Job ID = 2590859 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,180,841 reads read : 76,361,682 reads written : 38,180,841 reads 0-length : 38,180,841 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: 00:17:14 38180841 reads; of these: 38180841 (100.00%) were unpaired; of these: 3528340 (9.24%) aligned 0 times 24459913 (64.06%) aligned exactly 1 time 10192588 (26.70%) aligned >1 times 90.76% overall alignment rate Time searching: 00:17:14 Overall time: 00:17:14 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] 23354634 / 34652501 = 0.6740 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 00:11:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.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 00:11:07: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:11:07: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:11:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.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 00:11:08: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:11:08: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.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 00:11:09: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:11:09: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:11:14: 1000000 INFO @ Tue, 13 Aug 2019 00:11:15: 1000000 INFO @ Tue, 13 Aug 2019 00:11:16: 1000000 INFO @ Tue, 13 Aug 2019 00:11:21: 2000000 INFO @ Tue, 13 Aug 2019 00:11:22: 2000000 INFO @ Tue, 13 Aug 2019 00:11:24: 2000000 INFO @ Tue, 13 Aug 2019 00:11:27: 3000000 INFO @ Tue, 13 Aug 2019 00:11:28: 3000000 INFO @ Tue, 13 Aug 2019 00:11:31: 3000000 INFO @ Tue, 13 Aug 2019 00:11:34: 4000000 INFO @ Tue, 13 Aug 2019 00:11:35: 4000000 INFO @ Tue, 13 Aug 2019 00:11:38: 4000000 INFO @ Tue, 13 Aug 2019 00:11:41: 5000000 INFO @ Tue, 13 Aug 2019 00:11:42: 5000000 INFO @ Tue, 13 Aug 2019 00:11:46: 5000000 INFO @ Tue, 13 Aug 2019 00:11:47: 6000000 INFO @ Tue, 13 Aug 2019 00:11:48: 6000000 INFO @ Tue, 13 Aug 2019 00:11:53: 6000000 INFO @ Tue, 13 Aug 2019 00:11:54: 7000000 INFO @ Tue, 13 Aug 2019 00:11:55: 7000000 INFO @ Tue, 13 Aug 2019 00:12:00: 7000000 INFO @ Tue, 13 Aug 2019 00:12:00: 8000000 INFO @ Tue, 13 Aug 2019 00:12:01: 8000000 INFO @ Tue, 13 Aug 2019 00:12:07: 9000000 INFO @ Tue, 13 Aug 2019 00:12:07: 8000000 INFO @ Tue, 13 Aug 2019 00:12:08: 9000000 INFO @ Tue, 13 Aug 2019 00:12:13: 10000000 INFO @ Tue, 13 Aug 2019 00:12:14: 9000000 INFO @ Tue, 13 Aug 2019 00:12:14: 10000000 INFO @ Tue, 13 Aug 2019 00:12:20: 11000000 INFO @ Tue, 13 Aug 2019 00:12:21: 11000000 INFO @ Tue, 13 Aug 2019 00:12:21: 10000000 INFO @ Tue, 13 Aug 2019 00:12:22: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:12:22: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:12:22: #1 total tags in treatment: 11297867 INFO @ Tue, 13 Aug 2019 00:12:22: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:12:22: #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 00:12:22: #1 tags after filtering in treatment: 11297867 INFO @ Tue, 13 Aug 2019 00:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:12:22: #1 finished! INFO @ Tue, 13 Aug 2019 00:12:22: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:12:23: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:12:23: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:12:23: #1 total tags in treatment: 11297867 INFO @ Tue, 13 Aug 2019 00:12:23: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:12:23: #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 00:12:23: #1 tags after filtering in treatment: 11297867 INFO @ Tue, 13 Aug 2019 00:12:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:12:23: #1 finished! INFO @ Tue, 13 Aug 2019 00:12:23: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:12:24: #2 number of paired peaks: 3248 INFO @ Tue, 13 Aug 2019 00:12:24: start model_add_line... INFO @ Tue, 13 Aug 2019 00:12:24: start X-correlation... INFO @ Tue, 13 Aug 2019 00:12:24: end of X-cor INFO @ Tue, 13 Aug 2019 00:12:24: #2 finished! INFO @ Tue, 13 Aug 2019 00:12:24: #2 predicted fragment length is 148 bps INFO @ Tue, 13 Aug 2019 00:12:24: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 13 Aug 2019 00:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.05_model.r INFO @ Tue, 13 Aug 2019 00:12:24: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:12:25: #2 number of paired peaks: 3248 INFO @ Tue, 13 Aug 2019 00:12:25: start model_add_line... INFO @ Tue, 13 Aug 2019 00:12:25: start X-correlation... INFO @ Tue, 13 Aug 2019 00:12:25: end of X-cor INFO @ Tue, 13 Aug 2019 00:12:25: #2 finished! INFO @ Tue, 13 Aug 2019 00:12:25: #2 predicted fragment length is 148 bps INFO @ Tue, 13 Aug 2019 00:12:25: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 13 Aug 2019 00:12:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.10_model.r INFO @ Tue, 13 Aug 2019 00:12:25: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:12:28: 11000000 INFO @ Tue, 13 Aug 2019 00:12:31: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:12:31: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:12:31: #1 total tags in treatment: 11297867 INFO @ Tue, 13 Aug 2019 00:12:31: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:12:31: #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 00:12:31: #1 tags after filtering in treatment: 11297867 INFO @ Tue, 13 Aug 2019 00:12:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:12:31: #1 finished! INFO @ Tue, 13 Aug 2019 00:12:31: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:12:32: #2 number of paired peaks: 3248 INFO @ Tue, 13 Aug 2019 00:12:32: start model_add_line... INFO @ Tue, 13 Aug 2019 00:12:32: start X-correlation... INFO @ Tue, 13 Aug 2019 00:12:32: end of X-cor INFO @ Tue, 13 Aug 2019 00:12:32: #2 finished! INFO @ Tue, 13 Aug 2019 00:12:32: #2 predicted fragment length is 148 bps INFO @ Tue, 13 Aug 2019 00:12:32: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 13 Aug 2019 00:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.20_model.r INFO @ Tue, 13 Aug 2019 00:12:32: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:12:59: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:13:00: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:13:07: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.05_summits.bed INFO @ Tue, 13 Aug 2019 00:13:16: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9745 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.10_summits.bed INFO @ Tue, 13 Aug 2019 00:13:17: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6608 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:13:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:13:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:13:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011093/SRX5011093.20_summits.bed INFO @ Tue, 13 Aug 2019 00:13:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4225 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。