Job ID = 2640702 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,582,051 reads read : 65,164,102 reads written : 32,582,051 reads 0-length : 32,582,051 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:42 32582051 reads; of these: 32582051 (100.00%) were unpaired; of these: 967763 (2.97%) aligned 0 times 26494662 (81.32%) aligned exactly 1 time 5119626 (15.71%) aligned >1 times 97.03% overall alignment rate Time searching: 00:23:45 Overall time: 00:23:45 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] 2140114 / 31614288 = 0.0677 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.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 @ Sat, 24 Aug 2019 19:00:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:00:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:00:14: 1000000 INFO @ Sat, 24 Aug 2019 19:00:20: 2000000 INFO @ Sat, 24 Aug 2019 19:00:27: 3000000 INFO @ Sat, 24 Aug 2019 19:00:33: 4000000 INFO @ Sat, 24 Aug 2019 19:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.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 @ Sat, 24 Aug 2019 19:00:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:00:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:00:40: 5000000 INFO @ Sat, 24 Aug 2019 19:00:44: 1000000 INFO @ Sat, 24 Aug 2019 19:00:47: 6000000 INFO @ Sat, 24 Aug 2019 19:00:52: 2000000 INFO @ Sat, 24 Aug 2019 19:00:53: 7000000 INFO @ Sat, 24 Aug 2019 19:00:59: 3000000 INFO @ Sat, 24 Aug 2019 19:01:00: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:01:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.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 @ Sat, 24 Aug 2019 19:01:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:01:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:01:07: 4000000 INFO @ Sat, 24 Aug 2019 19:01:07: 9000000 INFO @ Sat, 24 Aug 2019 19:01:14: 10000000 INFO @ Sat, 24 Aug 2019 19:01:14: 1000000 INFO @ Sat, 24 Aug 2019 19:01:14: 5000000 INFO @ Sat, 24 Aug 2019 19:01:20: 11000000 INFO @ Sat, 24 Aug 2019 19:01:22: 2000000 INFO @ Sat, 24 Aug 2019 19:01:22: 6000000 INFO @ Sat, 24 Aug 2019 19:01:27: 12000000 INFO @ Sat, 24 Aug 2019 19:01:29: 3000000 INFO @ Sat, 24 Aug 2019 19:01:29: 7000000 INFO @ Sat, 24 Aug 2019 19:01:34: 13000000 INFO @ Sat, 24 Aug 2019 19:01:37: 4000000 INFO @ Sat, 24 Aug 2019 19:01:37: 8000000 INFO @ Sat, 24 Aug 2019 19:01:40: 14000000 INFO @ Sat, 24 Aug 2019 19:01:44: 5000000 INFO @ Sat, 24 Aug 2019 19:01:45: 9000000 INFO @ Sat, 24 Aug 2019 19:01:47: 15000000 INFO @ Sat, 24 Aug 2019 19:01:52: 6000000 INFO @ Sat, 24 Aug 2019 19:01:52: 10000000 INFO @ Sat, 24 Aug 2019 19:01:54: 16000000 INFO @ Sat, 24 Aug 2019 19:01:59: 7000000 INFO @ Sat, 24 Aug 2019 19:02:00: 11000000 INFO @ Sat, 24 Aug 2019 19:02:01: 17000000 INFO @ Sat, 24 Aug 2019 19:02:07: 8000000 INFO @ Sat, 24 Aug 2019 19:02:07: 12000000 INFO @ Sat, 24 Aug 2019 19:02:07: 18000000 INFO @ Sat, 24 Aug 2019 19:02:14: 19000000 INFO @ Sat, 24 Aug 2019 19:02:14: 9000000 INFO @ Sat, 24 Aug 2019 19:02:15: 13000000 INFO @ Sat, 24 Aug 2019 19:02:21: 20000000 INFO @ Sat, 24 Aug 2019 19:02:22: 10000000 INFO @ Sat, 24 Aug 2019 19:02:22: 14000000 INFO @ Sat, 24 Aug 2019 19:02:27: 21000000 INFO @ Sat, 24 Aug 2019 19:02:29: 11000000 INFO @ Sat, 24 Aug 2019 19:02:30: 15000000 INFO @ Sat, 24 Aug 2019 19:02:34: 22000000 INFO @ Sat, 24 Aug 2019 19:02:37: 12000000 INFO @ Sat, 24 Aug 2019 19:02:37: 16000000 INFO @ Sat, 24 Aug 2019 19:02:41: 23000000 INFO @ Sat, 24 Aug 2019 19:02:44: 13000000 INFO @ Sat, 24 Aug 2019 19:02:45: 17000000 INFO @ Sat, 24 Aug 2019 19:02:47: 24000000 INFO @ Sat, 24 Aug 2019 19:02:52: 14000000 INFO @ Sat, 24 Aug 2019 19:02:53: 18000000 INFO @ Sat, 24 Aug 2019 19:02:54: 25000000 INFO @ Sat, 24 Aug 2019 19:03:00: 15000000 INFO @ Sat, 24 Aug 2019 19:03:00: 19000000 INFO @ Sat, 24 Aug 2019 19:03:01: 26000000 INFO @ Sat, 24 Aug 2019 19:03:07: 16000000 INFO @ Sat, 24 Aug 2019 19:03:08: 20000000 INFO @ Sat, 24 Aug 2019 19:03:08: 27000000 INFO @ Sat, 24 Aug 2019 19:03:14: 28000000 INFO @ Sat, 24 Aug 2019 19:03:15: 17000000 INFO @ Sat, 24 Aug 2019 19:03:15: 21000000 INFO @ Sat, 24 Aug 2019 19:03:21: 29000000 INFO @ Sat, 24 Aug 2019 19:03:22: 18000000 INFO @ Sat, 24 Aug 2019 19:03:23: 22000000 INFO @ Sat, 24 Aug 2019 19:03:25: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:03:25: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:03:25: #1 total tags in treatment: 29474174 INFO @ Sat, 24 Aug 2019 19:03:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:03:26: #1 tags after filtering in treatment: 29473989 INFO @ Sat, 24 Aug 2019 19:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:03:26: #1 finished! INFO @ Sat, 24 Aug 2019 19:03:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:03:30: 19000000 INFO @ Sat, 24 Aug 2019 19:03:30: 23000000 INFO @ Sat, 24 Aug 2019 19:03:33: #2 number of paired peaks: 114220 INFO @ Sat, 24 Aug 2019 19:03:33: start model_add_line... INFO @ Sat, 24 Aug 2019 19:03:34: start X-correlation... INFO @ Sat, 24 Aug 2019 19:03:34: end of X-cor INFO @ Sat, 24 Aug 2019 19:03:34: #2 finished! INFO @ Sat, 24 Aug 2019 19:03:34: #2 predicted fragment length is 205 bps INFO @ Sat, 24 Aug 2019 19:03:34: #2 alternative fragment length(s) may be 4,205 bps INFO @ Sat, 24 Aug 2019 19:03:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.05_model.r INFO @ Sat, 24 Aug 2019 19:03:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:03:37: 20000000 INFO @ Sat, 24 Aug 2019 19:03:38: 24000000 INFO @ Sat, 24 Aug 2019 19:03:45: 21000000 INFO @ Sat, 24 Aug 2019 19:03:45: 25000000 INFO @ Sat, 24 Aug 2019 19:03:52: 22000000 INFO @ Sat, 24 Aug 2019 19:03:53: 26000000 INFO @ Sat, 24 Aug 2019 19:04:00: 23000000 INFO @ Sat, 24 Aug 2019 19:04:00: 27000000 INFO @ Sat, 24 Aug 2019 19:04:07: 24000000 INFO @ Sat, 24 Aug 2019 19:04:08: 28000000 INFO @ Sat, 24 Aug 2019 19:04:15: 25000000 INFO @ Sat, 24 Aug 2019 19:04:15: 29000000 INFO @ Sat, 24 Aug 2019 19:04:19: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:04:19: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:04:19: #1 total tags in treatment: 29474174 INFO @ Sat, 24 Aug 2019 19:04:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:04:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:04:20: #1 tags after filtering in treatment: 29473989 INFO @ Sat, 24 Aug 2019 19:04:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:04:20: #1 finished! INFO @ Sat, 24 Aug 2019 19:04:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:04:22: 26000000 INFO @ Sat, 24 Aug 2019 19:04:28: #2 number of paired peaks: 114220 INFO @ Sat, 24 Aug 2019 19:04:28: start model_add_line... INFO @ Sat, 24 Aug 2019 19:04:29: start X-correlation... INFO @ Sat, 24 Aug 2019 19:04:29: end of X-cor INFO @ Sat, 24 Aug 2019 19:04:29: #2 finished! INFO @ Sat, 24 Aug 2019 19:04:29: #2 predicted fragment length is 205 bps INFO @ Sat, 24 Aug 2019 19:04:29: #2 alternative fragment length(s) may be 4,205 bps INFO @ Sat, 24 Aug 2019 19:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.10_model.r INFO @ Sat, 24 Aug 2019 19:04:29: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:04:30: 27000000 INFO @ Sat, 24 Aug 2019 19:04:37: 28000000 INFO @ Sat, 24 Aug 2019 19:04:45: 29000000 INFO @ Sat, 24 Aug 2019 19:04:49: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:04:49: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:04:49: #1 total tags in treatment: 29474174 INFO @ Sat, 24 Aug 2019 19:04:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:04:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:04:50: #1 tags after filtering in treatment: 29473989 INFO @ Sat, 24 Aug 2019 19:04:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:04:50: #1 finished! INFO @ Sat, 24 Aug 2019 19:04:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:04:58: #2 number of paired peaks: 114220 INFO @ Sat, 24 Aug 2019 19:04:58: start model_add_line... INFO @ Sat, 24 Aug 2019 19:04:58: start X-correlation... INFO @ Sat, 24 Aug 2019 19:04:58: end of X-cor INFO @ Sat, 24 Aug 2019 19:04:58: #2 finished! INFO @ Sat, 24 Aug 2019 19:04:58: #2 predicted fragment length is 205 bps INFO @ Sat, 24 Aug 2019 19:04:58: #2 alternative fragment length(s) may be 4,205 bps INFO @ Sat, 24 Aug 2019 19:04:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.20_model.r INFO @ Sat, 24 Aug 2019 19:04:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:04:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:05:11: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:06:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:06:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:06:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.05_summits.bed INFO @ Sat, 24 Aug 2019 19:06:03: Done! pass1 - making usageList (138 chroms): 12 millis pass2 - checking and writing primary data (38758 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:06:06: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:06:35: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:07:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:07:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:07:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.10_summits.bed INFO @ Sat, 24 Aug 2019 19:07:02: Done! pass1 - making usageList (94 chroms): 9 millis pass2 - checking and writing primary data (21615 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:07:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:07:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:07:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375059/SRX5375059.20_summits.bed INFO @ Sat, 24 Aug 2019 19:07:25: Done! pass1 - making usageList (49 chroms): 3 millis pass2 - checking and writing primary data (7502 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。