Job ID = 2590503 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,640,890 reads read : 29,281,780 reads written : 14,640,890 reads 0-length : 14,640,890 spots read : 14,831,606 reads read : 29,663,212 reads written : 14,831,606 reads 0-length : 14,831,606 spots read : 14,867,968 reads read : 29,735,936 reads written : 14,867,968 reads 0-length : 14,867,968 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: 00:14:41 44340464 reads; of these: 44340464 (100.00%) were unpaired; of these: 1117145 (2.52%) aligned 0 times 34259113 (77.26%) aligned exactly 1 time 8964206 (20.22%) aligned >1 times 97.48% overall alignment rate Time searching: 00:14:41 Overall time: 00:14:41 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 20 files... [bam_rmdupse_core] 14503393 / 43223319 = 0.3355 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 22:45:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.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 22:45:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:45:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.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 22:45:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:45:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:45:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.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 22:45:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:45:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:45:24: 1000000 INFO @ Mon, 12 Aug 2019 22:45:25: 1000000 INFO @ Mon, 12 Aug 2019 22:45:27: 1000000 INFO @ Mon, 12 Aug 2019 22:45:31: 2000000 INFO @ Mon, 12 Aug 2019 22:45:32: 2000000 INFO @ Mon, 12 Aug 2019 22:45:35: 2000000 INFO @ Mon, 12 Aug 2019 22:45:38: 3000000 INFO @ Mon, 12 Aug 2019 22:45:39: 3000000 INFO @ Mon, 12 Aug 2019 22:45:43: 3000000 INFO @ Mon, 12 Aug 2019 22:45:45: 4000000 INFO @ Mon, 12 Aug 2019 22:45:46: 4000000 INFO @ Mon, 12 Aug 2019 22:45:51: 4000000 INFO @ Mon, 12 Aug 2019 22:45:52: 5000000 INFO @ Mon, 12 Aug 2019 22:45:53: 5000000 INFO @ Mon, 12 Aug 2019 22:45:59: 6000000 INFO @ Mon, 12 Aug 2019 22:45:59: 5000000 INFO @ Mon, 12 Aug 2019 22:46:00: 6000000 INFO @ Mon, 12 Aug 2019 22:46:05: 7000000 INFO @ Mon, 12 Aug 2019 22:46:06: 7000000 INFO @ Mon, 12 Aug 2019 22:46:07: 6000000 INFO @ Mon, 12 Aug 2019 22:46:12: 8000000 INFO @ Mon, 12 Aug 2019 22:46:13: 8000000 INFO @ Mon, 12 Aug 2019 22:46:14: 7000000 INFO @ Mon, 12 Aug 2019 22:46:19: 9000000 INFO @ Mon, 12 Aug 2019 22:46:20: 9000000 INFO @ Mon, 12 Aug 2019 22:46:22: 8000000 INFO @ Mon, 12 Aug 2019 22:46:26: 10000000 INFO @ Mon, 12 Aug 2019 22:46:27: 10000000 INFO @ Mon, 12 Aug 2019 22:46:30: 9000000 INFO @ Mon, 12 Aug 2019 22:46:33: 11000000 INFO @ Mon, 12 Aug 2019 22:46:34: 11000000 INFO @ Mon, 12 Aug 2019 22:46:38: 10000000 INFO @ Mon, 12 Aug 2019 22:46:40: 12000000 INFO @ Mon, 12 Aug 2019 22:46:41: 12000000 INFO @ Mon, 12 Aug 2019 22:46:45: 11000000 INFO @ Mon, 12 Aug 2019 22:46:47: 13000000 INFO @ Mon, 12 Aug 2019 22:46:47: 13000000 INFO @ Mon, 12 Aug 2019 22:46:53: 12000000 INFO @ Mon, 12 Aug 2019 22:46:53: 14000000 INFO @ Mon, 12 Aug 2019 22:46:54: 14000000 INFO @ Mon, 12 Aug 2019 22:47:00: 15000000 INFO @ Mon, 12 Aug 2019 22:47:01: 13000000 INFO @ Mon, 12 Aug 2019 22:47:01: 15000000 INFO @ Mon, 12 Aug 2019 22:47:07: 16000000 INFO @ Mon, 12 Aug 2019 22:47:08: 16000000 INFO @ Mon, 12 Aug 2019 22:47:09: 14000000 INFO @ Mon, 12 Aug 2019 22:47:14: 17000000 INFO @ Mon, 12 Aug 2019 22:47:15: 17000000 INFO @ Mon, 12 Aug 2019 22:47:16: 15000000 INFO @ Mon, 12 Aug 2019 22:47:21: 18000000 INFO @ Mon, 12 Aug 2019 22:47:22: 18000000 INFO @ Mon, 12 Aug 2019 22:47:24: 16000000 INFO @ Mon, 12 Aug 2019 22:47:28: 19000000 INFO @ Mon, 12 Aug 2019 22:47:28: 19000000 INFO @ Mon, 12 Aug 2019 22:47:32: 17000000 INFO @ Mon, 12 Aug 2019 22:47:34: 20000000 INFO @ Mon, 12 Aug 2019 22:47:35: 20000000 INFO @ Mon, 12 Aug 2019 22:47:40: 18000000 INFO @ Mon, 12 Aug 2019 22:47:41: 21000000 INFO @ Mon, 12 Aug 2019 22:47:42: 21000000 INFO @ Mon, 12 Aug 2019 22:47:47: 19000000 INFO @ Mon, 12 Aug 2019 22:47:48: 22000000 INFO @ Mon, 12 Aug 2019 22:47:49: 22000000 INFO @ Mon, 12 Aug 2019 22:47:55: 23000000 INFO @ Mon, 12 Aug 2019 22:47:55: 20000000 INFO @ Mon, 12 Aug 2019 22:47:56: 23000000 INFO @ Mon, 12 Aug 2019 22:48:02: 24000000 INFO @ Mon, 12 Aug 2019 22:48:02: 24000000 INFO @ Mon, 12 Aug 2019 22:48:03: 21000000 INFO @ Mon, 12 Aug 2019 22:48:09: 25000000 INFO @ Mon, 12 Aug 2019 22:48:09: 25000000 INFO @ Mon, 12 Aug 2019 22:48:10: 22000000 INFO @ Mon, 12 Aug 2019 22:48:15: 26000000 INFO @ Mon, 12 Aug 2019 22:48:16: 26000000 INFO @ Mon, 12 Aug 2019 22:48:18: 23000000 INFO @ Mon, 12 Aug 2019 22:48:22: 27000000 INFO @ Mon, 12 Aug 2019 22:48:23: 27000000 INFO @ Mon, 12 Aug 2019 22:48:26: 24000000 INFO @ Mon, 12 Aug 2019 22:48:29: 28000000 INFO @ Mon, 12 Aug 2019 22:48:30: 28000000 INFO @ Mon, 12 Aug 2019 22:48:34: 25000000 INFO @ Mon, 12 Aug 2019 22:48:34: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:48:34: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:48:34: #1 total tags in treatment: 28719926 INFO @ Mon, 12 Aug 2019 22:48:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:48:34: #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 22:48:35: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:48:35: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:48:35: #1 total tags in treatment: 28719926 INFO @ Mon, 12 Aug 2019 22:48:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:48:35: #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 22:48:35: #1 tags after filtering in treatment: 28719926 INFO @ Mon, 12 Aug 2019 22:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:48:35: #1 finished! INFO @ Mon, 12 Aug 2019 22:48:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:48:35: #1 tags after filtering in treatment: 28719926 INFO @ Mon, 12 Aug 2019 22:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:48:35: #1 finished! INFO @ Mon, 12 Aug 2019 22:48:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:48:38: #2 number of paired peaks: 2873 INFO @ Mon, 12 Aug 2019 22:48:38: start model_add_line... INFO @ Mon, 12 Aug 2019 22:48:38: start X-correlation... INFO @ Mon, 12 Aug 2019 22:48:38: end of X-cor INFO @ Mon, 12 Aug 2019 22:48:38: #2 finished! INFO @ Mon, 12 Aug 2019 22:48:38: #2 predicted fragment length is 217 bps INFO @ Mon, 12 Aug 2019 22:48:38: #2 alternative fragment length(s) may be 4,217 bps INFO @ Mon, 12 Aug 2019 22:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.05_model.r INFO @ Mon, 12 Aug 2019 22:48:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:48:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:48:38: #2 number of paired peaks: 2873 INFO @ Mon, 12 Aug 2019 22:48:38: start model_add_line... INFO @ Mon, 12 Aug 2019 22:48:39: start X-correlation... INFO @ Mon, 12 Aug 2019 22:48:39: end of X-cor INFO @ Mon, 12 Aug 2019 22:48:39: #2 finished! INFO @ Mon, 12 Aug 2019 22:48:39: #2 predicted fragment length is 217 bps INFO @ Mon, 12 Aug 2019 22:48:39: #2 alternative fragment length(s) may be 4,217 bps INFO @ Mon, 12 Aug 2019 22:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.10_model.r INFO @ Mon, 12 Aug 2019 22:48:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:48:41: 26000000 INFO @ Mon, 12 Aug 2019 22:48:49: 27000000 INFO @ Mon, 12 Aug 2019 22:48:56: 28000000 INFO @ Mon, 12 Aug 2019 22:49:02: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:49:02: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:49:02: #1 total tags in treatment: 28719926 INFO @ Mon, 12 Aug 2019 22:49:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:49:02: #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 22:49:03: #1 tags after filtering in treatment: 28719926 INFO @ Mon, 12 Aug 2019 22:49:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:49:03: #1 finished! INFO @ Mon, 12 Aug 2019 22:49:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:49:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:49:06: #2 number of paired peaks: 2873 INFO @ Mon, 12 Aug 2019 22:49:06: start model_add_line... INFO @ Mon, 12 Aug 2019 22:49:06: start X-correlation... INFO @ Mon, 12 Aug 2019 22:49:06: end of X-cor INFO @ Mon, 12 Aug 2019 22:49:06: #2 finished! INFO @ Mon, 12 Aug 2019 22:49:06: #2 predicted fragment length is 217 bps INFO @ Mon, 12 Aug 2019 22:49:06: #2 alternative fragment length(s) may be 4,217 bps INFO @ Mon, 12 Aug 2019 22:49:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.20_model.r INFO @ Mon, 12 Aug 2019 22:49:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:50:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:50:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:50:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:50:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.10_summits.bed INFO @ Mon, 12 Aug 2019 22:50:44: Done! INFO @ Mon, 12 Aug 2019 22:50:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:50:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.05_peaks.narrowPeak pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7853 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:50:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.05_summits.bed INFO @ Mon, 12 Aug 2019 22:50:44: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10253 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:51:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:51:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:51:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981730/SRX3981730.20_summits.bed INFO @ Mon, 12 Aug 2019 22:51:12: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5196 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。