Job ID = 11632718 sra ファイルのダウンロード中... Completed: 1394679K bytes transferred in 16 seconds (673708K 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 52629817 spots for /home/okishinya/chipatlas/results/rn6/SRX3782477/SRR6826295.sra Written 52629817 spots for /home/okishinya/chipatlas/results/rn6/SRX3782477/SRR6826295.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:25 52629817 reads; of these: 52629817 (100.00%) were unpaired; of these: 7855373 (14.93%) aligned 0 times 34882670 (66.28%) aligned exactly 1 time 9891774 (18.79%) aligned >1 times 85.07% overall alignment rate Time searching: 00:19:27 Overall time: 00:19:27 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 12 files... [bam_rmdupse_core] 3353780 / 44774444 = 0.0749 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 07:09:44: # Command line: callpeak -t SRX3782477.bam -f BAM -g 2.15e9 -n SRX3782477.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782477.20 # format = BAM # ChIP-seq file = ['SRX3782477.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 07:09:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:09:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:09:44: # Command line: callpeak -t SRX3782477.bam -f BAM -g 2.15e9 -n SRX3782477.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782477.05 # format = BAM # ChIP-seq file = ['SRX3782477.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 07:09:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:09:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:09:44: # Command line: callpeak -t SRX3782477.bam -f BAM -g 2.15e9 -n SRX3782477.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782477.10 # format = BAM # ChIP-seq file = ['SRX3782477.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 07:09:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:09:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:09:50: 1000000 INFO @ Fri, 15 Feb 2019 07:09:50: 1000000 INFO @ Fri, 15 Feb 2019 07:09:50: 1000000 INFO @ Fri, 15 Feb 2019 07:09:56: 2000000 INFO @ Fri, 15 Feb 2019 07:09:56: 2000000 INFO @ Fri, 15 Feb 2019 07:09:56: 2000000 INFO @ Fri, 15 Feb 2019 07:10:02: 3000000 INFO @ Fri, 15 Feb 2019 07:10:02: 3000000 INFO @ Fri, 15 Feb 2019 07:10:02: 3000000 INFO @ Fri, 15 Feb 2019 07:10:08: 4000000 INFO @ Fri, 15 Feb 2019 07:10:08: 4000000 INFO @ Fri, 15 Feb 2019 07:10:08: 4000000 INFO @ Fri, 15 Feb 2019 07:10:14: 5000000 INFO @ Fri, 15 Feb 2019 07:10:14: 5000000 INFO @ Fri, 15 Feb 2019 07:10:14: 5000000 INFO @ Fri, 15 Feb 2019 07:10:19: 6000000 INFO @ Fri, 15 Feb 2019 07:10:20: 6000000 INFO @ Fri, 15 Feb 2019 07:10:20: 6000000 INFO @ Fri, 15 Feb 2019 07:10:25: 7000000 INFO @ Fri, 15 Feb 2019 07:10:26: 7000000 INFO @ Fri, 15 Feb 2019 07:10:26: 7000000 INFO @ Fri, 15 Feb 2019 07:10:31: 8000000 INFO @ Fri, 15 Feb 2019 07:10:31: 8000000 INFO @ Fri, 15 Feb 2019 07:10:32: 8000000 INFO @ Fri, 15 Feb 2019 07:10:37: 9000000 INFO @ Fri, 15 Feb 2019 07:10:37: 9000000 INFO @ Fri, 15 Feb 2019 07:10:39: 9000000 INFO @ Fri, 15 Feb 2019 07:10:43: 10000000 INFO @ Fri, 15 Feb 2019 07:10:44: 10000000 INFO @ Fri, 15 Feb 2019 07:10:45: 10000000 INFO @ Fri, 15 Feb 2019 07:10:49: 11000000 INFO @ Fri, 15 Feb 2019 07:10:50: 11000000 INFO @ Fri, 15 Feb 2019 07:10:51: 11000000 INFO @ Fri, 15 Feb 2019 07:10:55: 12000000 INFO @ Fri, 15 Feb 2019 07:10:56: 12000000 INFO @ Fri, 15 Feb 2019 07:10:57: 12000000 INFO @ Fri, 15 Feb 2019 07:11:02: 13000000 INFO @ Fri, 15 Feb 2019 07:11:02: 13000000 INFO @ Fri, 15 Feb 2019 07:11:04: 13000000 INFO @ Fri, 15 Feb 2019 07:11:08: 14000000 INFO @ Fri, 15 Feb 2019 07:11:09: 14000000 INFO @ Fri, 15 Feb 2019 07:11:11: 14000000 INFO @ Fri, 15 Feb 2019 07:11:15: 15000000 INFO @ Fri, 15 Feb 2019 07:11:15: 15000000 INFO @ Fri, 15 Feb 2019 07:11:18: 15000000 INFO @ Fri, 15 Feb 2019 07:11:21: 16000000 INFO @ Fri, 15 Feb 2019 07:11:22: 16000000 INFO @ Fri, 15 Feb 2019 07:11:26: 16000000 INFO @ Fri, 15 Feb 2019 07:11:28: 17000000 INFO @ Fri, 15 Feb 2019 07:11:28: 17000000 INFO @ Fri, 15 Feb 2019 07:11:33: 17000000 INFO @ Fri, 15 Feb 2019 07:11:34: 18000000 INFO @ Fri, 15 Feb 2019 07:11:35: 18000000 INFO @ Fri, 15 Feb 2019 07:11:40: 18000000 INFO @ Fri, 15 Feb 2019 07:11:41: 19000000 INFO @ Fri, 15 Feb 2019 07:11:41: 19000000 INFO @ Fri, 15 Feb 2019 07:11:47: 19000000 INFO @ Fri, 15 Feb 2019 07:11:47: 20000000 INFO @ Fri, 15 Feb 2019 07:11:48: 20000000 INFO @ Fri, 15 Feb 2019 07:11:54: 20000000 INFO @ Fri, 15 Feb 2019 07:11:54: 21000000 INFO @ Fri, 15 Feb 2019 07:11:54: 21000000 INFO @ Fri, 15 Feb 2019 07:12:00: 22000000 INFO @ Fri, 15 Feb 2019 07:12:00: 22000000 INFO @ Fri, 15 Feb 2019 07:12:01: 21000000 INFO @ Fri, 15 Feb 2019 07:12:07: 23000000 INFO @ Fri, 15 Feb 2019 07:12:07: 23000000 INFO @ Fri, 15 Feb 2019 07:12:08: 22000000 INFO @ Fri, 15 Feb 2019 07:12:13: 24000000 INFO @ Fri, 15 Feb 2019 07:12:13: 24000000 INFO @ Fri, 15 Feb 2019 07:12:14: 23000000 INFO @ Fri, 15 Feb 2019 07:12:19: 25000000 INFO @ Fri, 15 Feb 2019 07:12:20: 25000000 INFO @ Fri, 15 Feb 2019 07:12:21: 24000000 INFO @ Fri, 15 Feb 2019 07:12:26: 26000000 INFO @ Fri, 15 Feb 2019 07:12:26: 26000000 INFO @ Fri, 15 Feb 2019 07:12:28: 25000000 INFO @ Fri, 15 Feb 2019 07:12:32: 27000000 INFO @ Fri, 15 Feb 2019 07:12:32: 27000000 INFO @ Fri, 15 Feb 2019 07:12:35: 26000000 INFO @ Fri, 15 Feb 2019 07:12:39: 28000000 INFO @ Fri, 15 Feb 2019 07:12:39: 28000000 INFO @ Fri, 15 Feb 2019 07:12:42: 27000000 INFO @ Fri, 15 Feb 2019 07:12:45: 29000000 INFO @ Fri, 15 Feb 2019 07:12:45: 29000000 INFO @ Fri, 15 Feb 2019 07:12:49: 28000000 INFO @ Fri, 15 Feb 2019 07:12:51: 30000000 INFO @ Fri, 15 Feb 2019 07:12:52: 30000000 INFO @ Fri, 15 Feb 2019 07:12:56: 29000000 INFO @ Fri, 15 Feb 2019 07:12:58: 31000000 INFO @ Fri, 15 Feb 2019 07:12:58: 31000000 INFO @ Fri, 15 Feb 2019 07:13:03: 30000000 INFO @ Fri, 15 Feb 2019 07:13:04: 32000000 INFO @ Fri, 15 Feb 2019 07:13:05: 32000000 INFO @ Fri, 15 Feb 2019 07:13:10: 31000000 INFO @ Fri, 15 Feb 2019 07:13:11: 33000000 INFO @ Fri, 15 Feb 2019 07:13:11: 33000000 INFO @ Fri, 15 Feb 2019 07:13:17: 32000000 INFO @ Fri, 15 Feb 2019 07:13:17: 34000000 INFO @ Fri, 15 Feb 2019 07:13:18: 34000000 INFO @ Fri, 15 Feb 2019 07:13:24: 35000000 INFO @ Fri, 15 Feb 2019 07:13:24: 35000000 INFO @ Fri, 15 Feb 2019 07:13:24: 33000000 INFO @ Fri, 15 Feb 2019 07:13:30: 36000000 INFO @ Fri, 15 Feb 2019 07:13:31: 36000000 INFO @ Fri, 15 Feb 2019 07:13:31: 34000000 INFO @ Fri, 15 Feb 2019 07:13:37: 37000000 INFO @ Fri, 15 Feb 2019 07:13:37: 37000000 INFO @ Fri, 15 Feb 2019 07:13:38: 35000000 INFO @ Fri, 15 Feb 2019 07:13:43: 38000000 INFO @ Fri, 15 Feb 2019 07:13:44: 38000000 INFO @ Fri, 15 Feb 2019 07:13:45: 36000000 INFO @ Fri, 15 Feb 2019 07:13:50: 39000000 INFO @ Fri, 15 Feb 2019 07:13:51: 39000000 INFO @ Fri, 15 Feb 2019 07:13:53: 37000000 INFO @ Fri, 15 Feb 2019 07:13:57: 40000000 INFO @ Fri, 15 Feb 2019 07:13:58: 40000000 INFO @ Fri, 15 Feb 2019 07:14:01: 38000000 INFO @ Fri, 15 Feb 2019 07:14:05: 41000000 INFO @ Fri, 15 Feb 2019 07:14:05: 41000000 INFO @ Fri, 15 Feb 2019 07:14:08: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:14:08: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:14:08: #1 total tags in treatment: 41420664 INFO @ Fri, 15 Feb 2019 07:14:08: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:14:08: #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 07:14:08: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:14:08: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:14:08: #1 total tags in treatment: 41420664 INFO @ Fri, 15 Feb 2019 07:14:08: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:14:08: #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 07:14:09: 39000000 INFO @ Fri, 15 Feb 2019 07:14:09: #1 tags after filtering in treatment: 41420571 INFO @ Fri, 15 Feb 2019 07:14:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:14:09: #1 finished! INFO @ Fri, 15 Feb 2019 07:14:09: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:14:09: #1 tags after filtering in treatment: 41420571 INFO @ Fri, 15 Feb 2019 07:14:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:14:09: #1 finished! INFO @ Fri, 15 Feb 2019 07:14:09: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:14:13: #2 number of paired peaks: 12044 INFO @ Fri, 15 Feb 2019 07:14:13: start model_add_line... INFO @ Fri, 15 Feb 2019 07:14:13: start X-correlation... INFO @ Fri, 15 Feb 2019 07:14:13: end of X-cor INFO @ Fri, 15 Feb 2019 07:14:13: #2 finished! INFO @ Fri, 15 Feb 2019 07:14:13: #2 predicted fragment length is 167 bps INFO @ Fri, 15 Feb 2019 07:14:13: #2 alternative fragment length(s) may be 49,129,141,146,167 bps INFO @ Fri, 15 Feb 2019 07:14:13: #2.2 Generate R script for model : SRX3782477.05_model.r INFO @ Fri, 15 Feb 2019 07:14:13: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:14:14: #2 number of paired peaks: 12044 INFO @ Fri, 15 Feb 2019 07:14:14: start model_add_line... INFO @ Fri, 15 Feb 2019 07:14:14: start X-correlation... INFO @ Fri, 15 Feb 2019 07:14:14: end of X-cor INFO @ Fri, 15 Feb 2019 07:14:14: #2 finished! INFO @ Fri, 15 Feb 2019 07:14:14: #2 predicted fragment length is 167 bps INFO @ Fri, 15 Feb 2019 07:14:14: #2 alternative fragment length(s) may be 49,129,141,146,167 bps INFO @ Fri, 15 Feb 2019 07:14:14: #2.2 Generate R script for model : SRX3782477.20_model.r INFO @ Fri, 15 Feb 2019 07:14:14: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:14:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:14:16: 40000000 INFO @ Fri, 15 Feb 2019 07:14:23: 41000000 INFO @ Fri, 15 Feb 2019 07:14:27: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:14:27: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:14:27: #1 total tags in treatment: 41420664 INFO @ Fri, 15 Feb 2019 07:14:27: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:14:27: #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 07:14:28: #1 tags after filtering in treatment: 41420571 INFO @ Fri, 15 Feb 2019 07:14:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:14:28: #1 finished! INFO @ Fri, 15 Feb 2019 07:14:28: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:14:32: #2 number of paired peaks: 12044 INFO @ Fri, 15 Feb 2019 07:14:32: start model_add_line... INFO @ Fri, 15 Feb 2019 07:14:32: start X-correlation... INFO @ Fri, 15 Feb 2019 07:14:32: end of X-cor INFO @ Fri, 15 Feb 2019 07:14:32: #2 finished! INFO @ Fri, 15 Feb 2019 07:14:32: #2 predicted fragment length is 167 bps INFO @ Fri, 15 Feb 2019 07:14:32: #2 alternative fragment length(s) may be 49,129,141,146,167 bps INFO @ Fri, 15 Feb 2019 07:14:32: #2.2 Generate R script for model : SRX3782477.10_model.r INFO @ Fri, 15 Feb 2019 07:14:32: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:14:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:15:53: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:15:58: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:16:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:16:50: #4 Write output xls file... SRX3782477.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:16:50: #4 Write peak in narrowPeak format file... SRX3782477.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:16:50: #4 Write summits bed file... SRX3782477.20_summits.bed INFO @ Fri, 15 Feb 2019 07:16:50: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (299 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:17:04: #4 Write output xls file... SRX3782477.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:17:04: #4 Write peak in narrowPeak format file... SRX3782477.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:17:04: #4 Write summits bed file... SRX3782477.10_summits.bed INFO @ Fri, 15 Feb 2019 07:17:04: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (554 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:17:05: #4 Write output xls file... SRX3782477.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:17:05: #4 Write peak in narrowPeak format file... SRX3782477.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:17:05: #4 Write summits bed file... SRX3782477.05_summits.bed INFO @ Fri, 15 Feb 2019 07:17:05: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (1211 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。