Job ID = 11632708 sra ファイルのダウンロード中... Completed: 1428067K bytes transferred in 17 seconds (650363K 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 55217242 spots for /home/okishinya/chipatlas/results/rn6/SRX3782467/SRR6826285.sra Written 55217242 spots for /home/okishinya/chipatlas/results/rn6/SRX3782467/SRR6826285.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:22:29 55217242 reads; of these: 55217242 (100.00%) were unpaired; of these: 4806844 (8.71%) aligned 0 times 39168724 (70.94%) aligned exactly 1 time 11241674 (20.36%) aligned >1 times 91.29% overall alignment rate Time searching: 00:22:33 Overall time: 00:22:33 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] 4864733 / 50410398 = 0.0965 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 07:01:06: # Command line: callpeak -t SRX3782467.bam -f BAM -g 2.15e9 -n SRX3782467.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782467.10 # format = BAM # ChIP-seq file = ['SRX3782467.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 07:01:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:01:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:01:06: # Command line: callpeak -t SRX3782467.bam -f BAM -g 2.15e9 -n SRX3782467.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782467.20 # format = BAM # ChIP-seq file = ['SRX3782467.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 07:01:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:01:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:01:06: # Command line: callpeak -t SRX3782467.bam -f BAM -g 2.15e9 -n SRX3782467.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782467.05 # format = BAM # ChIP-seq file = ['SRX3782467.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 07:01:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:01:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:01:13: 1000000 INFO @ Fri, 15 Feb 2019 07:01:13: 1000000 INFO @ Fri, 15 Feb 2019 07:01:13: 1000000 INFO @ Fri, 15 Feb 2019 07:01:19: 2000000 INFO @ Fri, 15 Feb 2019 07:01:19: 2000000 INFO @ Fri, 15 Feb 2019 07:01:20: 2000000 INFO @ Fri, 15 Feb 2019 07:01:25: 3000000 INFO @ Fri, 15 Feb 2019 07:01:26: 3000000 INFO @ Fri, 15 Feb 2019 07:01:26: 3000000 INFO @ Fri, 15 Feb 2019 07:01:32: 4000000 INFO @ Fri, 15 Feb 2019 07:01:32: 4000000 INFO @ Fri, 15 Feb 2019 07:01:33: 4000000 INFO @ Fri, 15 Feb 2019 07:01:39: 5000000 INFO @ Fri, 15 Feb 2019 07:01:39: 5000000 INFO @ Fri, 15 Feb 2019 07:01:39: 5000000 INFO @ Fri, 15 Feb 2019 07:01:45: 6000000 INFO @ Fri, 15 Feb 2019 07:01:45: 6000000 INFO @ Fri, 15 Feb 2019 07:01:46: 6000000 INFO @ Fri, 15 Feb 2019 07:01:52: 7000000 INFO @ Fri, 15 Feb 2019 07:01:52: 7000000 INFO @ Fri, 15 Feb 2019 07:01:53: 7000000 INFO @ Fri, 15 Feb 2019 07:01:59: 8000000 INFO @ Fri, 15 Feb 2019 07:01:59: 8000000 INFO @ Fri, 15 Feb 2019 07:01:59: 8000000 INFO @ Fri, 15 Feb 2019 07:02:05: 9000000 INFO @ Fri, 15 Feb 2019 07:02:06: 9000000 INFO @ Fri, 15 Feb 2019 07:02:06: 9000000 INFO @ Fri, 15 Feb 2019 07:02:12: 10000000 INFO @ Fri, 15 Feb 2019 07:02:13: 10000000 INFO @ Fri, 15 Feb 2019 07:02:13: 10000000 INFO @ Fri, 15 Feb 2019 07:02:19: 11000000 INFO @ Fri, 15 Feb 2019 07:02:19: 11000000 INFO @ Fri, 15 Feb 2019 07:02:20: 11000000 INFO @ Fri, 15 Feb 2019 07:02:26: 12000000 INFO @ Fri, 15 Feb 2019 07:02:26: 12000000 INFO @ Fri, 15 Feb 2019 07:02:26: 12000000 INFO @ Fri, 15 Feb 2019 07:02:33: 13000000 INFO @ Fri, 15 Feb 2019 07:02:33: 13000000 INFO @ Fri, 15 Feb 2019 07:02:33: 13000000 INFO @ Fri, 15 Feb 2019 07:02:39: 14000000 INFO @ Fri, 15 Feb 2019 07:02:40: 14000000 INFO @ Fri, 15 Feb 2019 07:02:40: 14000000 INFO @ Fri, 15 Feb 2019 07:02:46: 15000000 INFO @ Fri, 15 Feb 2019 07:02:46: 15000000 INFO @ Fri, 15 Feb 2019 07:02:47: 15000000 INFO @ Fri, 15 Feb 2019 07:02:53: 16000000 INFO @ Fri, 15 Feb 2019 07:02:53: 16000000 INFO @ Fri, 15 Feb 2019 07:02:54: 16000000 INFO @ Fri, 15 Feb 2019 07:03:00: 17000000 INFO @ Fri, 15 Feb 2019 07:03:00: 17000000 INFO @ Fri, 15 Feb 2019 07:03:01: 17000000 INFO @ Fri, 15 Feb 2019 07:03:07: 18000000 INFO @ Fri, 15 Feb 2019 07:03:07: 18000000 INFO @ Fri, 15 Feb 2019 07:03:08: 18000000 INFO @ Fri, 15 Feb 2019 07:03:13: 19000000 INFO @ Fri, 15 Feb 2019 07:03:14: 19000000 INFO @ Fri, 15 Feb 2019 07:03:15: 19000000 INFO @ Fri, 15 Feb 2019 07:03:20: 20000000 INFO @ Fri, 15 Feb 2019 07:03:21: 20000000 INFO @ Fri, 15 Feb 2019 07:03:22: 20000000 INFO @ Fri, 15 Feb 2019 07:03:27: 21000000 INFO @ Fri, 15 Feb 2019 07:03:28: 21000000 INFO @ Fri, 15 Feb 2019 07:03:29: 21000000 INFO @ Fri, 15 Feb 2019 07:03:33: 22000000 INFO @ Fri, 15 Feb 2019 07:03:35: 22000000 INFO @ Fri, 15 Feb 2019 07:03:36: 22000000 INFO @ Fri, 15 Feb 2019 07:03:40: 23000000 INFO @ Fri, 15 Feb 2019 07:03:42: 23000000 INFO @ Fri, 15 Feb 2019 07:03:43: 23000000 INFO @ Fri, 15 Feb 2019 07:03:47: 24000000 INFO @ Fri, 15 Feb 2019 07:03:48: 24000000 INFO @ Fri, 15 Feb 2019 07:03:50: 24000000 INFO @ Fri, 15 Feb 2019 07:03:53: 25000000 INFO @ Fri, 15 Feb 2019 07:03:55: 25000000 INFO @ Fri, 15 Feb 2019 07:03:57: 25000000 INFO @ Fri, 15 Feb 2019 07:04:00: 26000000 INFO @ Fri, 15 Feb 2019 07:04:02: 26000000 INFO @ Fri, 15 Feb 2019 07:04:04: 26000000 INFO @ Fri, 15 Feb 2019 07:04:07: 27000000 INFO @ Fri, 15 Feb 2019 07:04:09: 27000000 INFO @ Fri, 15 Feb 2019 07:04:11: 27000000 INFO @ Fri, 15 Feb 2019 07:04:14: 28000000 INFO @ Fri, 15 Feb 2019 07:04:15: 28000000 INFO @ Fri, 15 Feb 2019 07:04:18: 28000000 INFO @ Fri, 15 Feb 2019 07:04:20: 29000000 INFO @ Fri, 15 Feb 2019 07:04:22: 29000000 INFO @ Fri, 15 Feb 2019 07:04:25: 29000000 INFO @ Fri, 15 Feb 2019 07:04:27: 30000000 INFO @ Fri, 15 Feb 2019 07:04:29: 30000000 INFO @ Fri, 15 Feb 2019 07:04:32: 30000000 INFO @ Fri, 15 Feb 2019 07:04:34: 31000000 INFO @ Fri, 15 Feb 2019 07:04:35: 31000000 INFO @ Fri, 15 Feb 2019 07:04:38: 31000000 INFO @ Fri, 15 Feb 2019 07:04:40: 32000000 INFO @ Fri, 15 Feb 2019 07:04:42: 32000000 INFO @ Fri, 15 Feb 2019 07:04:45: 32000000 INFO @ Fri, 15 Feb 2019 07:04:47: 33000000 INFO @ Fri, 15 Feb 2019 07:04:49: 33000000 INFO @ Fri, 15 Feb 2019 07:04:52: 33000000 INFO @ Fri, 15 Feb 2019 07:04:54: 34000000 INFO @ Fri, 15 Feb 2019 07:04:56: 34000000 INFO @ Fri, 15 Feb 2019 07:04:59: 34000000 INFO @ Fri, 15 Feb 2019 07:05:00: 35000000 INFO @ Fri, 15 Feb 2019 07:05:02: 35000000 INFO @ Fri, 15 Feb 2019 07:05:06: 35000000 INFO @ Fri, 15 Feb 2019 07:05:07: 36000000 INFO @ Fri, 15 Feb 2019 07:05:09: 36000000 INFO @ Fri, 15 Feb 2019 07:05:13: 36000000 INFO @ Fri, 15 Feb 2019 07:05:14: 37000000 INFO @ Fri, 15 Feb 2019 07:05:16: 37000000 INFO @ Fri, 15 Feb 2019 07:05:19: 37000000 INFO @ Fri, 15 Feb 2019 07:05:20: 38000000 INFO @ Fri, 15 Feb 2019 07:05:22: 38000000 INFO @ Fri, 15 Feb 2019 07:05:26: 38000000 INFO @ Fri, 15 Feb 2019 07:05:27: 39000000 INFO @ Fri, 15 Feb 2019 07:05:29: 39000000 INFO @ Fri, 15 Feb 2019 07:05:33: 39000000 INFO @ Fri, 15 Feb 2019 07:05:34: 40000000 INFO @ Fri, 15 Feb 2019 07:05:36: 40000000 INFO @ Fri, 15 Feb 2019 07:05:40: 40000000 INFO @ Fri, 15 Feb 2019 07:05:41: 41000000 INFO @ Fri, 15 Feb 2019 07:05:43: 41000000 INFO @ Fri, 15 Feb 2019 07:05:47: 41000000 INFO @ Fri, 15 Feb 2019 07:05:47: 42000000 INFO @ Fri, 15 Feb 2019 07:05:49: 42000000 INFO @ Fri, 15 Feb 2019 07:05:54: 42000000 INFO @ Fri, 15 Feb 2019 07:05:54: 43000000 INFO @ Fri, 15 Feb 2019 07:05:56: 43000000 INFO @ Fri, 15 Feb 2019 07:06:01: 43000000 INFO @ Fri, 15 Feb 2019 07:06:01: 44000000 INFO @ Fri, 15 Feb 2019 07:06:03: 44000000 INFO @ Fri, 15 Feb 2019 07:06:08: 44000000 INFO @ Fri, 15 Feb 2019 07:06:08: 45000000 INFO @ Fri, 15 Feb 2019 07:06:10: 45000000 INFO @ Fri, 15 Feb 2019 07:06:12: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:06:12: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:06:12: #1 total tags in treatment: 45545665 INFO @ Fri, 15 Feb 2019 07:06:12: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:06:12: #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 07:06:13: #1 tags after filtering in treatment: 45545569 INFO @ Fri, 15 Feb 2019 07:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:06:13: #1 finished! INFO @ Fri, 15 Feb 2019 07:06:13: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:06:14: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:06:14: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:06:14: #1 total tags in treatment: 45545665 INFO @ Fri, 15 Feb 2019 07:06:14: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:06:14: #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 07:06:14: 45000000 INFO @ Fri, 15 Feb 2019 07:06:15: #1 tags after filtering in treatment: 45545569 INFO @ Fri, 15 Feb 2019 07:06:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:06:15: #1 finished! INFO @ Fri, 15 Feb 2019 07:06:15: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:06:18: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:06:18: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:06:18: #1 total tags in treatment: 45545665 INFO @ Fri, 15 Feb 2019 07:06:18: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:06:18: #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 07:06:19: #2 number of paired peaks: 36088 INFO @ Fri, 15 Feb 2019 07:06:19: start model_add_line... INFO @ Fri, 15 Feb 2019 07:06:20: #1 tags after filtering in treatment: 45545569 INFO @ Fri, 15 Feb 2019 07:06:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:06:20: #1 finished! INFO @ Fri, 15 Feb 2019 07:06:20: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:06:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:06:20: start X-correlation... INFO @ Fri, 15 Feb 2019 07:06:20: end of X-cor INFO @ Fri, 15 Feb 2019 07:06:20: #2 finished! INFO @ Fri, 15 Feb 2019 07:06:20: #2 predicted fragment length is 248 bps INFO @ Fri, 15 Feb 2019 07:06:20: #2 alternative fragment length(s) may be 248 bps INFO @ Fri, 15 Feb 2019 07:06:20: #2.2 Generate R script for model : SRX3782467.05_model.r INFO @ Fri, 15 Feb 2019 07:06:20: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:06:20: #2 number of paired peaks: 36088 INFO @ Fri, 15 Feb 2019 07:06:20: start model_add_line... INFO @ Fri, 15 Feb 2019 07:06:21: start X-correlation... INFO @ Fri, 15 Feb 2019 07:06:21: end of X-cor INFO @ Fri, 15 Feb 2019 07:06:21: #2 finished! INFO @ Fri, 15 Feb 2019 07:06:21: #2 predicted fragment length is 248 bps INFO @ Fri, 15 Feb 2019 07:06:21: #2 alternative fragment length(s) may be 248 bps INFO @ Fri, 15 Feb 2019 07:06:21: #2.2 Generate R script for model : SRX3782467.20_model.r INFO @ Fri, 15 Feb 2019 07:06:21: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:06:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:06:25: #2 number of paired peaks: 36088 INFO @ Fri, 15 Feb 2019 07:06:25: start model_add_line... INFO @ Fri, 15 Feb 2019 07:06:25: start X-correlation... INFO @ Fri, 15 Feb 2019 07:06:25: end of X-cor INFO @ Fri, 15 Feb 2019 07:06:25: #2 finished! INFO @ Fri, 15 Feb 2019 07:06:25: #2 predicted fragment length is 248 bps INFO @ Fri, 15 Feb 2019 07:06:25: #2 alternative fragment length(s) may be 248 bps INFO @ Fri, 15 Feb 2019 07:06:25: #2.2 Generate R script for model : SRX3782467.10_model.r INFO @ Fri, 15 Feb 2019 07:06:25: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:06:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:08:15: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:08:17: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:08:28: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:09:30: #4 Write output xls file... SRX3782467.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:09:30: #4 Write peak in narrowPeak format file... SRX3782467.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:09:30: #4 Write summits bed file... SRX3782467.05_summits.bed INFO @ Fri, 15 Feb 2019 07:09:30: Done! pass1 - making usageList (91 chroms): 9 millis pass2 - checking and writing primary data (21665 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:09:33: #4 Write output xls file... SRX3782467.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:09:33: #4 Write peak in narrowPeak format file... SRX3782467.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:09:33: #4 Write summits bed file... SRX3782467.20_summits.bed INFO @ Fri, 15 Feb 2019 07:09:33: Done! pass1 - making usageList (37 chroms): 6 millis pass2 - checking and writing primary data (2847 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:09:43: #4 Write output xls file... SRX3782467.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:09:44: #4 Write peak in narrowPeak format file... SRX3782467.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:09:44: #4 Write summits bed file... SRX3782467.10_summits.bed INFO @ Fri, 15 Feb 2019 07:09:44: Done! pass1 - making usageList (60 chroms): 6 millis pass2 - checking and writing primary data (9832 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。