Job ID = 2590928 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,593,623 reads read : 15,593,623 reads written : 15,593,623 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: 00:04:45 15593623 reads; of these: 15593623 (100.00%) were unpaired; of these: 754002 (4.84%) aligned 0 times 12505598 (80.20%) aligned exactly 1 time 2334023 (14.97%) aligned >1 times 95.16% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1761595 / 14839621 = 0.1187 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 @ Tue, 13 Aug 2019 00:11:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.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 @ Tue, 13 Aug 2019 00:11:17: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:11:17: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:11:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.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 @ Tue, 13 Aug 2019 00:11:17: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:11:17: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:11:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.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 @ Tue, 13 Aug 2019 00:11:18: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:11:18: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:11:26: 1000000 INFO @ Tue, 13 Aug 2019 00:11:29: 1000000 INFO @ Tue, 13 Aug 2019 00:11:30: 1000000 INFO @ Tue, 13 Aug 2019 00:11:34: 2000000 INFO @ Tue, 13 Aug 2019 00:11:40: 2000000 INFO @ Tue, 13 Aug 2019 00:11:41: 2000000 INFO @ Tue, 13 Aug 2019 00:11:43: 3000000 INFO @ Tue, 13 Aug 2019 00:11:51: 3000000 INFO @ Tue, 13 Aug 2019 00:11:51: 4000000 INFO @ Tue, 13 Aug 2019 00:11:52: 3000000 INFO @ Tue, 13 Aug 2019 00:12:00: 5000000 INFO @ Tue, 13 Aug 2019 00:12:01: 4000000 INFO @ Tue, 13 Aug 2019 00:12:02: 4000000 INFO @ Tue, 13 Aug 2019 00:12:09: 6000000 INFO @ Tue, 13 Aug 2019 00:12:13: 5000000 INFO @ Tue, 13 Aug 2019 00:12:14: 5000000 INFO @ Tue, 13 Aug 2019 00:12:19: 7000000 INFO @ Tue, 13 Aug 2019 00:12:24: 6000000 INFO @ Tue, 13 Aug 2019 00:12:25: 6000000 INFO @ Tue, 13 Aug 2019 00:12:28: 8000000 INFO @ Tue, 13 Aug 2019 00:12:36: 7000000 INFO @ Tue, 13 Aug 2019 00:12:37: 7000000 INFO @ Tue, 13 Aug 2019 00:12:38: 9000000 INFO @ Tue, 13 Aug 2019 00:12:47: 10000000 INFO @ Tue, 13 Aug 2019 00:12:47: 8000000 INFO @ Tue, 13 Aug 2019 00:12:48: 8000000 INFO @ Tue, 13 Aug 2019 00:12:56: 11000000 INFO @ Tue, 13 Aug 2019 00:12:58: 9000000 INFO @ Tue, 13 Aug 2019 00:12:59: 9000000 INFO @ Tue, 13 Aug 2019 00:13:06: 12000000 INFO @ Tue, 13 Aug 2019 00:13:09: 10000000 INFO @ Tue, 13 Aug 2019 00:13:10: 10000000 INFO @ Tue, 13 Aug 2019 00:13:15: 13000000 INFO @ Tue, 13 Aug 2019 00:13:16: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:13:16: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:13:16: #1 total tags in treatment: 13078026 INFO @ Tue, 13 Aug 2019 00:13:16: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:13:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:13:16: #1 tags after filtering in treatment: 13078026 INFO @ Tue, 13 Aug 2019 00:13:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:13:16: #1 finished! INFO @ Tue, 13 Aug 2019 00:13:16: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:13:18: #2 number of paired peaks: 7163 INFO @ Tue, 13 Aug 2019 00:13:18: start model_add_line... INFO @ Tue, 13 Aug 2019 00:13:18: start X-correlation... INFO @ Tue, 13 Aug 2019 00:13:19: end of X-cor INFO @ Tue, 13 Aug 2019 00:13:19: #2 finished! INFO @ Tue, 13 Aug 2019 00:13:19: #2 predicted fragment length is 166 bps INFO @ Tue, 13 Aug 2019 00:13:19: #2 alternative fragment length(s) may be 2,153,166 bps INFO @ Tue, 13 Aug 2019 00:13:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.05_model.r INFO @ Tue, 13 Aug 2019 00:13:19: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:13:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:13:20: 11000000 INFO @ Tue, 13 Aug 2019 00:13:21: 11000000 INFO @ Tue, 13 Aug 2019 00:13:31: 12000000 INFO @ Tue, 13 Aug 2019 00:13:32: 12000000 INFO @ Tue, 13 Aug 2019 00:13:42: 13000000 INFO @ Tue, 13 Aug 2019 00:13:42: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:13:42: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:13:42: #1 total tags in treatment: 13078026 INFO @ Tue, 13 Aug 2019 00:13:42: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:13:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:13:42: 13000000 INFO @ Tue, 13 Aug 2019 00:13:43: #1 tags after filtering in treatment: 13078026 INFO @ Tue, 13 Aug 2019 00:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:13:43: #1 finished! INFO @ Tue, 13 Aug 2019 00:13:43: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:13:43: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:13:43: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:13:43: #1 total tags in treatment: 13078026 INFO @ Tue, 13 Aug 2019 00:13:43: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:13:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:13:43: #1 tags after filtering in treatment: 13078026 INFO @ Tue, 13 Aug 2019 00:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:13:43: #1 finished! INFO @ Tue, 13 Aug 2019 00:13:43: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:13:45: #2 number of paired peaks: 7163 INFO @ Tue, 13 Aug 2019 00:13:45: start model_add_line... INFO @ Tue, 13 Aug 2019 00:13:45: start X-correlation... INFO @ Tue, 13 Aug 2019 00:13:45: end of X-cor INFO @ Tue, 13 Aug 2019 00:13:45: #2 finished! INFO @ Tue, 13 Aug 2019 00:13:45: #2 predicted fragment length is 166 bps INFO @ Tue, 13 Aug 2019 00:13:45: #2 alternative fragment length(s) may be 2,153,166 bps INFO @ Tue, 13 Aug 2019 00:13:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.10_model.r INFO @ Tue, 13 Aug 2019 00:13:45: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:13:45: #2 number of paired peaks: 7163 INFO @ Tue, 13 Aug 2019 00:13:45: start model_add_line... INFO @ Tue, 13 Aug 2019 00:13:46: start X-correlation... INFO @ Tue, 13 Aug 2019 00:13:46: end of X-cor INFO @ Tue, 13 Aug 2019 00:13:46: #2 finished! INFO @ Tue, 13 Aug 2019 00:13:46: #2 predicted fragment length is 166 bps INFO @ Tue, 13 Aug 2019 00:13:46: #2 alternative fragment length(s) may be 2,153,166 bps INFO @ Tue, 13 Aug 2019 00:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.20_model.r INFO @ Tue, 13 Aug 2019 00:13:46: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:13:58: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:14:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:14:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:14:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.05_summits.bed INFO @ Tue, 13 Aug 2019 00:14:17: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6757 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:14:24: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:14:25: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:14:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:14:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:14:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.10_summits.bed INFO @ Tue, 13 Aug 2019 00:14:42: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4298 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:14:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:14:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:14:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5431040/SRX5431040.20_summits.bed INFO @ Tue, 13 Aug 2019 00:14:42: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1461 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。