Job ID = 11632713 sra ファイルのダウンロード中... Completed: 1035859K bytes transferred in 14 seconds (602452K 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 68327945 spots for /home/okishinya/chipatlas/results/rn6/SRX3782472/SRR6826290.sra Written 68327945 spots for /home/okishinya/chipatlas/results/rn6/SRX3782472/SRR6826290.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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:27:20 68327945 reads; of these: 68327945 (100.00%) were unpaired; of these: 4091026 (5.99%) aligned 0 times 50105396 (73.33%) aligned exactly 1 time 14131523 (20.68%) aligned >1 times 94.01% overall alignment rate Time searching: 00:27:25 Overall time: 00:27:25 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] 7163824 / 64236919 = 0.1115 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 07:10:08: # Command line: callpeak -t SRX3782472.bam -f BAM -g 2.15e9 -n SRX3782472.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782472.20 # format = BAM # ChIP-seq file = ['SRX3782472.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 07:10:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:10:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:10:08: # Command line: callpeak -t SRX3782472.bam -f BAM -g 2.15e9 -n SRX3782472.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782472.10 # format = BAM # ChIP-seq file = ['SRX3782472.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 07:10:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:10:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:10:08: # Command line: callpeak -t SRX3782472.bam -f BAM -g 2.15e9 -n SRX3782472.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782472.05 # format = BAM # ChIP-seq file = ['SRX3782472.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 07:10:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:10:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:10:14: 1000000 INFO @ Fri, 15 Feb 2019 07:10:14: 1000000 INFO @ Fri, 15 Feb 2019 07:10:15: 1000000 INFO @ Fri, 15 Feb 2019 07:10:20: 2000000 INFO @ Fri, 15 Feb 2019 07:10:21: 2000000 INFO @ Fri, 15 Feb 2019 07:10:21: 2000000 INFO @ Fri, 15 Feb 2019 07:10:26: 3000000 INFO @ Fri, 15 Feb 2019 07:10:27: 3000000 INFO @ Fri, 15 Feb 2019 07:10:27: 3000000 INFO @ Fri, 15 Feb 2019 07:10:32: 4000000 INFO @ Fri, 15 Feb 2019 07:10:33: 4000000 INFO @ Fri, 15 Feb 2019 07:10:34: 4000000 INFO @ Fri, 15 Feb 2019 07:10:38: 5000000 INFO @ Fri, 15 Feb 2019 07:10:39: 5000000 INFO @ Fri, 15 Feb 2019 07:10:40: 5000000 INFO @ Fri, 15 Feb 2019 07:10:44: 6000000 INFO @ Fri, 15 Feb 2019 07:10:45: 6000000 INFO @ Fri, 15 Feb 2019 07:10:47: 6000000 INFO @ Fri, 15 Feb 2019 07:10:50: 7000000 INFO @ Fri, 15 Feb 2019 07:10:52: 7000000 INFO @ Fri, 15 Feb 2019 07:10:53: 7000000 INFO @ Fri, 15 Feb 2019 07:10:55: 8000000 INFO @ Fri, 15 Feb 2019 07:10:58: 8000000 INFO @ Fri, 15 Feb 2019 07:11:00: 8000000 INFO @ Fri, 15 Feb 2019 07:11:01: 9000000 INFO @ Fri, 15 Feb 2019 07:11:04: 9000000 INFO @ Fri, 15 Feb 2019 07:11:06: 9000000 INFO @ Fri, 15 Feb 2019 07:11:07: 10000000 INFO @ Fri, 15 Feb 2019 07:11:10: 10000000 INFO @ Fri, 15 Feb 2019 07:11:13: 10000000 INFO @ Fri, 15 Feb 2019 07:11:13: 11000000 INFO @ Fri, 15 Feb 2019 07:11:17: 11000000 INFO @ Fri, 15 Feb 2019 07:11:19: 12000000 INFO @ Fri, 15 Feb 2019 07:11:19: 11000000 INFO @ Fri, 15 Feb 2019 07:11:23: 12000000 INFO @ Fri, 15 Feb 2019 07:11:25: 13000000 INFO @ Fri, 15 Feb 2019 07:11:26: 12000000 INFO @ Fri, 15 Feb 2019 07:11:29: 13000000 INFO @ Fri, 15 Feb 2019 07:11:31: 14000000 INFO @ Fri, 15 Feb 2019 07:11:32: 13000000 INFO @ Fri, 15 Feb 2019 07:11:35: 14000000 INFO @ Fri, 15 Feb 2019 07:11:36: 15000000 INFO @ Fri, 15 Feb 2019 07:11:39: 14000000 INFO @ Fri, 15 Feb 2019 07:11:41: 15000000 INFO @ Fri, 15 Feb 2019 07:11:42: 16000000 INFO @ Fri, 15 Feb 2019 07:11:45: 15000000 INFO @ Fri, 15 Feb 2019 07:11:48: 16000000 INFO @ Fri, 15 Feb 2019 07:11:48: 17000000 INFO @ Fri, 15 Feb 2019 07:11:52: 16000000 INFO @ Fri, 15 Feb 2019 07:11:54: 18000000 INFO @ Fri, 15 Feb 2019 07:11:54: 17000000 INFO @ Fri, 15 Feb 2019 07:11:58: 17000000 INFO @ Fri, 15 Feb 2019 07:12:00: 19000000 INFO @ Fri, 15 Feb 2019 07:12:00: 18000000 INFO @ Fri, 15 Feb 2019 07:12:05: 18000000 INFO @ Fri, 15 Feb 2019 07:12:06: 20000000 INFO @ Fri, 15 Feb 2019 07:12:07: 19000000 INFO @ Fri, 15 Feb 2019 07:12:11: 19000000 INFO @ Fri, 15 Feb 2019 07:12:11: 21000000 INFO @ Fri, 15 Feb 2019 07:12:13: 20000000 INFO @ Fri, 15 Feb 2019 07:12:17: 22000000 INFO @ Fri, 15 Feb 2019 07:12:18: 20000000 INFO @ Fri, 15 Feb 2019 07:12:19: 21000000 INFO @ Fri, 15 Feb 2019 07:12:23: 23000000 INFO @ Fri, 15 Feb 2019 07:12:24: 21000000 INFO @ Fri, 15 Feb 2019 07:12:25: 22000000 INFO @ Fri, 15 Feb 2019 07:12:29: 24000000 INFO @ Fri, 15 Feb 2019 07:12:31: 22000000 INFO @ Fri, 15 Feb 2019 07:12:31: 23000000 INFO @ Fri, 15 Feb 2019 07:12:35: 25000000 INFO @ Fri, 15 Feb 2019 07:12:37: 23000000 INFO @ Fri, 15 Feb 2019 07:12:38: 24000000 INFO @ Fri, 15 Feb 2019 07:12:41: 26000000 INFO @ Fri, 15 Feb 2019 07:12:44: 25000000 INFO @ Fri, 15 Feb 2019 07:12:44: 24000000 INFO @ Fri, 15 Feb 2019 07:12:47: 27000000 INFO @ Fri, 15 Feb 2019 07:12:50: 26000000 INFO @ Fri, 15 Feb 2019 07:12:51: 25000000 INFO @ Fri, 15 Feb 2019 07:12:53: 28000000 INFO @ Fri, 15 Feb 2019 07:12:56: 27000000 INFO @ Fri, 15 Feb 2019 07:12:57: 26000000 INFO @ Fri, 15 Feb 2019 07:12:58: 29000000 INFO @ Fri, 15 Feb 2019 07:13:02: 28000000 INFO @ Fri, 15 Feb 2019 07:13:04: 27000000 INFO @ Fri, 15 Feb 2019 07:13:04: 30000000 INFO @ Fri, 15 Feb 2019 07:13:08: 29000000 INFO @ Fri, 15 Feb 2019 07:13:10: 31000000 INFO @ Fri, 15 Feb 2019 07:13:10: 28000000 INFO @ Fri, 15 Feb 2019 07:13:15: 30000000 INFO @ Fri, 15 Feb 2019 07:13:16: 32000000 INFO @ Fri, 15 Feb 2019 07:13:17: 29000000 INFO @ Fri, 15 Feb 2019 07:13:21: 31000000 INFO @ Fri, 15 Feb 2019 07:13:22: 33000000 INFO @ Fri, 15 Feb 2019 07:13:23: 30000000 INFO @ Fri, 15 Feb 2019 07:13:27: 32000000 INFO @ Fri, 15 Feb 2019 07:13:28: 34000000 INFO @ Fri, 15 Feb 2019 07:13:30: 31000000 INFO @ Fri, 15 Feb 2019 07:13:33: 33000000 INFO @ Fri, 15 Feb 2019 07:13:34: 35000000 INFO @ Fri, 15 Feb 2019 07:13:37: 32000000 INFO @ Fri, 15 Feb 2019 07:13:39: 34000000 INFO @ Fri, 15 Feb 2019 07:13:40: 36000000 INFO @ Fri, 15 Feb 2019 07:13:43: 33000000 INFO @ Fri, 15 Feb 2019 07:13:46: 37000000 INFO @ Fri, 15 Feb 2019 07:13:46: 35000000 INFO @ Fri, 15 Feb 2019 07:13:50: 34000000 INFO @ Fri, 15 Feb 2019 07:13:51: 38000000 INFO @ Fri, 15 Feb 2019 07:13:52: 36000000 INFO @ Fri, 15 Feb 2019 07:13:57: 35000000 INFO @ Fri, 15 Feb 2019 07:13:57: 39000000 INFO @ Fri, 15 Feb 2019 07:13:58: 37000000 INFO @ Fri, 15 Feb 2019 07:14:03: 40000000 INFO @ Fri, 15 Feb 2019 07:14:03: 36000000 INFO @ Fri, 15 Feb 2019 07:14:05: 38000000 INFO @ Fri, 15 Feb 2019 07:14:09: 41000000 INFO @ Fri, 15 Feb 2019 07:14:10: 37000000 INFO @ Fri, 15 Feb 2019 07:14:11: 39000000 INFO @ Fri, 15 Feb 2019 07:14:15: 42000000 INFO @ Fri, 15 Feb 2019 07:14:17: 38000000 INFO @ Fri, 15 Feb 2019 07:14:17: 40000000 INFO @ Fri, 15 Feb 2019 07:14:21: 43000000 INFO @ Fri, 15 Feb 2019 07:14:23: 39000000 INFO @ Fri, 15 Feb 2019 07:14:23: 41000000 INFO @ Fri, 15 Feb 2019 07:14:26: 44000000 INFO @ Fri, 15 Feb 2019 07:14:29: 42000000 INFO @ Fri, 15 Feb 2019 07:14:30: 40000000 INFO @ Fri, 15 Feb 2019 07:14:32: 45000000 INFO @ Fri, 15 Feb 2019 07:14:36: 43000000 INFO @ Fri, 15 Feb 2019 07:14:36: 41000000 INFO @ Fri, 15 Feb 2019 07:14:38: 46000000 INFO @ Fri, 15 Feb 2019 07:14:42: 44000000 INFO @ Fri, 15 Feb 2019 07:14:43: 42000000 INFO @ Fri, 15 Feb 2019 07:14:44: 47000000 INFO @ Fri, 15 Feb 2019 07:14:48: 45000000 INFO @ Fri, 15 Feb 2019 07:14:49: 43000000 INFO @ Fri, 15 Feb 2019 07:14:50: 48000000 INFO @ Fri, 15 Feb 2019 07:14:54: 46000000 INFO @ Fri, 15 Feb 2019 07:14:56: 49000000 INFO @ Fri, 15 Feb 2019 07:14:56: 44000000 INFO @ Fri, 15 Feb 2019 07:15:00: 47000000 INFO @ Fri, 15 Feb 2019 07:15:01: 50000000 INFO @ Fri, 15 Feb 2019 07:15:02: 45000000 INFO @ Fri, 15 Feb 2019 07:15:06: 48000000 INFO @ Fri, 15 Feb 2019 07:15:07: 51000000 INFO @ Fri, 15 Feb 2019 07:15:08: 46000000 INFO @ Fri, 15 Feb 2019 07:15:12: 49000000 INFO @ Fri, 15 Feb 2019 07:15:13: 52000000 INFO @ Fri, 15 Feb 2019 07:15:15: 47000000 INFO @ Fri, 15 Feb 2019 07:15:18: 50000000 INFO @ Fri, 15 Feb 2019 07:15:19: 53000000 INFO @ Fri, 15 Feb 2019 07:15:21: 48000000 INFO @ Fri, 15 Feb 2019 07:15:24: 51000000 INFO @ Fri, 15 Feb 2019 07:15:25: 54000000 INFO @ Fri, 15 Feb 2019 07:15:28: 49000000 INFO @ Fri, 15 Feb 2019 07:15:30: 52000000 INFO @ Fri, 15 Feb 2019 07:15:31: 55000000 INFO @ Fri, 15 Feb 2019 07:15:34: 50000000 INFO @ Fri, 15 Feb 2019 07:15:36: 53000000 INFO @ Fri, 15 Feb 2019 07:15:36: 56000000 INFO @ Fri, 15 Feb 2019 07:15:40: 51000000 INFO @ Fri, 15 Feb 2019 07:15:42: 54000000 INFO @ Fri, 15 Feb 2019 07:15:42: 57000000 INFO @ Fri, 15 Feb 2019 07:15:43: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:15:43: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:15:43: #1 total tags in treatment: 57073095 INFO @ Fri, 15 Feb 2019 07:15:43: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:15:43: #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 07:15:45: #1 tags after filtering in treatment: 57073032 INFO @ Fri, 15 Feb 2019 07:15:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:15:45: #1 finished! INFO @ Fri, 15 Feb 2019 07:15:45: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:15:47: 52000000 INFO @ Fri, 15 Feb 2019 07:15:48: 55000000 INFO @ Fri, 15 Feb 2019 07:15:51: #2 number of paired peaks: 38815 INFO @ Fri, 15 Feb 2019 07:15:51: start model_add_line... INFO @ Fri, 15 Feb 2019 07:15:52: start X-correlation... INFO @ Fri, 15 Feb 2019 07:15:52: end of X-cor INFO @ Fri, 15 Feb 2019 07:15:52: #2 finished! INFO @ Fri, 15 Feb 2019 07:15:52: #2 predicted fragment length is 340 bps INFO @ Fri, 15 Feb 2019 07:15:52: #2 alternative fragment length(s) may be 340 bps INFO @ Fri, 15 Feb 2019 07:15:52: #2.2 Generate R script for model : SRX3782472.05_model.r INFO @ Fri, 15 Feb 2019 07:15:52: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:15:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:15:53: 53000000 INFO @ Fri, 15 Feb 2019 07:15:54: 56000000 INFO @ Fri, 15 Feb 2019 07:16:00: 54000000 INFO @ Fri, 15 Feb 2019 07:16:00: 57000000 INFO @ Fri, 15 Feb 2019 07:16:01: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:16:01: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:16:01: #1 total tags in treatment: 57073095 INFO @ Fri, 15 Feb 2019 07:16:01: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:16:01: #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 07:16:02: #1 tags after filtering in treatment: 57073032 INFO @ Fri, 15 Feb 2019 07:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:16:02: #1 finished! INFO @ Fri, 15 Feb 2019 07:16:02: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:16:06: 55000000 INFO @ Fri, 15 Feb 2019 07:16:10: #2 number of paired peaks: 38815 INFO @ Fri, 15 Feb 2019 07:16:10: start model_add_line... INFO @ Fri, 15 Feb 2019 07:16:10: start X-correlation... INFO @ Fri, 15 Feb 2019 07:16:10: end of X-cor INFO @ Fri, 15 Feb 2019 07:16:10: #2 finished! INFO @ Fri, 15 Feb 2019 07:16:10: #2 predicted fragment length is 340 bps INFO @ Fri, 15 Feb 2019 07:16:10: #2 alternative fragment length(s) may be 340 bps INFO @ Fri, 15 Feb 2019 07:16:10: #2.2 Generate R script for model : SRX3782472.20_model.r INFO @ Fri, 15 Feb 2019 07:16:10: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:16:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:16:12: 56000000 INFO @ Fri, 15 Feb 2019 07:16:18: 57000000 INFO @ Fri, 15 Feb 2019 07:16:19: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:16:19: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:16:19: #1 total tags in treatment: 57073095 INFO @ Fri, 15 Feb 2019 07:16:19: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:16:19: #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 07:16:21: #1 tags after filtering in treatment: 57073032 INFO @ Fri, 15 Feb 2019 07:16:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:16:21: #1 finished! INFO @ Fri, 15 Feb 2019 07:16:21: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:16:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:16:27: #2 number of paired peaks: 38815 INFO @ Fri, 15 Feb 2019 07:16:27: start model_add_line... INFO @ Fri, 15 Feb 2019 07:16:28: start X-correlation... INFO @ Fri, 15 Feb 2019 07:16:28: end of X-cor INFO @ Fri, 15 Feb 2019 07:16:28: #2 finished! INFO @ Fri, 15 Feb 2019 07:16:28: #2 predicted fragment length is 340 bps INFO @ Fri, 15 Feb 2019 07:16:28: #2 alternative fragment length(s) may be 340 bps INFO @ Fri, 15 Feb 2019 07:16:28: #2.2 Generate R script for model : SRX3782472.10_model.r INFO @ Fri, 15 Feb 2019 07:16:28: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:16:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:18:34: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:18:47: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:18:56: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:20:00: #4 Write output xls file... SRX3782472.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:20:00: #4 Write peak in narrowPeak format file... SRX3782472.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:20:00: #4 Write summits bed file... SRX3782472.05_summits.bed INFO @ Fri, 15 Feb 2019 07:20:01: Done! pass1 - making usageList (109 chroms): 11 millis pass2 - checking and writing primary data (18410 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:20:23: #4 Write output xls file... SRX3782472.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:20:23: #4 Write peak in narrowPeak format file... SRX3782472.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:20:23: #4 Write summits bed file... SRX3782472.20_summits.bed INFO @ Fri, 15 Feb 2019 07:20:23: Done! pass1 - making usageList (79 chroms): 8 millis pass2 - checking and writing primary data (11312 records, 4 fields): 95 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:20:24: #4 Write output xls file... SRX3782472.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:20:24: #4 Write peak in narrowPeak format file... SRX3782472.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:20:25: #4 Write summits bed file... SRX3782472.10_summits.bed INFO @ Fri, 15 Feb 2019 07:20:25: Done! pass1 - making usageList (93 chroms): 13 millis pass2 - checking and writing primary data (14325 records, 4 fields): 37 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。