Job ID = 11632709 sra ファイルのダウンロード中... Completed: 892834K bytes transferred in 10 seconds (667832K 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 58862168 spots for /home/okishinya/chipatlas/results/rn6/SRX3782468/SRR6826286.sra Written 58862168 spots for /home/okishinya/chipatlas/results/rn6/SRX3782468/SRR6826286.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: 00:00:00 Multiseed full-index search: 00:22:11 58862168 reads; of these: 58862168 (100.00%) were unpaired; of these: 3113901 (5.29%) aligned 0 times 45648113 (77.55%) aligned exactly 1 time 10100154 (17.16%) aligned >1 times 94.71% overall alignment rate Time searching: 00:22:15 Overall time: 00:22:15 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] 7017084 / 55748267 = 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 07:07:28: # Command line: callpeak -t SRX3782468.bam -f BAM -g 2.15e9 -n SRX3782468.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782468.10 # format = BAM # ChIP-seq file = ['SRX3782468.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 07:07:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:07:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:07:28: # Command line: callpeak -t SRX3782468.bam -f BAM -g 2.15e9 -n SRX3782468.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782468.20 # format = BAM # ChIP-seq file = ['SRX3782468.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 07:07:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:07:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:07:28: # Command line: callpeak -t SRX3782468.bam -f BAM -g 2.15e9 -n SRX3782468.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782468.05 # format = BAM # ChIP-seq file = ['SRX3782468.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 07:07:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:07:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:07:33: 1000000 INFO @ Fri, 15 Feb 2019 07:07:33: 1000000 INFO @ Fri, 15 Feb 2019 07:07:33: 1000000 INFO @ Fri, 15 Feb 2019 07:07:39: 2000000 INFO @ Fri, 15 Feb 2019 07:07:39: 2000000 INFO @ Fri, 15 Feb 2019 07:07:39: 2000000 INFO @ Fri, 15 Feb 2019 07:07:44: 3000000 INFO @ Fri, 15 Feb 2019 07:07:45: 3000000 INFO @ Fri, 15 Feb 2019 07:07:45: 3000000 INFO @ Fri, 15 Feb 2019 07:07:50: 4000000 INFO @ Fri, 15 Feb 2019 07:07:50: 4000000 INFO @ Fri, 15 Feb 2019 07:07:51: 4000000 INFO @ Fri, 15 Feb 2019 07:07:56: 5000000 INFO @ Fri, 15 Feb 2019 07:07:56: 5000000 INFO @ Fri, 15 Feb 2019 07:07:57: 5000000 INFO @ Fri, 15 Feb 2019 07:08:01: 6000000 INFO @ Fri, 15 Feb 2019 07:08:02: 6000000 INFO @ Fri, 15 Feb 2019 07:08:03: 6000000 INFO @ Fri, 15 Feb 2019 07:08:07: 7000000 INFO @ Fri, 15 Feb 2019 07:08:08: 7000000 INFO @ Fri, 15 Feb 2019 07:08:08: 7000000 INFO @ Fri, 15 Feb 2019 07:08:12: 8000000 INFO @ Fri, 15 Feb 2019 07:08:13: 8000000 INFO @ Fri, 15 Feb 2019 07:08:14: 8000000 INFO @ Fri, 15 Feb 2019 07:08:18: 9000000 INFO @ Fri, 15 Feb 2019 07:08:19: 9000000 INFO @ Fri, 15 Feb 2019 07:08:20: 9000000 INFO @ Fri, 15 Feb 2019 07:08:23: 10000000 INFO @ Fri, 15 Feb 2019 07:08:25: 10000000 INFO @ Fri, 15 Feb 2019 07:08:27: 10000000 INFO @ Fri, 15 Feb 2019 07:08:29: 11000000 INFO @ Fri, 15 Feb 2019 07:08:32: 11000000 INFO @ Fri, 15 Feb 2019 07:08:33: 11000000 INFO @ Fri, 15 Feb 2019 07:08:34: 12000000 INFO @ Fri, 15 Feb 2019 07:08:39: 12000000 INFO @ Fri, 15 Feb 2019 07:08:40: 13000000 INFO @ Fri, 15 Feb 2019 07:08:40: 12000000 INFO @ Fri, 15 Feb 2019 07:08:45: 13000000 INFO @ Fri, 15 Feb 2019 07:08:45: 14000000 INFO @ Fri, 15 Feb 2019 07:08:47: 13000000 INFO @ Fri, 15 Feb 2019 07:08:51: 15000000 INFO @ Fri, 15 Feb 2019 07:08:52: 14000000 INFO @ Fri, 15 Feb 2019 07:08:53: 14000000 INFO @ Fri, 15 Feb 2019 07:08:56: 16000000 INFO @ Fri, 15 Feb 2019 07:08:58: 15000000 INFO @ Fri, 15 Feb 2019 07:09:00: 15000000 INFO @ Fri, 15 Feb 2019 07:09:02: 17000000 INFO @ Fri, 15 Feb 2019 07:09:04: 16000000 INFO @ Fri, 15 Feb 2019 07:09:06: 16000000 INFO @ Fri, 15 Feb 2019 07:09:08: 18000000 INFO @ Fri, 15 Feb 2019 07:09:09: 17000000 INFO @ Fri, 15 Feb 2019 07:09:12: 17000000 INFO @ Fri, 15 Feb 2019 07:09:14: 19000000 INFO @ Fri, 15 Feb 2019 07:09:15: 18000000 INFO @ Fri, 15 Feb 2019 07:09:18: 18000000 INFO @ Fri, 15 Feb 2019 07:09:20: 20000000 INFO @ Fri, 15 Feb 2019 07:09:20: 19000000 INFO @ Fri, 15 Feb 2019 07:09:24: 19000000 INFO @ Fri, 15 Feb 2019 07:09:26: 20000000 INFO @ Fri, 15 Feb 2019 07:09:26: 21000000 INFO @ Fri, 15 Feb 2019 07:09:29: 20000000 INFO @ Fri, 15 Feb 2019 07:09:31: 21000000 INFO @ Fri, 15 Feb 2019 07:09:32: 22000000 INFO @ Fri, 15 Feb 2019 07:09:35: 21000000 INFO @ Fri, 15 Feb 2019 07:09:37: 22000000 INFO @ Fri, 15 Feb 2019 07:09:39: 23000000 INFO @ Fri, 15 Feb 2019 07:09:42: 22000000 INFO @ Fri, 15 Feb 2019 07:09:42: 23000000 INFO @ Fri, 15 Feb 2019 07:09:45: 24000000 INFO @ Fri, 15 Feb 2019 07:09:48: 23000000 INFO @ Fri, 15 Feb 2019 07:09:48: 24000000 INFO @ Fri, 15 Feb 2019 07:09:51: 25000000 INFO @ Fri, 15 Feb 2019 07:09:54: 25000000 INFO @ Fri, 15 Feb 2019 07:09:54: 24000000 INFO @ Fri, 15 Feb 2019 07:09:57: 26000000 INFO @ Fri, 15 Feb 2019 07:09:59: 26000000 INFO @ Fri, 15 Feb 2019 07:10:00: 25000000 INFO @ Fri, 15 Feb 2019 07:10:03: 27000000 INFO @ Fri, 15 Feb 2019 07:10:04: 27000000 INFO @ Fri, 15 Feb 2019 07:10:05: 26000000 INFO @ Fri, 15 Feb 2019 07:10:09: 28000000 INFO @ Fri, 15 Feb 2019 07:10:10: 28000000 INFO @ Fri, 15 Feb 2019 07:10:11: 27000000 INFO @ Fri, 15 Feb 2019 07:10:15: 29000000 INFO @ Fri, 15 Feb 2019 07:10:16: 29000000 INFO @ Fri, 15 Feb 2019 07:10:18: 28000000 INFO @ Fri, 15 Feb 2019 07:10:21: 30000000 INFO @ Fri, 15 Feb 2019 07:10:22: 30000000 INFO @ Fri, 15 Feb 2019 07:10:24: 29000000 INFO @ Fri, 15 Feb 2019 07:10:27: 31000000 INFO @ Fri, 15 Feb 2019 07:10:28: 31000000 INFO @ Fri, 15 Feb 2019 07:10:30: 30000000 INFO @ Fri, 15 Feb 2019 07:10:33: 32000000 INFO @ Fri, 15 Feb 2019 07:10:34: 32000000 INFO @ Fri, 15 Feb 2019 07:10:37: 31000000 INFO @ Fri, 15 Feb 2019 07:10:38: 33000000 INFO @ Fri, 15 Feb 2019 07:10:39: 33000000 INFO @ Fri, 15 Feb 2019 07:10:43: 32000000 INFO @ Fri, 15 Feb 2019 07:10:44: 34000000 INFO @ Fri, 15 Feb 2019 07:10:45: 34000000 INFO @ Fri, 15 Feb 2019 07:10:48: 33000000 INFO @ Fri, 15 Feb 2019 07:10:50: 35000000 INFO @ Fri, 15 Feb 2019 07:10:51: 35000000 INFO @ Fri, 15 Feb 2019 07:10:54: 34000000 INFO @ Fri, 15 Feb 2019 07:10:56: 36000000 INFO @ Fri, 15 Feb 2019 07:10:57: 36000000 INFO @ Fri, 15 Feb 2019 07:11:00: 35000000 INFO @ Fri, 15 Feb 2019 07:11:02: 37000000 INFO @ Fri, 15 Feb 2019 07:11:03: 37000000 INFO @ Fri, 15 Feb 2019 07:11:05: 36000000 INFO @ Fri, 15 Feb 2019 07:11:07: 38000000 INFO @ Fri, 15 Feb 2019 07:11:09: 38000000 INFO @ Fri, 15 Feb 2019 07:11:11: 37000000 INFO @ Fri, 15 Feb 2019 07:11:13: 39000000 INFO @ Fri, 15 Feb 2019 07:11:15: 39000000 INFO @ Fri, 15 Feb 2019 07:11:17: 38000000 INFO @ Fri, 15 Feb 2019 07:11:19: 40000000 INFO @ Fri, 15 Feb 2019 07:11:21: 40000000 INFO @ Fri, 15 Feb 2019 07:11:23: 39000000 INFO @ Fri, 15 Feb 2019 07:11:25: 41000000 INFO @ Fri, 15 Feb 2019 07:11:26: 41000000 INFO @ Fri, 15 Feb 2019 07:11:28: 40000000 INFO @ Fri, 15 Feb 2019 07:11:30: 42000000 INFO @ Fri, 15 Feb 2019 07:11:32: 42000000 INFO @ Fri, 15 Feb 2019 07:11:34: 41000000 INFO @ Fri, 15 Feb 2019 07:11:36: 43000000 INFO @ Fri, 15 Feb 2019 07:11:38: 43000000 INFO @ Fri, 15 Feb 2019 07:11:40: 42000000 INFO @ Fri, 15 Feb 2019 07:11:42: 44000000 INFO @ Fri, 15 Feb 2019 07:11:44: 44000000 INFO @ Fri, 15 Feb 2019 07:11:45: 43000000 INFO @ Fri, 15 Feb 2019 07:11:48: 45000000 INFO @ Fri, 15 Feb 2019 07:11:50: 45000000 INFO @ Fri, 15 Feb 2019 07:11:51: 44000000 INFO @ Fri, 15 Feb 2019 07:11:53: 46000000 INFO @ Fri, 15 Feb 2019 07:11:55: 46000000 INFO @ Fri, 15 Feb 2019 07:11:57: 45000000 INFO @ Fri, 15 Feb 2019 07:11:59: 47000000 INFO @ Fri, 15 Feb 2019 07:12:01: 47000000 INFO @ Fri, 15 Feb 2019 07:12:04: 46000000 INFO @ Fri, 15 Feb 2019 07:12:05: 48000000 INFO @ Fri, 15 Feb 2019 07:12:07: 48000000 INFO @ Fri, 15 Feb 2019 07:12:10: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:12:10: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:12:10: #1 total tags in treatment: 48731183 INFO @ Fri, 15 Feb 2019 07:12:10: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:12:10: #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 07:12:10: 47000000 INFO @ Fri, 15 Feb 2019 07:12:11: #1 tags after filtering in treatment: 48731069 INFO @ Fri, 15 Feb 2019 07:12:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:12:11: #1 finished! INFO @ Fri, 15 Feb 2019 07:12:11: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:12:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:12:12: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:12:12: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:12:12: #1 total tags in treatment: 48731183 INFO @ Fri, 15 Feb 2019 07:12:12: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:12:12: #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 07:12:13: #1 tags after filtering in treatment: 48731069 INFO @ Fri, 15 Feb 2019 07:12:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:12:13: #1 finished! INFO @ Fri, 15 Feb 2019 07:12:13: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:12:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:12:16: 48000000 INFO @ Fri, 15 Feb 2019 07:12:18: #2 number of paired peaks: 50546 INFO @ Fri, 15 Feb 2019 07:12:18: start model_add_line... INFO @ Fri, 15 Feb 2019 07:12:19: start X-correlation... INFO @ Fri, 15 Feb 2019 07:12:19: end of X-cor INFO @ Fri, 15 Feb 2019 07:12:19: #2 finished! INFO @ Fri, 15 Feb 2019 07:12:19: #2 predicted fragment length is 379 bps INFO @ Fri, 15 Feb 2019 07:12:19: #2 alternative fragment length(s) may be 379 bps INFO @ Fri, 15 Feb 2019 07:12:19: #2.2 Generate R script for model : SRX3782468.05_model.r INFO @ Fri, 15 Feb 2019 07:12:19: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:12:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:12:20: #2 number of paired peaks: 50546 INFO @ Fri, 15 Feb 2019 07:12:20: start model_add_line... INFO @ Fri, 15 Feb 2019 07:12:21: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:12:21: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:12:21: #1 total tags in treatment: 48731183 INFO @ Fri, 15 Feb 2019 07:12:21: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:12:21: #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 07:12:21: start X-correlation... INFO @ Fri, 15 Feb 2019 07:12:21: end of X-cor INFO @ Fri, 15 Feb 2019 07:12:21: #2 finished! INFO @ Fri, 15 Feb 2019 07:12:21: #2 predicted fragment length is 379 bps INFO @ Fri, 15 Feb 2019 07:12:21: #2 alternative fragment length(s) may be 379 bps INFO @ Fri, 15 Feb 2019 07:12:21: #2.2 Generate R script for model : SRX3782468.10_model.r INFO @ Fri, 15 Feb 2019 07:12:21: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:12:23: #1 tags after filtering in treatment: 48731069 INFO @ Fri, 15 Feb 2019 07:12:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:12:23: #1 finished! INFO @ Fri, 15 Feb 2019 07:12:23: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:12:30: #2 number of paired peaks: 50546 INFO @ Fri, 15 Feb 2019 07:12:30: start model_add_line... INFO @ Fri, 15 Feb 2019 07:12:31: start X-correlation... INFO @ Fri, 15 Feb 2019 07:12:31: end of X-cor INFO @ Fri, 15 Feb 2019 07:12:31: #2 finished! INFO @ Fri, 15 Feb 2019 07:12:31: #2 predicted fragment length is 379 bps INFO @ Fri, 15 Feb 2019 07:12:31: #2 alternative fragment length(s) may be 379 bps INFO @ Fri, 15 Feb 2019 07:12:31: #2.2 Generate R script for model : SRX3782468.20_model.r INFO @ Fri, 15 Feb 2019 07:12:31: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:14:49: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:14:55: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:15:17: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:16:10: #4 Write output xls file... SRX3782468.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:16:10: #4 Write peak in narrowPeak format file... SRX3782468.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:16:10: #4 Write summits bed file... SRX3782468.05_summits.bed INFO @ Fri, 15 Feb 2019 07:16:10: Done! pass1 - making usageList (112 chroms): 7 millis pass2 - checking and writing primary data (22545 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:16:15: #4 Write output xls file... SRX3782468.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:16:16: #4 Write peak in narrowPeak format file... SRX3782468.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:16:16: #4 Write summits bed file... SRX3782468.10_summits.bed INFO @ Fri, 15 Feb 2019 07:16:16: Done! pass1 - making usageList (99 chroms): 6 millis pass2 - checking and writing primary data (17962 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:16:45: #4 Write output xls file... SRX3782468.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:16:45: #4 Write peak in narrowPeak format file... SRX3782468.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:16:45: #4 Write summits bed file... SRX3782468.20_summits.bed INFO @ Fri, 15 Feb 2019 07:16:45: Done! pass1 - making usageList (82 chroms): 5 millis pass2 - checking and writing primary data (14456 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。