Job ID = 10453668 sra ファイルのダウンロード中... Completed: 603561K bytes transferred in 12 seconds (408398K 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 34355623 spots for /home/okishinya/chipatlas/results/rn6/SRX3478273/SRR6384652.sra Written 34355623 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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:13:05 34355623 reads; of these: 34355623 (100.00%) were unpaired; of these: 1910194 (5.56%) aligned 0 times 23844902 (69.41%) aligned exactly 1 time 8600527 (25.03%) aligned >1 times 94.44% overall alignment rate Time searching: 01:13:11 Overall time: 01:13:11 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 16 files... [bam_rmdupse_core] 5167736 / 32445429 = 0.1593 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 18:09:40: # Command line: callpeak -t SRX3478273.bam -f BAM -g 2.15e9 -n SRX3478273.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3478273.10 # format = BAM # ChIP-seq file = ['SRX3478273.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 18:09:40: # Command line: callpeak -t SRX3478273.bam -f BAM -g 2.15e9 -n SRX3478273.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3478273.20 # format = BAM # ChIP-seq file = ['SRX3478273.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 18:09:40: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:09:40: # Command line: callpeak -t SRX3478273.bam -f BAM -g 2.15e9 -n SRX3478273.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3478273.05 # format = BAM # ChIP-seq file = ['SRX3478273.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 18:09:40: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:09:40: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:09:40: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:09:40: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:09:40: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:09:52: 1000000 INFO @ Thu, 08 Feb 2018 18:09:52: 1000000 INFO @ Thu, 08 Feb 2018 18:09:56: 1000000 INFO @ Thu, 08 Feb 2018 18:10:08: 2000000 INFO @ Thu, 08 Feb 2018 18:10:09: 2000000 INFO @ Thu, 08 Feb 2018 18:10:14: 2000000 INFO @ Thu, 08 Feb 2018 18:10:23: 3000000 INFO @ Thu, 08 Feb 2018 18:10:25: 3000000 INFO @ Thu, 08 Feb 2018 18:10:28: 3000000 INFO @ Thu, 08 Feb 2018 18:10:40: 4000000 INFO @ Thu, 08 Feb 2018 18:10:42: 4000000 INFO @ Thu, 08 Feb 2018 18:10:46: 4000000 INFO @ Thu, 08 Feb 2018 18:10:56: 5000000 INFO @ Thu, 08 Feb 2018 18:10:59: 5000000 INFO @ Thu, 08 Feb 2018 18:11:04: 5000000 INFO @ Thu, 08 Feb 2018 18:11:13: 6000000 INFO @ Thu, 08 Feb 2018 18:11:16: 6000000 INFO @ Thu, 08 Feb 2018 18:11:21: 6000000 INFO @ Thu, 08 Feb 2018 18:11:30: 7000000 INFO @ Thu, 08 Feb 2018 18:11:34: 7000000 INFO @ Thu, 08 Feb 2018 18:11:39: 7000000 INFO @ Thu, 08 Feb 2018 18:11:46: 8000000 INFO @ Thu, 08 Feb 2018 18:11:52: 8000000 INFO @ Thu, 08 Feb 2018 18:11:55: 8000000 INFO @ Thu, 08 Feb 2018 18:12:01: 9000000 INFO @ Thu, 08 Feb 2018 18:12:05: 9000000 INFO @ Thu, 08 Feb 2018 18:12:08: 9000000 INFO @ Thu, 08 Feb 2018 18:12:15: 10000000 INFO @ Thu, 08 Feb 2018 18:12:19: 10000000 INFO @ Thu, 08 Feb 2018 18:12:21: 10000000 INFO @ Thu, 08 Feb 2018 18:12:30: 11000000 INFO @ Thu, 08 Feb 2018 18:12:32: 11000000 INFO @ Thu, 08 Feb 2018 18:12:33: 11000000 INFO @ Thu, 08 Feb 2018 18:12:43: 12000000 INFO @ Thu, 08 Feb 2018 18:12:45: 12000000 INFO @ Thu, 08 Feb 2018 18:12:46: 12000000 INFO @ Thu, 08 Feb 2018 18:12:57: 13000000 INFO @ Thu, 08 Feb 2018 18:12:58: 13000000 INFO @ Thu, 08 Feb 2018 18:12:58: 13000000 INFO @ Thu, 08 Feb 2018 18:13:10: 14000000 INFO @ Thu, 08 Feb 2018 18:13:12: 14000000 INFO @ Thu, 08 Feb 2018 18:13:14: 14000000 INFO @ Thu, 08 Feb 2018 18:13:22: 15000000 INFO @ Thu, 08 Feb 2018 18:13:26: 15000000 INFO @ Thu, 08 Feb 2018 18:13:31: 15000000 INFO @ Thu, 08 Feb 2018 18:13:36: 16000000 INFO @ Thu, 08 Feb 2018 18:13:42: 16000000 INFO @ Thu, 08 Feb 2018 18:13:46: 16000000 INFO @ Thu, 08 Feb 2018 18:13:49: 17000000 INFO @ Thu, 08 Feb 2018 18:13:55: 17000000 INFO @ Thu, 08 Feb 2018 18:14:02: 17000000 INFO @ Thu, 08 Feb 2018 18:14:03: 18000000 INFO @ Thu, 08 Feb 2018 18:14:09: 18000000 INFO @ Thu, 08 Feb 2018 18:14:14: 19000000 INFO @ Thu, 08 Feb 2018 18:14:17: 18000000 INFO @ Thu, 08 Feb 2018 18:14:24: 19000000 INFO @ Thu, 08 Feb 2018 18:14:28: 20000000 INFO @ Thu, 08 Feb 2018 18:14:34: 19000000 INFO @ Thu, 08 Feb 2018 18:14:40: 21000000 INFO @ Thu, 08 Feb 2018 18:14:40: 20000000 INFO @ Thu, 08 Feb 2018 18:14:50: 20000000 INFO @ Thu, 08 Feb 2018 18:14:53: 22000000 INFO @ Thu, 08 Feb 2018 18:14:55: 21000000 INFO @ Thu, 08 Feb 2018 18:15:05: 23000000 INFO @ Thu, 08 Feb 2018 18:15:07: 21000000 INFO @ Thu, 08 Feb 2018 18:15:11: 22000000 INFO @ Thu, 08 Feb 2018 18:15:19: 24000000 INFO @ Thu, 08 Feb 2018 18:15:21: 22000000 INFO @ Thu, 08 Feb 2018 18:15:29: 23000000 INFO @ Thu, 08 Feb 2018 18:15:31: 25000000 INFO @ Thu, 08 Feb 2018 18:15:34: 23000000 INFO @ Thu, 08 Feb 2018 18:15:44: 26000000 INFO @ Thu, 08 Feb 2018 18:15:48: 24000000 INFO @ Thu, 08 Feb 2018 18:15:48: 24000000 INFO @ Thu, 08 Feb 2018 18:15:57: 27000000 INFO @ Thu, 08 Feb 2018 18:16:00: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:16:00: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:16:00: #1 total tags in treatment: 27277693 INFO @ Thu, 08 Feb 2018 18:16:00: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:16:00: #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 18:16:01: #1 tags after filtering in treatment: 27277575 INFO @ Thu, 08 Feb 2018 18:16:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:16:01: #1 finished! INFO @ Thu, 08 Feb 2018 18:16:01: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:16:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:16:02: 25000000 INFO @ Thu, 08 Feb 2018 18:16:07: #2 number of paired peaks: 43004 INFO @ Thu, 08 Feb 2018 18:16:07: start model_add_line... INFO @ Thu, 08 Feb 2018 18:16:07: 25000000 INFO @ Thu, 08 Feb 2018 18:16:07: start X-correlation... INFO @ Thu, 08 Feb 2018 18:16:07: end of X-cor INFO @ Thu, 08 Feb 2018 18:16:07: #2 finished! INFO @ Thu, 08 Feb 2018 18:16:07: #2 predicted fragment length is 150 bps INFO @ Thu, 08 Feb 2018 18:16:07: #2 alternative fragment length(s) may be 4,150 bps INFO @ Thu, 08 Feb 2018 18:16:07: #2.2 Generate R script for model : SRX3478273.20_model.r INFO @ Thu, 08 Feb 2018 18:16:07: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:16:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:16:16: 26000000 INFO @ Thu, 08 Feb 2018 18:16:25: 26000000 INFO @ Thu, 08 Feb 2018 18:16:30: 27000000 INFO @ Thu, 08 Feb 2018 18:16:34: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:16:34: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:16:34: #1 total tags in treatment: 27277693 INFO @ Thu, 08 Feb 2018 18:16:34: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:16:34: #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 18:16:36: #1 tags after filtering in treatment: 27277575 INFO @ Thu, 08 Feb 2018 18:16:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:16:36: #1 finished! INFO @ Thu, 08 Feb 2018 18:16:36: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:16:41: #2 number of paired peaks: 43004 INFO @ Thu, 08 Feb 2018 18:16:41: start model_add_line... INFO @ Thu, 08 Feb 2018 18:16:42: start X-correlation... INFO @ Thu, 08 Feb 2018 18:16:42: end of X-cor INFO @ Thu, 08 Feb 2018 18:16:42: #2 finished! INFO @ Thu, 08 Feb 2018 18:16:42: #2 predicted fragment length is 150 bps INFO @ Thu, 08 Feb 2018 18:16:42: #2 alternative fragment length(s) may be 4,150 bps INFO @ Thu, 08 Feb 2018 18:16:42: #2.2 Generate R script for model : SRX3478273.10_model.r INFO @ Thu, 08 Feb 2018 18:16:42: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:16:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:16:42: 27000000 INFO @ Thu, 08 Feb 2018 18:16:47: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:16:47: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:16:47: #1 total tags in treatment: 27277693 INFO @ Thu, 08 Feb 2018 18:16:47: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:16:47: #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 18:16:48: #1 tags after filtering in treatment: 27277575 INFO @ Thu, 08 Feb 2018 18:16:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:16:48: #1 finished! INFO @ Thu, 08 Feb 2018 18:16:48: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:16:54: #2 number of paired peaks: 43004 INFO @ Thu, 08 Feb 2018 18:16:54: start model_add_line... INFO @ Thu, 08 Feb 2018 18:16:54: start X-correlation... INFO @ Thu, 08 Feb 2018 18:16:54: end of X-cor INFO @ Thu, 08 Feb 2018 18:16:54: #2 finished! INFO @ Thu, 08 Feb 2018 18:16:54: #2 predicted fragment length is 150 bps INFO @ Thu, 08 Feb 2018 18:16:54: #2 alternative fragment length(s) may be 4,150 bps INFO @ Thu, 08 Feb 2018 18:16:54: #2.2 Generate R script for model : SRX3478273.05_model.r INFO @ Thu, 08 Feb 2018 18:16:54: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:17:36: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:18:11: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:18:27: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:18:30: #4 Write output xls file... SRX3478273.20_peaks.xls INFO @ Thu, 08 Feb 2018 18:18:30: #4 Write peak in narrowPeak format file... SRX3478273.20_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:18:30: #4 Write summits bed file... SRX3478273.20_summits.bed INFO @ Thu, 08 Feb 2018 18:18:30: Done! pass1 - making usageList (29 chroms): 4 millis pass2 - checking and writing primary data (262 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 18:19:05: #4 Write output xls file... SRX3478273.10_peaks.xls INFO @ Thu, 08 Feb 2018 18:19:05: #4 Write peak in narrowPeak format file... SRX3478273.10_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:19:05: #4 Write summits bed file... SRX3478273.10_summits.bed INFO @ Thu, 08 Feb 2018 18:19:05: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (1009 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 18:19:34: #4 Write output xls file... SRX3478273.05_peaks.xls INFO @ Thu, 08 Feb 2018 18:19:34: #4 Write peak in narrowPeak format file... SRX3478273.05_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:19:34: #4 Write summits bed file... SRX3478273.05_summits.bed INFO @ Thu, 08 Feb 2018 18:19:34: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (5824 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。