Job ID = 2590658 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,843,529 reads read : 65,687,058 reads written : 32,843,529 reads 0-length : 32,843,529 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: 00:11:36 32843529 reads; of these: 32843529 (100.00%) were unpaired; of these: 4781596 (14.56%) aligned 0 times 21205510 (64.57%) aligned exactly 1 time 6856423 (20.88%) aligned >1 times 85.44% overall alignment rate Time searching: 00:11:36 Overall time: 00:11:36 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 12 files... [bam_rmdupse_core] 14485309 / 28061933 = 0.5162 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 23:21:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.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 23:21:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:21:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.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 23:21:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:21:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.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 23:21:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:21:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:21:59: 1000000 INFO @ Mon, 12 Aug 2019 23:22:02: 1000000 INFO @ Mon, 12 Aug 2019 23:22:02: 1000000 INFO @ Mon, 12 Aug 2019 23:22:07: 2000000 INFO @ Mon, 12 Aug 2019 23:22:10: 2000000 INFO @ Mon, 12 Aug 2019 23:22:11: 2000000 INFO @ Mon, 12 Aug 2019 23:22:15: 3000000 INFO @ Mon, 12 Aug 2019 23:22:18: 3000000 INFO @ Mon, 12 Aug 2019 23:22:21: 3000000 INFO @ Mon, 12 Aug 2019 23:22:23: 4000000 INFO @ Mon, 12 Aug 2019 23:22:26: 4000000 INFO @ Mon, 12 Aug 2019 23:22:31: 4000000 INFO @ Mon, 12 Aug 2019 23:22:31: 5000000 INFO @ Mon, 12 Aug 2019 23:22:34: 5000000 INFO @ Mon, 12 Aug 2019 23:22:39: 6000000 INFO @ Mon, 12 Aug 2019 23:22:40: 5000000 INFO @ Mon, 12 Aug 2019 23:22:42: 6000000 INFO @ Mon, 12 Aug 2019 23:22:47: 7000000 INFO @ Mon, 12 Aug 2019 23:22:50: 7000000 INFO @ Mon, 12 Aug 2019 23:22:50: 6000000 INFO @ Mon, 12 Aug 2019 23:22:55: 8000000 INFO @ Mon, 12 Aug 2019 23:22:58: 8000000 INFO @ Mon, 12 Aug 2019 23:23:00: 7000000 INFO @ Mon, 12 Aug 2019 23:23:03: 9000000 INFO @ Mon, 12 Aug 2019 23:23:06: 9000000 INFO @ Mon, 12 Aug 2019 23:23:10: 8000000 INFO @ Mon, 12 Aug 2019 23:23:11: 10000000 INFO @ Mon, 12 Aug 2019 23:23:14: 10000000 INFO @ Mon, 12 Aug 2019 23:23:19: 11000000 INFO @ Mon, 12 Aug 2019 23:23:20: 9000000 INFO @ Mon, 12 Aug 2019 23:23:22: 11000000 INFO @ Mon, 12 Aug 2019 23:23:27: 12000000 INFO @ Mon, 12 Aug 2019 23:23:29: 10000000 INFO @ Mon, 12 Aug 2019 23:23:30: 12000000 INFO @ Mon, 12 Aug 2019 23:23:35: 13000000 INFO @ Mon, 12 Aug 2019 23:23:38: 13000000 INFO @ Mon, 12 Aug 2019 23:23:39: 11000000 INFO @ Mon, 12 Aug 2019 23:23:40: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:23:40: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:23:40: #1 total tags in treatment: 13576624 INFO @ Mon, 12 Aug 2019 23:23:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:23:40: #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 23:23:40: #1 tags after filtering in treatment: 13576624 INFO @ Mon, 12 Aug 2019 23:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:23:40: #1 finished! INFO @ Mon, 12 Aug 2019 23:23:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:23:42: #2 number of paired peaks: 1558 INFO @ Mon, 12 Aug 2019 23:23:42: start model_add_line... INFO @ Mon, 12 Aug 2019 23:23:42: start X-correlation... INFO @ Mon, 12 Aug 2019 23:23:42: end of X-cor INFO @ Mon, 12 Aug 2019 23:23:42: #2 finished! INFO @ Mon, 12 Aug 2019 23:23:42: #2 predicted fragment length is 134 bps INFO @ Mon, 12 Aug 2019 23:23:42: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 12 Aug 2019 23:23:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.05_model.r INFO @ Mon, 12 Aug 2019 23:23:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:23:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:23:43: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:23:43: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:23:43: #1 total tags in treatment: 13576624 INFO @ Mon, 12 Aug 2019 23:23:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:23:43: #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 23:23:43: #1 tags after filtering in treatment: 13576624 INFO @ Mon, 12 Aug 2019 23:23:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:23:43: #1 finished! INFO @ Mon, 12 Aug 2019 23:23:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:23:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:23:44: #2 number of paired peaks: 1558 INFO @ Mon, 12 Aug 2019 23:23:44: start model_add_line... INFO @ Mon, 12 Aug 2019 23:23:44: start X-correlation... INFO @ Mon, 12 Aug 2019 23:23:44: end of X-cor INFO @ Mon, 12 Aug 2019 23:23:44: #2 finished! INFO @ Mon, 12 Aug 2019 23:23:44: #2 predicted fragment length is 134 bps INFO @ Mon, 12 Aug 2019 23:23:44: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 12 Aug 2019 23:23:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.20_model.r INFO @ Mon, 12 Aug 2019 23:23:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:23:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:23:49: 12000000 INFO @ Mon, 12 Aug 2019 23:23:58: 13000000 INFO @ Mon, 12 Aug 2019 23:24:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:24:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:24:04: #1 total tags in treatment: 13576624 INFO @ Mon, 12 Aug 2019 23:24:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:24:04: #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 23:24:04: #1 tags after filtering in treatment: 13576624 INFO @ Mon, 12 Aug 2019 23:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:24:04: #1 finished! INFO @ Mon, 12 Aug 2019 23:24:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:24:05: #2 number of paired peaks: 1558 INFO @ Mon, 12 Aug 2019 23:24:05: start model_add_line... INFO @ Mon, 12 Aug 2019 23:24:06: start X-correlation... INFO @ Mon, 12 Aug 2019 23:24:06: end of X-cor INFO @ Mon, 12 Aug 2019 23:24:06: #2 finished! INFO @ Mon, 12 Aug 2019 23:24:06: #2 predicted fragment length is 134 bps INFO @ Mon, 12 Aug 2019 23:24:06: #2 alternative fragment length(s) may be 134 bps INFO @ Mon, 12 Aug 2019 23:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.10_model.r INFO @ Mon, 12 Aug 2019 23:24:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:24:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:24:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:24:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:24:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:24:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.05_summits.bed INFO @ Mon, 12 Aug 2019 23:24:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11693 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:24:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:24:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:24:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.20_summits.bed INFO @ Mon, 12 Aug 2019 23:24:42: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3954 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:24:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:25:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:25:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:25:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011009/SRX5011009.10_summits.bed INFO @ Mon, 12 Aug 2019 23:25:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7504 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。