Job ID = 2590669 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,506,346 reads read : 47,012,692 reads written : 23,506,346 reads 0-length : 23,506,346 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: 00:09:17 23506346 reads; of these: 23506346 (100.00%) were unpaired; of these: 1960473 (8.34%) aligned 0 times 16818817 (71.55%) aligned exactly 1 time 4727056 (20.11%) aligned >1 times 91.66% overall alignment rate Time searching: 00:09:17 Overall time: 00:09:17 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] 10635672 / 21545873 = 0.4936 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 23:19:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.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 23:19:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:19:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:19:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.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 23:19:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:19:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:19:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.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 23:19:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:19:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:19:26: 1000000 INFO @ Mon, 12 Aug 2019 23:19:26: 1000000 INFO @ Mon, 12 Aug 2019 23:19:27: 1000000 INFO @ Mon, 12 Aug 2019 23:19:33: 2000000 INFO @ Mon, 12 Aug 2019 23:19:34: 2000000 INFO @ Mon, 12 Aug 2019 23:19:35: 2000000 INFO @ Mon, 12 Aug 2019 23:19:40: 3000000 INFO @ Mon, 12 Aug 2019 23:19:42: 3000000 INFO @ Mon, 12 Aug 2019 23:19:43: 3000000 INFO @ Mon, 12 Aug 2019 23:19:48: 4000000 INFO @ Mon, 12 Aug 2019 23:19:50: 4000000 INFO @ Mon, 12 Aug 2019 23:19:52: 4000000 INFO @ Mon, 12 Aug 2019 23:19:55: 5000000 INFO @ Mon, 12 Aug 2019 23:20:00: 5000000 INFO @ Mon, 12 Aug 2019 23:20:03: 5000000 INFO @ Mon, 12 Aug 2019 23:20:04: 6000000 INFO @ Mon, 12 Aug 2019 23:20:08: 6000000 INFO @ Mon, 12 Aug 2019 23:20:11: 7000000 INFO @ Mon, 12 Aug 2019 23:20:11: 6000000 INFO @ Mon, 12 Aug 2019 23:20:15: 7000000 INFO @ Mon, 12 Aug 2019 23:20:18: 8000000 INFO @ Mon, 12 Aug 2019 23:20:20: 7000000 INFO @ Mon, 12 Aug 2019 23:20:22: 8000000 INFO @ Mon, 12 Aug 2019 23:20:24: 9000000 INFO @ Mon, 12 Aug 2019 23:20:28: 8000000 INFO @ Mon, 12 Aug 2019 23:20:29: 9000000 INFO @ Mon, 12 Aug 2019 23:20:31: 10000000 INFO @ Mon, 12 Aug 2019 23:20:37: 10000000 INFO @ Mon, 12 Aug 2019 23:20:37: 9000000 INFO @ Mon, 12 Aug 2019 23:20:38: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:20:38: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:20:38: #1 total tags in treatment: 10910201 INFO @ Mon, 12 Aug 2019 23:20:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:20:38: #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 23:20:38: #1 tags after filtering in treatment: 10910201 INFO @ Mon, 12 Aug 2019 23:20:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:20:38: #1 finished! INFO @ Mon, 12 Aug 2019 23:20:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:20:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:20:39: #2 number of paired peaks: 2563 INFO @ Mon, 12 Aug 2019 23:20:39: start model_add_line... INFO @ Mon, 12 Aug 2019 23:20:39: start X-correlation... INFO @ Mon, 12 Aug 2019 23:20:39: end of X-cor INFO @ Mon, 12 Aug 2019 23:20:39: #2 finished! INFO @ Mon, 12 Aug 2019 23:20:39: #2 predicted fragment length is 210 bps INFO @ Mon, 12 Aug 2019 23:20:39: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 12 Aug 2019 23:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.20_model.r INFO @ Mon, 12 Aug 2019 23:20:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:20:43: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:20:43: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:20:43: #1 total tags in treatment: 10910201 INFO @ Mon, 12 Aug 2019 23:20:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:20:43: #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 23:20:43: #1 tags after filtering in treatment: 10910201 INFO @ Mon, 12 Aug 2019 23:20:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:20:43: #1 finished! INFO @ Mon, 12 Aug 2019 23:20:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:20:45: 10000000 INFO @ Mon, 12 Aug 2019 23:20:45: #2 number of paired peaks: 2563 INFO @ Mon, 12 Aug 2019 23:20:45: start model_add_line... INFO @ Mon, 12 Aug 2019 23:20:45: start X-correlation... INFO @ Mon, 12 Aug 2019 23:20:45: end of X-cor INFO @ Mon, 12 Aug 2019 23:20:45: #2 finished! INFO @ Mon, 12 Aug 2019 23:20:45: #2 predicted fragment length is 210 bps INFO @ Mon, 12 Aug 2019 23:20:45: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 12 Aug 2019 23:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.05_model.r INFO @ Mon, 12 Aug 2019 23:20:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:20:52: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:20:52: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:20:52: #1 total tags in treatment: 10910201 INFO @ Mon, 12 Aug 2019 23:20:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:20:52: #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 23:20:52: #1 tags after filtering in treatment: 10910201 INFO @ Mon, 12 Aug 2019 23:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:20:52: #1 finished! INFO @ Mon, 12 Aug 2019 23:20:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:20:53: #2 number of paired peaks: 2563 INFO @ Mon, 12 Aug 2019 23:20:53: start model_add_line... INFO @ Mon, 12 Aug 2019 23:20:54: start X-correlation... INFO @ Mon, 12 Aug 2019 23:20:54: end of X-cor INFO @ Mon, 12 Aug 2019 23:20:54: #2 finished! INFO @ Mon, 12 Aug 2019 23:20:54: #2 predicted fragment length is 210 bps INFO @ Mon, 12 Aug 2019 23:20:54: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 12 Aug 2019 23:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.10_model.r INFO @ Mon, 12 Aug 2019 23:20:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:21:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:21:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:21:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.20_summits.bed INFO @ Mon, 12 Aug 2019 23:21:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4366 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:21:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:21:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:21:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.05_summits.bed INFO @ Mon, 12 Aug 2019 23:21:39: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9866 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011018/SRX5011018.10_summits.bed INFO @ Mon, 12 Aug 2019 23:21:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7162 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。