @ Fri, 15 Feb 2019 07:22:55: 39000000 INFO @ Fri, 15 Feb 2019 07:22:55: 37000000 INFO @ Fri, 15 Feb 2019 07:23:01: 39000000 INFO @ Fri, 15 Feb 2019 07:23:01: 40000000 INFO @ Fri, 15 Feb 2019 07:23:02: 38000000 INFO @ Fri, 15 Feb 2019 07:23:07: 40000000 INFO @ Fri, 15 Feb 2019 07:23:08: 41000000 INFO @ Fri, 15 Feb 2019 07:23:09: 39000000 INFO @ Fri, 15 Feb 2019 07:23:14: 41000000 INFO @ Fri, 15 Feb 2019 07:23:14: 42000000 INFO @ Fri, 15 Feb 2019 07:23:16: 40000000 INFO @ Fri, 15 Feb 2019 07:23:21: 43000000 INFO @ Fri, 15 Feb 2019 07:23:21: 42000000 INFO @ Fri, 15 Feb 2019 07:23:23: 41000000 INFO @ Fri, 15 Feb 2019 07:23:28: 44000000 INFO @ Fri, 15 Feb 2019 07:23:28: 43000000 INFO @ Fri, 15 Feb 2019 07:23:30: 42000000 INFO @ Fri, 15 Feb 2019 07:23:34: 45000000 INFO @ Fri, 15 Feb 2019 07:23:35: 44000000 INFO @ Fri, 15 Feb 2019 07:23:37: 43000000 INFO @ Fri, 15 Feb 2019 07:23:41: 46000000 INFO @ Fri, 15 Feb 2019 07:23:41: 45000000 INFO @ Fri, 15 Feb 2019 07:23:44: 44000000 INFO @ Fri, 15 Feb 2019 07:23:48: 47000000 INFO @ Fri, 15 Feb 2019 07:23:50: 46000000 INFO @ Fri, 15 Feb 2019 07:23:53: 45000000 INFO @ Fri, 15 Feb 2019 07:23:56: 48000000 INFO @ Fri, 15 Feb 2019 07:23:57: 47000000 INFO @ Fri, 15 Feb 2019 07:24:00: 46000000 INFO @ Fri, 15 Feb 2019 07:24:02: 49000000 INFO @ Fri, 15 Feb 2019 07:24:04: 48000000 INFO @ Fri, 15 Feb 2019 07:24:05: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:24:05: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:24:05: #1 total tags in treatment: 49351797 INFO @ Fri, 15 Feb 2019 07:24:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:24:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:24:06: #1 tags after filtering in treatment: 49351693 INFO @ Fri, 15 Feb 2019 07:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:24:06: #1 finished! INFO @ Fri, 15 Feb 2019 07:24:06: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:24:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:24:07: 47000000 INFO @ Fri, 15 Feb 2019 07:24:10: 49000000 INFO @ Fri, 15 Feb 2019 07:24:11: #2 number of paired peaks: 16730 INFO @ Fri, 15 Feb 2019 07:24:11: start model_add_line... INFO @ Fri, 15 Feb 2019 07:24:12: start X-correlation... INFO @ Fri, 15 Feb 2019 07:24:12: end of X-cor INFO @ Fri, 15 Feb 2019 07:24:12: #2 finished! INFO @ Fri, 15 Feb 2019 07:24:12: #2 predicted fragment length is 196 bps INFO @ Fri, 15 Feb 2019 07:24:12: #2 alternative fragment length(s) may be 187,196 bps INFO @ Fri, 15 Feb 2019 07:24:12: #2.2 Generate R script for model : SRX3782478.10_model.r INFO @ Fri, 15 Feb 2019 07:24:12: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:24:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:24:13: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:24:13: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:24:13: #1 total tags in treatment: 49351797 INFO @ Fri, 15 Feb 2019 07:24:13: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:24:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:24:14: 48000000 INFO @ Fri, 15 Feb 2019 07:24:14: #1 tags after filtering in treatment: 49351693 INFO @ Fri, 15 Feb 2019 07:24:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:24:14: #1 finished! INFO @ Fri, 15 Feb 2019 07:24:14: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:24:19: #2 number of paired peaks: 16730 INFO @ Fri, 15 Feb 2019 07:24:19: start model_add_line... INFO @ Fri, 15 Feb 2019 07:24:20: start X-correlation... INFO @ Fri, 15 Feb 2019 07:24:20: end of X-cor INFO @ Fri, 15 Feb 2019 07:24:20: #2 finished! INFO @ Fri, 15 Feb 2019 07:24:20: #2 predicted fragment length is 196 bps INFO @ Fri, 15 Feb 2019 07:24:20: #2 alternative fragment length(s) may be 187,196 bps INFO @ Fri, 15 Feb 2019 07:24:20: #2.2 Generate R script for model : SRX3782478.05_model.r INFO @ Fri, 15 Feb 2019 07:24:20: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:24:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:24:21: 49000000 INFO @ Fri, 15 Feb 2019 07:24:23: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:24:23: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:24:23: #1 total tags in treatment: 49351797 INFO @ Fri, 15 Feb 2019 07:24:23: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:24:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:24:25: #1 tags after filtering in treatment: 49351693 INFO @ Fri, 15 Feb 2019 07:24:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:24:25: #1 finished! INFO @ Fri, 15 Feb 2019 07:24:25: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:24:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:24:29: #2 number of paired peaks: 16730 INFO @ Fri, 15 Feb 2019 07:24:29: start model_add_line... INFO @ Fri, 15 Feb 2019 07:24:30: start X-correlation... INFO @ Fri, 15 Feb 2019 07:24:30: end of X-cor INFO @ Fri, 15 Feb 2019 07:24:30: #2 finished! INFO @ Fri, 15 Feb 2019 07:24:30: #2 predicted fragment length is 196 bps INFO @ Fri, 15 Feb 2019 07:24:30: #2 alternative fragment length(s) may be 187,196 bps INFO @ Fri, 15 Feb 2019 07:24:30: #2.2 Generate R script for model : SRX3782478.20_model.r INFO @ Fri, 15 Feb 2019 07:24:30: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:24:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:26:18: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:26:19: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:26:34: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:27:27: #4 Write output xls file... SRX3782478.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:27:27: #4 Write peak in narrowPeak format file... SRX3782478.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:27:27: #4 Write summits bed file... SRX3782478.10_summits.bed INFO @ Fri, 15 Feb 2019 07:27:27: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (722 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:27:31: #4 Write output xls file... SRX3782478.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:27:31: #4 Write peak in narrowPeak format file... SRX3782478.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:27:31: #4 Write summits bed file... SRX3782478.05_summits.bed INFO @ Fri, 15 Feb 2019 07:27:31: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (3613 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:27:39: #4 Write output xls file... SRX3782478.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:27:39: #4 Write peak in narrowPeak format file... SRX3782478.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:27:39: #4 Write summits bed file... SRX3782478.20_summits.bed INFO @ Fri, 15 Feb 2019 07:27:39: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。