Job ID = 11632721 sra ファイルのダウンロード中... Completed: 753590K bytes transferred in 9 seconds (654989K 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 51428352 spots for /home/okishinya/chipatlas/results/rn6/SRX3782480/SRR6826298.sra Written 51428352 spots for /home/okishinya/chipatlas/results/rn6/SRX3782480/SRR6826298.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: 00:00:01 Multiseed full-index search: 00:23:19 51428352 reads; of these: 51428352 (100.00%) were unpaired; of these: 3029590 (5.89%) aligned 0 times 36647397 (71.26%) aligned exactly 1 time 11751365 (22.85%) aligned >1 times 94.11% overall alignment rate Time searching: 00:23:23 Overall time: 00:23:24 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] 1704808 / 48398762 = 0.0352 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 08:13:32: # Command line: callpeak -t SRX3782480.bam -f BAM -g 2.15e9 -n SRX3782480.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782480.20 # format = BAM # ChIP-seq file = ['SRX3782480.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 08:13:32: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:13:32: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:13:32: # Command line: callpeak -t SRX3782480.bam -f BAM -g 2.15e9 -n SRX3782480.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782480.05 # format = BAM # ChIP-seq file = ['SRX3782480.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 08:13:32: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:13:32: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:13:32: # Command line: callpeak -t SRX3782480.bam -f BAM -g 2.15e9 -n SRX3782480.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782480.10 # format = BAM # ChIP-seq file = ['SRX3782480.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 08:13:32: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:13:32: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:13:39: 1000000 INFO @ Fri, 15 Feb 2019 08:13:40: 1000000 INFO @ Fri, 15 Feb 2019 08:13:40: 1000000 INFO @ Fri, 15 Feb 2019 08:13:46: 2000000 INFO @ Fri, 15 Feb 2019 08:13:47: 2000000 INFO @ Fri, 15 Feb 2019 08:13:47: 2000000 INFO @ Fri, 15 Feb 2019 08:13:53: 3000000 INFO @ Fri, 15 Feb 2019 08:13:54: 3000000 INFO @ Fri, 15 Feb 2019 08:13:54: 3000000 INFO @ Fri, 15 Feb 2019 08:14:00: 4000000 INFO @ Fri, 15 Feb 2019 08:14:01: 4000000 INFO @ Fri, 15 Feb 2019 08:14:01: 4000000 INFO @ Fri, 15 Feb 2019 08:14:07: 5000000 INFO @ Fri, 15 Feb 2019 08:14:09: 5000000 INFO @ Fri, 15 Feb 2019 08:14:09: 5000000 INFO @ Fri, 15 Feb 2019 08:14:14: 6000000 INFO @ Fri, 15 Feb 2019 08:14:16: 6000000 INFO @ Fri, 15 Feb 2019 08:14:16: 6000000 INFO @ Fri, 15 Feb 2019 08:14:21: 7000000 INFO @ Fri, 15 Feb 2019 08:14:24: 7000000 INFO @ Fri, 15 Feb 2019 08:14:24: 7000000 INFO @ Fri, 15 Feb 2019 08:14:27: 8000000 INFO @ Fri, 15 Feb 2019 08:14:31: 8000000 INFO @ Fri, 15 Feb 2019 08:14:31: 8000000 INFO @ Fri, 15 Feb 2019 08:14:34: 9000000 INFO @ Fri, 15 Feb 2019 08:14:39: 9000000 INFO @ Fri, 15 Feb 2019 08:14:39: 9000000 INFO @ Fri, 15 Feb 2019 08:14:42: 10000000 INFO @ Fri, 15 Feb 2019 08:14:48: 10000000 INFO @ Fri, 15 Feb 2019 08:14:48: 10000000 INFO @ Fri, 15 Feb 2019 08:14:50: 11000000 INFO @ Fri, 15 Feb 2019 08:14:56: 11000000 INFO @ Fri, 15 Feb 2019 08:14:56: 11000000 INFO @ Fri, 15 Feb 2019 08:14:58: 12000000 INFO @ Fri, 15 Feb 2019 08:15:06: 12000000 INFO @ Fri, 15 Feb 2019 08:15:06: 12000000 INFO @ Fri, 15 Feb 2019 08:15:08: 13000000 INFO @ Fri, 15 Feb 2019 08:15:15: 13000000 INFO @ Fri, 15 Feb 2019 08:15:15: 13000000 INFO @ Fri, 15 Feb 2019 08:15:17: 14000000 INFO @ Fri, 15 Feb 2019 08:15:24: 14000000 INFO @ Fri, 15 Feb 2019 08:15:24: 14000000 INFO @ Fri, 15 Feb 2019 08:15:26: 15000000 INFO @ Fri, 15 Feb 2019 08:15:34: 15000000 INFO @ Fri, 15 Feb 2019 08:15:34: 15000000 INFO @ Fri, 15 Feb 2019 08:15:34: 16000000 INFO @ Fri, 15 Feb 2019 08:15:42: 17000000 INFO @ Fri, 15 Feb 2019 08:15:42: 16000000 INFO @ Fri, 15 Feb 2019 08:15:42: 16000000 INFO @ Fri, 15 Feb 2019 08:15:51: 18000000 INFO @ Fri, 15 Feb 2019 08:15:51: 17000000 INFO @ Fri, 15 Feb 2019 08:15:51: 17000000 INFO @ Fri, 15 Feb 2019 08:15:59: 18000000 INFO @ Fri, 15 Feb 2019 08:15:59: 18000000 INFO @ Fri, 15 Feb 2019 08:15:59: 19000000 INFO @ Fri, 15 Feb 2019 08:16:06: 19000000 INFO @ Fri, 15 Feb 2019 08:16:06: 19000000 INFO @ Fri, 15 Feb 2019 08:16:07: 20000000 INFO @ Fri, 15 Feb 2019 08:16:14: 20000000 INFO @ Fri, 15 Feb 2019 08:16:14: 20000000 INFO @ Fri, 15 Feb 2019 08:16:16: 21000000 INFO @ Fri, 15 Feb 2019 08:16:20: 21000000 INFO @ Fri, 15 Feb 2019 08:16:20: 21000000 INFO @ Fri, 15 Feb 2019 08:16:24: 22000000 INFO @ Fri, 15 Feb 2019 08:16:27: 22000000 INFO @ Fri, 15 Feb 2019 08:16:29: 22000000 INFO @ Fri, 15 Feb 2019 08:16:33: 23000000 INFO @ Fri, 15 Feb 2019 08:16:34: 23000000 INFO @ Fri, 15 Feb 2019 08:16:38: 23000000 INFO @ Fri, 15 Feb 2019 08:16:40: 24000000 INFO @ Fri, 15 Feb 2019 08:16:41: 24000000 INFO @ Fri, 15 Feb 2019 08:16:44: 24000000 INFO @ Fri, 15 Feb 2019 08:16:47: 25000000 INFO @ Fri, 15 Feb 2019 08:16:48: 25000000 INFO @ Fri, 15 Feb 2019 08:16:51: 25000000 INFO @ Fri, 15 Feb 2019 08:16:55: 26000000 INFO @ Fri, 15 Feb 2019 08:16:55: 26000000 INFO @ Fri, 15 Feb 2019 08:16:58: 26000000 INFO @ Fri, 15 Feb 2019 08:17:02: 27000000 INFO @ Fri, 15 Feb 2019 08:17:02: 27000000 INFO @ Fri, 15 Feb 2019 08:17:05: 27000000 INFO @ Fri, 15 Feb 2019 08:17:09: 28000000 INFO @ Fri, 15 Feb 2019 08:17:09: 28000000 INFO @ Fri, 15 Feb 2019 08:17:12: 28000000 INFO @ Fri, 15 Feb 2019 08:17:16: 29000000 INFO @ Fri, 15 Feb 2019 08:17:16: 29000000 INFO @ Fri, 15 Feb 2019 08:17:19: 29000000 INFO @ Fri, 15 Feb 2019 08:17:22: 30000000 INFO @ Fri, 15 Feb 2019 08:17:23: 30000000 INFO @ Fri, 15 Feb 2019 08:17:25: 30000000 INFO @ Fri, 15 Feb 2019 08:17:29: 31000000 INFO @ Fri, 15 Feb 2019 08:17:29: 31000000 INFO @ Fri, 15 Feb 2019 08:17:32: 31000000 INFO @ Fri, 15 Feb 2019 08:17:36: 32000000 INFO @ Fri, 15 Feb 2019 08:17:37: 32000000 INFO @ Fri, 15 Feb 2019 08:17:39: 32000000 INFO @ Fri, 15 Feb 2019 08:17:44: 33000000 INFO @ Fri, 15 Feb 2019 08:17:45: 33000000 INFO @ Fri, 15 Feb 2019 08:17:46: 33000000 INFO @ Fri, 15 Feb 2019 08:17:52: 34000000 INFO @ Fri, 15 Feb 2019 08:17:53: 34000000 INFO @ Fri, 15 Feb 2019 08:17:54: 34000000 INFO @ Fri, 15 Feb 2019 08:18:00: 35000000 INFO @ Fri, 15 Feb 2019 08:18:01: 35000000 INFO @ Fri, 15 Feb 2019 08:18:02: 35000000 INFO @ Fri, 15 Feb 2019 08:18:07: 36000000 INFO @ Fri, 15 Feb 2019 08:18:08: 36000000 INFO @ Fri, 15 Feb 2019 08:18:10: 36000000 INFO @ Fri, 15 Feb 2019 08:18:15: 37000000 INFO @ Fri, 15 Feb 2019 08:18:15: 37000000 INFO @ Fri, 15 Feb 2019 08:18:19: 37000000 INFO @ Fri, 15 Feb 2019 08:18:22: 38000000 INFO @ Fri, 15 Feb 2019 08:18:22: 38000000 INFO @ Fri, 15 Feb 2019 08:18:27: 38000000 INFO @ Fri, 15 Feb 2019 08:18:29: 39000000 INFO @ Fri, 15 Feb 2019 08:18:30: 39000000 INFO @ Fri, 15 Feb 2019 08:18:37: 39000000 INFO @ Fri, 15 Feb 2019 08:18:38: 40000000 INFO @ Fri, 15 Feb 2019 08:18:39: 40000000 INFO @ Fri, 15 Feb 2019 08:18:47: 41000000 INFO @ Fri, 15 Feb 2019 08:18:47: 40000000 INFO @ Fri, 15 Feb 2019 08:18:48: 41000000 INFO @ Fri, 15 Feb 2019 08:18:55: 42000000 INFO @ Fri, 15 Feb 2019 08:18:57: 42000000 INFO @ Fri, 15 Feb 2019 08:18:57: 41000000 INFO @ Fri, 15 Feb 2019 08:19:04: 43000000 INFO @ Fri, 15 Feb 2019 08:19:06: 43000000 INFO @ Fri, 15 Feb 2019 08:19:07: 42000000 INFO @ Fri, 15 Feb 2019 08:19:14: 44000000 INFO @ Fri, 15 Feb 2019 08:19:14: 44000000 INFO @ Fri, 15 Feb 2019 08:19:18: 43000000 INFO @ Fri, 15 Feb 2019 08:19:24: 45000000 INFO @ Fri, 15 Feb 2019 08:19:25: 45000000 INFO @ Fri, 15 Feb 2019 08:19:29: 44000000 INFO @ Fri, 15 Feb 2019 08:19:33: 46000000 INFO @ Fri, 15 Feb 2019 08:19:36: 46000000 INFO @ Fri, 15 Feb 2019 08:19:39: 45000000 INFO @ Fri, 15 Feb 2019 08:19:39: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 08:19:39: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 08:19:39: #1 total tags in treatment: 46693954 INFO @ Fri, 15 Feb 2019 08:19:39: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:19:39: #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 08:19:41: #1 tags after filtering in treatment: 46693879 INFO @ Fri, 15 Feb 2019 08:19:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:19:41: #1 finished! INFO @ Fri, 15 Feb 2019 08:19:41: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:19:41: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 08:19:41: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 08:19:41: #1 total tags in treatment: 46693954 INFO @ Fri, 15 Feb 2019 08:19:41: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:19:41: #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 08:19:43: #1 tags after filtering in treatment: 46693879 INFO @ Fri, 15 Feb 2019 08:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:19:43: #1 finished! INFO @ Fri, 15 Feb 2019 08:19:43: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:19:44: #2 number of paired peaks: 3789 INFO @ Fri, 15 Feb 2019 08:19:44: start model_add_line... INFO @ Fri, 15 Feb 2019 08:19:45: start X-correlation... INFO @ Fri, 15 Feb 2019 08:19:45: end of X-cor INFO @ Fri, 15 Feb 2019 08:19:45: #2 finished! INFO @ Fri, 15 Feb 2019 08:19:45: #2 predicted fragment length is 39 bps INFO @ Fri, 15 Feb 2019 08:19:45: #2 alternative fragment length(s) may be 39,392,583 bps INFO @ Fri, 15 Feb 2019 08:19:45: #2.2 Generate R script for model : SRX3782480.10_model.r WARNING @ Fri, 15 Feb 2019 08:19:45: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:19:45: #2 You may need to consider one of the other alternative d(s): 39,392,583 WARNING @ Fri, 15 Feb 2019 08:19:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 08:19:45: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:19:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:19:46: 46000000 INFO @ Fri, 15 Feb 2019 08:19:47: #2 number of paired peaks: 3789 INFO @ Fri, 15 Feb 2019 08:19:47: start model_add_line... INFO @ Fri, 15 Feb 2019 08:19:48: start X-correlation... INFO @ Fri, 15 Feb 2019 08:19:48: end of X-cor INFO @ Fri, 15 Feb 2019 08:19:48: #2 finished! INFO @ Fri, 15 Feb 2019 08:19:48: #2 predicted fragment length is 39 bps INFO @ Fri, 15 Feb 2019 08:19:48: #2 alternative fragment length(s) may be 39,392,583 bps INFO @ Fri, 15 Feb 2019 08:19:48: #2.2 Generate R script for model : SRX3782480.05_model.r WARNING @ Fri, 15 Feb 2019 08:19:48: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:19:48: #2 You may need to consider one of the other alternative d(s): 39,392,583 WARNING @ Fri, 15 Feb 2019 08:19:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 08:19:48: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:19:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:19:51: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 08:19:51: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 08:19:51: #1 total tags in treatment: 46693954 INFO @ Fri, 15 Feb 2019 08:19:51: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:19:51: #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 08:19:53: #1 tags after filtering in treatment: 46693879 INFO @ Fri, 15 Feb 2019 08:19:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:19:53: #1 finished! INFO @ Fri, 15 Feb 2019 08:19:53: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:19:57: #2 number of paired peaks: 3789 INFO @ Fri, 15 Feb 2019 08:19:57: start model_add_line... INFO @ Fri, 15 Feb 2019 08:19:57: start X-correlation... INFO @ Fri, 15 Feb 2019 08:19:57: end of X-cor INFO @ Fri, 15 Feb 2019 08:19:57: #2 finished! INFO @ Fri, 15 Feb 2019 08:19:57: #2 predicted fragment length is 39 bps INFO @ Fri, 15 Feb 2019 08:19:57: #2 alternative fragment length(s) may be 39,392,583 bps INFO @ Fri, 15 Feb 2019 08:19:57: #2.2 Generate R script for model : SRX3782480.20_model.r WARNING @ Fri, 15 Feb 2019 08:19:57: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:19:57: #2 You may need to consider one of the other alternative d(s): 39,392,583 WARNING @ Fri, 15 Feb 2019 08:19:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 08:19:57: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:19:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:21:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:21:32: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:21:45: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:22:36: #4 Write output xls file... SRX3782480.05_peaks.xls INFO @ Fri, 15 Feb 2019 08:22:36: #4 Write peak in narrowPeak format file... SRX3782480.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:22:36: #4 Write summits bed file... SRX3782480.05_summits.bed INFO @ Fri, 15 Feb 2019 08:22:36: Done! pass1 - making usageList (51 chroms): 4 millis pass2 - checking and writing primary data (2064 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:22:37: #4 Write output xls file... SRX3782480.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:22:37: #4 Write peak in narrowPeak format file... SRX3782480.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:22:37: #4 Write summits bed file... SRX3782480.10_summits.bed INFO @ Fri, 15 Feb 2019 08:22:37: Done! pass1 - making usageList (39 chroms): 3 millis pass2 - checking and writing primary data (1186 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:22:49: #4 Write output xls file... SRX3782480.20_peaks.xls INFO @ Fri, 15 Feb 2019 08:22:49: #4 Write peak in narrowPeak format file... SRX3782480.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:22:49: #4 Write summits bed file... SRX3782480.20_summits.bed INFO @ Fri, 15 Feb 2019 08:22:49: Done! pass1 - making usageList (29 chroms): 5 millis pass2 - checking and writing primary data (514 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。