Job ID = 2590721 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 45,045,790 reads read : 90,091,580 reads written : 45,045,790 reads 0-length : 45,045,790 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:22 45045790 reads; of these: 45045790 (100.00%) were unpaired; of these: 6802781 (15.10%) aligned 0 times 28252813 (62.72%) aligned exactly 1 time 9990196 (22.18%) aligned >1 times 84.90% overall alignment rate Time searching: 00:16:22 Overall time: 00:16:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 21052923 / 38243009 = 0.5505 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 @ Mon, 12 Aug 2019 23:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:42:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:42:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:42:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:28: 1000000 INFO @ Mon, 12 Aug 2019 23:42:29: 1000000 INFO @ Mon, 12 Aug 2019 23:42:32: 1000000 INFO @ Mon, 12 Aug 2019 23:42:36: 2000000 INFO @ Mon, 12 Aug 2019 23:42:37: 2000000 INFO @ Mon, 12 Aug 2019 23:42:42: 2000000 INFO @ Mon, 12 Aug 2019 23:42:43: 3000000 INFO @ Mon, 12 Aug 2019 23:42:45: 3000000 INFO @ Mon, 12 Aug 2019 23:42:51: 4000000 INFO @ Mon, 12 Aug 2019 23:42:51: 3000000 INFO @ Mon, 12 Aug 2019 23:42:53: 4000000 INFO @ Mon, 12 Aug 2019 23:42:58: 5000000 INFO @ Mon, 12 Aug 2019 23:43:01: 5000000 INFO @ Mon, 12 Aug 2019 23:43:01: 4000000 INFO @ Mon, 12 Aug 2019 23:43:06: 6000000 INFO @ Mon, 12 Aug 2019 23:43:09: 6000000 INFO @ Mon, 12 Aug 2019 23:43:11: 5000000 INFO @ Mon, 12 Aug 2019 23:43:14: 7000000 INFO @ Mon, 12 Aug 2019 23:43:17: 7000000 INFO @ Mon, 12 Aug 2019 23:43:20: 6000000 INFO @ Mon, 12 Aug 2019 23:43:21: 8000000 INFO @ Mon, 12 Aug 2019 23:43:25: 8000000 INFO @ Mon, 12 Aug 2019 23:43:29: 9000000 INFO @ Mon, 12 Aug 2019 23:43:30: 7000000 INFO @ Mon, 12 Aug 2019 23:43:33: 9000000 INFO @ Mon, 12 Aug 2019 23:43:37: 10000000 INFO @ Mon, 12 Aug 2019 23:43:40: 8000000 INFO @ Mon, 12 Aug 2019 23:43:40: 10000000 INFO @ Mon, 12 Aug 2019 23:43:44: 11000000 INFO @ Mon, 12 Aug 2019 23:43:48: 11000000 INFO @ Mon, 12 Aug 2019 23:43:49: 9000000 INFO @ Mon, 12 Aug 2019 23:43:52: 12000000 INFO @ Mon, 12 Aug 2019 23:43:56: 12000000 INFO @ Mon, 12 Aug 2019 23:43:59: 10000000 INFO @ Mon, 12 Aug 2019 23:44:00: 13000000 INFO @ Mon, 12 Aug 2019 23:44:04: 13000000 INFO @ Mon, 12 Aug 2019 23:44:09: 11000000 INFO @ Mon, 12 Aug 2019 23:44:11: 14000000 INFO @ Mon, 12 Aug 2019 23:44:12: 14000000 INFO @ Mon, 12 Aug 2019 23:44:20: 12000000 INFO @ Mon, 12 Aug 2019 23:44:21: 15000000 INFO @ Mon, 12 Aug 2019 23:44:22: 15000000 INFO @ Mon, 12 Aug 2019 23:44:29: 16000000 INFO @ Mon, 12 Aug 2019 23:44:30: 16000000 INFO @ Mon, 12 Aug 2019 23:44:30: 13000000 INFO @ Mon, 12 Aug 2019 23:44:37: 17000000 INFO @ Mon, 12 Aug 2019 23:44:38: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:44:38: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:44:38: #1 total tags in treatment: 17190086 INFO @ Mon, 12 Aug 2019 23:44:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:44:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:44:38: #1 tags after filtering in treatment: 17190086 INFO @ Mon, 12 Aug 2019 23:44:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:44:38: #1 finished! INFO @ Mon, 12 Aug 2019 23:44:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:44:39: 17000000 INFO @ Mon, 12 Aug 2019 23:44:40: #2 number of paired peaks: 1519 INFO @ Mon, 12 Aug 2019 23:44:40: start model_add_line... INFO @ Mon, 12 Aug 2019 23:44:40: start X-correlation... INFO @ Mon, 12 Aug 2019 23:44:40: end of X-cor INFO @ Mon, 12 Aug 2019 23:44:40: #2 finished! INFO @ Mon, 12 Aug 2019 23:44:40: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 23:44:40: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 23:44:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.10_model.r INFO @ Mon, 12 Aug 2019 23:44:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:44:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:44:40: 14000000 INFO @ Mon, 12 Aug 2019 23:44:41: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:44:41: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:44:41: #1 total tags in treatment: 17190086 INFO @ Mon, 12 Aug 2019 23:44:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:44:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:44:41: #1 tags after filtering in treatment: 17190086 INFO @ Mon, 12 Aug 2019 23:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:44:41: #1 finished! INFO @ Mon, 12 Aug 2019 23:44:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:44:43: #2 number of paired peaks: 1519 INFO @ Mon, 12 Aug 2019 23:44:43: start model_add_line... INFO @ Mon, 12 Aug 2019 23:44:43: start X-correlation... INFO @ Mon, 12 Aug 2019 23:44:43: end of X-cor INFO @ Mon, 12 Aug 2019 23:44:43: #2 finished! INFO @ Mon, 12 Aug 2019 23:44:43: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 23:44:43: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 23:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.05_model.r INFO @ Mon, 12 Aug 2019 23:44:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:44:50: 15000000 INFO @ Mon, 12 Aug 2019 23:44:59: 16000000 INFO @ Mon, 12 Aug 2019 23:45:09: 17000000 INFO @ Mon, 12 Aug 2019 23:45:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:45:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:45:10: #1 total tags in treatment: 17190086 INFO @ Mon, 12 Aug 2019 23:45:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:45:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:45:11: #1 tags after filtering in treatment: 17190086 INFO @ Mon, 12 Aug 2019 23:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:45:11: #1 finished! INFO @ Mon, 12 Aug 2019 23:45:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:45:12: #2 number of paired peaks: 1519 INFO @ Mon, 12 Aug 2019 23:45:12: start model_add_line... INFO @ Mon, 12 Aug 2019 23:45:12: start X-correlation... INFO @ Mon, 12 Aug 2019 23:45:12: end of X-cor INFO @ Mon, 12 Aug 2019 23:45:12: #2 finished! INFO @ Mon, 12 Aug 2019 23:45:12: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 23:45:12: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 23:45:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.20_model.r INFO @ Mon, 12 Aug 2019 23:45:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:45:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:45:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.10_summits.bed INFO @ Mon, 12 Aug 2019 23:45:55: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7438 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.05_summits.bed INFO @ Mon, 12 Aug 2019 23:45:59: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (11798 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:46:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011031/SRX5011031.20_summits.bed INFO @ Mon, 12 Aug 2019 23:46:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4070 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。