Job ID = 10453666 sra ファイルのダウンロード中... Completed: 757839K bytes transferred in 14 seconds (415713K 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... Written 43639446 spots for /home/okishinya/chipatlas/results/rn6/SRX3478271/SRR6384650.sra Written 43639446 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 01:26:04 43639446 reads; of these: 43639446 (100.00%) were unpaired; of these: 1539913 (3.53%) aligned 0 times 29655510 (67.96%) aligned exactly 1 time 12444023 (28.52%) aligned >1 times 96.47% overall alignment rate Time searching: 01:26:11 Overall time: 01:26:11 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] 12834865 / 42099533 = 0.3049 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 @ Thu, 08 Feb 2018 18:11:54: # Command line: callpeak -t SRX3478271.bam -f BAM -g 2.15e9 -n SRX3478271.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3478271.10 # format = BAM # ChIP-seq file = ['SRX3478271.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 @ Thu, 08 Feb 2018 18:11:54: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:11:54: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:11:54: # Command line: callpeak -t SRX3478271.bam -f BAM -g 2.15e9 -n SRX3478271.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3478271.05 # format = BAM # ChIP-seq file = ['SRX3478271.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 @ Thu, 08 Feb 2018 18:11:54: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:11:54: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:11:54: # Command line: callpeak -t SRX3478271.bam -f BAM -g 2.15e9 -n SRX3478271.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3478271.20 # format = BAM # ChIP-seq file = ['SRX3478271.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 @ Thu, 08 Feb 2018 18:11:54: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:11:54: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:12:10: 1000000 INFO @ Thu, 08 Feb 2018 18:12:10: 1000000 INFO @ Thu, 08 Feb 2018 18:12:10: 1000000 INFO @ Thu, 08 Feb 2018 18:12:27: 2000000 INFO @ Thu, 08 Feb 2018 18:12:27: 2000000 INFO @ Thu, 08 Feb 2018 18:12:27: 2000000 INFO @ Thu, 08 Feb 2018 18:12:39: 3000000 INFO @ Thu, 08 Feb 2018 18:12:39: 3000000 INFO @ Thu, 08 Feb 2018 18:12:41: 3000000 INFO @ Thu, 08 Feb 2018 18:12:55: 4000000 INFO @ Thu, 08 Feb 2018 18:12:55: 4000000 INFO @ Thu, 08 Feb 2018 18:12:56: 4000000 INFO @ Thu, 08 Feb 2018 18:13:09: 5000000 INFO @ Thu, 08 Feb 2018 18:13:09: 5000000 INFO @ Thu, 08 Feb 2018 18:13:10: 5000000 INFO @ Thu, 08 Feb 2018 18:13:25: 6000000 INFO @ Thu, 08 Feb 2018 18:13:25: 6000000 INFO @ Thu, 08 Feb 2018 18:13:25: 6000000 INFO @ Thu, 08 Feb 2018 18:13:39: 7000000 INFO @ Thu, 08 Feb 2018 18:13:39: 7000000 INFO @ Thu, 08 Feb 2018 18:13:39: 7000000 INFO @ Thu, 08 Feb 2018 18:13:54: 8000000 INFO @ Thu, 08 Feb 2018 18:13:54: 8000000 INFO @ Thu, 08 Feb 2018 18:13:55: 8000000 INFO @ Thu, 08 Feb 2018 18:14:09: 9000000 INFO @ Thu, 08 Feb 2018 18:14:09: 9000000 INFO @ Thu, 08 Feb 2018 18:14:09: 9000000 INFO @ Thu, 08 Feb 2018 18:14:24: 10000000 INFO @ Thu, 08 Feb 2018 18:14:25: 10000000 INFO @ Thu, 08 Feb 2018 18:14:25: 10000000 INFO @ Thu, 08 Feb 2018 18:14:39: 11000000 INFO @ Thu, 08 Feb 2018 18:14:40: 11000000 INFO @ Thu, 08 Feb 2018 18:14:40: 11000000 INFO @ Thu, 08 Feb 2018 18:14:54: 12000000 INFO @ Thu, 08 Feb 2018 18:14:54: 12000000 INFO @ Thu, 08 Feb 2018 18:14:54: 12000000 INFO @ Thu, 08 Feb 2018 18:15:08: 13000000 INFO @ Thu, 08 Feb 2018 18:15:09: 13000000 INFO @ Thu, 08 Feb 2018 18:15:09: 13000000 INFO @ Thu, 08 Feb 2018 18:15:18: 14000000 INFO @ Thu, 08 Feb 2018 18:15:22: 14000000 INFO @ Thu, 08 Feb 2018 18:15:22: 14000000 INFO @ Thu, 08 Feb 2018 18:15:29: 15000000 INFO @ Thu, 08 Feb 2018 18:15:38: 15000000 INFO @ Thu, 08 Feb 2018 18:15:38: 15000000 INFO @ Thu, 08 Feb 2018 18:15:42: 16000000 INFO @ Thu, 08 Feb 2018 18:15:51: 16000000 INFO @ Thu, 08 Feb 2018 18:15:51: 16000000 INFO @ Thu, 08 Feb 2018 18:15:55: 17000000 INFO @ Thu, 08 Feb 2018 18:16:07: 17000000 INFO @ Thu, 08 Feb 2018 18:16:07: 17000000 INFO @ Thu, 08 Feb 2018 18:16:09: 18000000 INFO @ Thu, 08 Feb 2018 18:16:21: 19000000 INFO @ Thu, 08 Feb 2018 18:16:21: 18000000 INFO @ Thu, 08 Feb 2018 18:16:21: 18000000 INFO @ Thu, 08 Feb 2018 18:16:36: 19000000 INFO @ Thu, 08 Feb 2018 18:16:37: 19000000 INFO @ Thu, 08 Feb 2018 18:16:37: 20000000 INFO @ Thu, 08 Feb 2018 18:16:48: 20000000 INFO @ Thu, 08 Feb 2018 18:16:52: 20000000 INFO @ Thu, 08 Feb 2018 18:16:56: 21000000 INFO @ Thu, 08 Feb 2018 18:17:02: 21000000 INFO @ Thu, 08 Feb 2018 18:17:05: 21000000 INFO @ Thu, 08 Feb 2018 18:17:12: 22000000 INFO @ Thu, 08 Feb 2018 18:17:13: 22000000 INFO @ Thu, 08 Feb 2018 18:17:19: 22000000 INFO @ Thu, 08 Feb 2018 18:17:26: 23000000 INFO @ Thu, 08 Feb 2018 18:17:29: 23000000 INFO @ Thu, 08 Feb 2018 18:17:33: 23000000 INFO @ Thu, 08 Feb 2018 18:17:38: 24000000 INFO @ Thu, 08 Feb 2018 18:17:46: 24000000 INFO @ Thu, 08 Feb 2018 18:17:46: 24000000 INFO @ Thu, 08 Feb 2018 18:17:51: 25000000 INFO @ Thu, 08 Feb 2018 18:18:00: 25000000 INFO @ Thu, 08 Feb 2018 18:18:03: 26000000 INFO @ Thu, 08 Feb 2018 18:18:03: 25000000 INFO @ Thu, 08 Feb 2018 18:18:13: 26000000 INFO @ Thu, 08 Feb 2018 18:18:15: 27000000 INFO @ Thu, 08 Feb 2018 18:18:19: 26000000 INFO @ Thu, 08 Feb 2018 18:18:27: 27000000 INFO @ Thu, 08 Feb 2018 18:18:28: 28000000 INFO @ Thu, 08 Feb 2018 18:18:34: 27000000 INFO @ Thu, 08 Feb 2018 18:18:40: 28000000 INFO @ Thu, 08 Feb 2018 18:18:41: 29000000 INFO @ Thu, 08 Feb 2018 18:18:46: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:18:46: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:18:46: #1 total tags in treatment: 29264668 INFO @ Thu, 08 Feb 2018 18:18:46: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:18:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:18:47: #1 tags after filtering in treatment: 29264570 INFO @ Thu, 08 Feb 2018 18:18:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:18:47: #1 finished! INFO @ Thu, 08 Feb 2018 18:18:47: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:18:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:18:49: 28000000 INFO @ Thu, 08 Feb 2018 18:18:52: #2 number of paired peaks: 17400 INFO @ Thu, 08 Feb 2018 18:18:52: start model_add_line... INFO @ Thu, 08 Feb 2018 18:18:52: start X-correlation... INFO @ Thu, 08 Feb 2018 18:18:52: end of X-cor INFO @ Thu, 08 Feb 2018 18:18:52: #2 finished! INFO @ Thu, 08 Feb 2018 18:18:52: #2 predicted fragment length is 107 bps INFO @ Thu, 08 Feb 2018 18:18:52: #2 alternative fragment length(s) may be 4,107 bps INFO @ Thu, 08 Feb 2018 18:18:52: #2.2 Generate R script for model : SRX3478271.10_model.r INFO @ Thu, 08 Feb 2018 18:18:52: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:18:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:18:54: 29000000 INFO @ Thu, 08 Feb 2018 18:18:57: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:18:57: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:18:57: #1 total tags in treatment: 29264668 INFO @ Thu, 08 Feb 2018 18:18:57: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:18:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:18:58: #1 tags after filtering in treatment: 29264570 INFO @ Thu, 08 Feb 2018 18:18:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:18:58: #1 finished! INFO @ Thu, 08 Feb 2018 18:18:58: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:18:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:19:02: #2 number of paired peaks: 17400 INFO @ Thu, 08 Feb 2018 18:19:02: start model_add_line... INFO @ Thu, 08 Feb 2018 18:19:03: start X-correlation... INFO @ Thu, 08 Feb 2018 18:19:03: end of X-cor INFO @ Thu, 08 Feb 2018 18:19:03: #2 finished! INFO @ Thu, 08 Feb 2018 18:19:03: #2 predicted fragment length is 107 bps INFO @ Thu, 08 Feb 2018 18:19:03: #2 alternative fragment length(s) may be 4,107 bps INFO @ Thu, 08 Feb 2018 18:19:03: #2.2 Generate R script for model : SRX3478271.05_model.r INFO @ Thu, 08 Feb 2018 18:19:03: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:19:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:19:04: 29000000 INFO @ Thu, 08 Feb 2018 18:19:08: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:19:08: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:19:08: #1 total tags in treatment: 29264668 INFO @ Thu, 08 Feb 2018 18:19:08: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:19:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:19:10: #1 tags after filtering in treatment: 29264570 INFO @ Thu, 08 Feb 2018 18:19:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:19:10: #1 finished! INFO @ Thu, 08 Feb 2018 18:19:10: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:19:14: #2 number of paired peaks: 17400 INFO @ Thu, 08 Feb 2018 18:19:14: start model_add_line... INFO @ Thu, 08 Feb 2018 18:19:14: start X-correlation... INFO @ Thu, 08 Feb 2018 18:19:14: end of X-cor INFO @ Thu, 08 Feb 2018 18:19:14: #2 finished! INFO @ Thu, 08 Feb 2018 18:19:14: #2 predicted fragment length is 107 bps INFO @ Thu, 08 Feb 2018 18:19:14: #2 alternative fragment length(s) may be 4,107 bps INFO @ Thu, 08 Feb 2018 18:19:14: #2.2 Generate R script for model : SRX3478271.20_model.r INFO @ Thu, 08 Feb 2018 18:19:14: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:19:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:20:27: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:20:36: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:20:46: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:21:24: #4 Write output xls file... SRX3478271.10_peaks.xls INFO @ Thu, 08 Feb 2018 18:21:24: #4 Write peak in narrowPeak format file... SRX3478271.10_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:21:24: #4 Write summits bed file... SRX3478271.10_summits.bed INFO @ Thu, 08 Feb 2018 18:21:24: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (697 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 18:21:34: #4 Write output xls file... SRX3478271.05_peaks.xls INFO @ Thu, 08 Feb 2018 18:21:34: #4 Write peak in narrowPeak format file... SRX3478271.05_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:21:34: #4 Write summits bed file... SRX3478271.05_summits.bed INFO @ Thu, 08 Feb 2018 18:21:34: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (1535 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 18:21:43: #4 Write output xls file... SRX3478271.20_peaks.xls INFO @ Thu, 08 Feb 2018 18:21:43: #4 Write peak in narrowPeak format file... SRX3478271.20_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:21:43: #4 Write summits bed file... SRX3478271.20_summits.bed INFO @ Thu, 08 Feb 2018 18:21:44: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (302 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。