Job ID = 1294003 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,231,400 reads read : 28,231,400 reads written : 28,231,400 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:10:48 28231400 reads; of these: 28231400 (100.00%) were unpaired; of these: 5538875 (19.62%) aligned 0 times 15616500 (55.32%) aligned exactly 1 time 7076025 (25.06%) aligned >1 times 80.38% overall alignment rate Time searching: 00:10:48 Overall time: 00:10:48 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] 3780147 / 22692525 = 0.1666 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, 03 Jun 2019 04:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.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, 03 Jun 2019 04:20:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:20:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.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, 03 Jun 2019 04:20:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:20:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.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, 03 Jun 2019 04:20:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:20:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:20:53: 1000000 INFO @ Mon, 03 Jun 2019 04:20:54: 1000000 INFO @ Mon, 03 Jun 2019 04:20:54: 1000000 INFO @ Mon, 03 Jun 2019 04:21:02: 2000000 INFO @ Mon, 03 Jun 2019 04:21:02: 2000000 INFO @ Mon, 03 Jun 2019 04:21:02: 2000000 INFO @ Mon, 03 Jun 2019 04:21:10: 3000000 INFO @ Mon, 03 Jun 2019 04:21:11: 3000000 INFO @ Mon, 03 Jun 2019 04:21:11: 3000000 INFO @ Mon, 03 Jun 2019 04:21:19: 4000000 INFO @ Mon, 03 Jun 2019 04:21:20: 4000000 INFO @ Mon, 03 Jun 2019 04:21:20: 4000000 INFO @ Mon, 03 Jun 2019 04:21:28: 5000000 INFO @ Mon, 03 Jun 2019 04:21:28: 5000000 INFO @ Mon, 03 Jun 2019 04:21:28: 5000000 INFO @ Mon, 03 Jun 2019 04:21:36: 6000000 INFO @ Mon, 03 Jun 2019 04:21:37: 6000000 INFO @ Mon, 03 Jun 2019 04:21:37: 6000000 INFO @ Mon, 03 Jun 2019 04:21:45: 7000000 INFO @ Mon, 03 Jun 2019 04:21:46: 7000000 INFO @ Mon, 03 Jun 2019 04:21:46: 7000000 INFO @ Mon, 03 Jun 2019 04:21:53: 8000000 INFO @ Mon, 03 Jun 2019 04:21:55: 8000000 INFO @ Mon, 03 Jun 2019 04:21:55: 8000000 INFO @ Mon, 03 Jun 2019 04:22:02: 9000000 INFO @ Mon, 03 Jun 2019 04:22:03: 9000000 INFO @ Mon, 03 Jun 2019 04:22:03: 9000000 INFO @ Mon, 03 Jun 2019 04:22:10: 10000000 INFO @ Mon, 03 Jun 2019 04:22:12: 10000000 INFO @ Mon, 03 Jun 2019 04:22:12: 10000000 INFO @ Mon, 03 Jun 2019 04:22:19: 11000000 INFO @ Mon, 03 Jun 2019 04:22:21: 11000000 INFO @ Mon, 03 Jun 2019 04:22:21: 11000000 INFO @ Mon, 03 Jun 2019 04:22:27: 12000000 INFO @ Mon, 03 Jun 2019 04:22:29: 12000000 INFO @ Mon, 03 Jun 2019 04:22:30: 12000000 INFO @ Mon, 03 Jun 2019 04:22:36: 13000000 INFO @ Mon, 03 Jun 2019 04:22:38: 13000000 INFO @ Mon, 03 Jun 2019 04:22:38: 13000000 INFO @ Mon, 03 Jun 2019 04:22:45: 14000000 INFO @ Mon, 03 Jun 2019 04:22:47: 14000000 INFO @ Mon, 03 Jun 2019 04:22:47: 14000000 INFO @ Mon, 03 Jun 2019 04:22:53: 15000000 INFO @ Mon, 03 Jun 2019 04:22:56: 15000000 INFO @ Mon, 03 Jun 2019 04:22:56: 15000000 INFO @ Mon, 03 Jun 2019 04:23:02: 16000000 INFO @ Mon, 03 Jun 2019 04:23:04: 16000000 INFO @ Mon, 03 Jun 2019 04:23:05: 16000000 INFO @ Mon, 03 Jun 2019 04:23:10: 17000000 INFO @ Mon, 03 Jun 2019 04:23:13: 17000000 INFO @ Mon, 03 Jun 2019 04:23:13: 17000000 INFO @ Mon, 03 Jun 2019 04:23:19: 18000000 INFO @ Mon, 03 Jun 2019 04:23:22: 18000000 INFO @ Mon, 03 Jun 2019 04:23:22: 18000000 INFO @ Mon, 03 Jun 2019 04:23:27: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 04:23:27: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 04:23:27: #1 total tags in treatment: 18912378 INFO @ Mon, 03 Jun 2019 04:23:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:23:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:23:27: #1 tags after filtering in treatment: 18912378 INFO @ Mon, 03 Jun 2019 04:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:23:27: #1 finished! INFO @ Mon, 03 Jun 2019 04:23:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:23:29: #2 number of paired peaks: 1040 INFO @ Mon, 03 Jun 2019 04:23:29: start model_add_line... INFO @ Mon, 03 Jun 2019 04:23:29: start X-correlation... INFO @ Mon, 03 Jun 2019 04:23:29: end of X-cor INFO @ Mon, 03 Jun 2019 04:23:29: #2 finished! INFO @ Mon, 03 Jun 2019 04:23:29: #2 predicted fragment length is 113 bps INFO @ Mon, 03 Jun 2019 04:23:29: #2 alternative fragment length(s) may be 113 bps INFO @ Mon, 03 Jun 2019 04:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.05_model.r INFO @ Mon, 03 Jun 2019 04:23:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:23:30: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 04:23:30: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 04:23:30: #1 total tags in treatment: 18912378 INFO @ Mon, 03 Jun 2019 04:23:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:23:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:23:30: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 04:23:30: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 04:23:30: #1 total tags in treatment: 18912378 INFO @ Mon, 03 Jun 2019 04:23:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:23:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:23:30: #1 tags after filtering in treatment: 18912378 INFO @ Mon, 03 Jun 2019 04:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:23:30: #1 finished! INFO @ Mon, 03 Jun 2019 04:23:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:23:31: #1 tags after filtering in treatment: 18912378 INFO @ Mon, 03 Jun 2019 04:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:23:31: #1 finished! INFO @ Mon, 03 Jun 2019 04:23:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:23:32: #2 number of paired peaks: 1040 INFO @ Mon, 03 Jun 2019 04:23:32: start model_add_line... INFO @ Mon, 03 Jun 2019 04:23:32: start X-correlation... INFO @ Mon, 03 Jun 2019 04:23:32: end of X-cor INFO @ Mon, 03 Jun 2019 04:23:32: #2 finished! INFO @ Mon, 03 Jun 2019 04:23:32: #2 predicted fragment length is 113 bps INFO @ Mon, 03 Jun 2019 04:23:32: #2 alternative fragment length(s) may be 113 bps INFO @ Mon, 03 Jun 2019 04:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.20_model.r INFO @ Mon, 03 Jun 2019 04:23:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:23:32: #2 number of paired peaks: 1040 INFO @ Mon, 03 Jun 2019 04:23:32: start model_add_line... INFO @ Mon, 03 Jun 2019 04:23:33: start X-correlation... INFO @ Mon, 03 Jun 2019 04:23:33: end of X-cor INFO @ Mon, 03 Jun 2019 04:23:33: #2 finished! INFO @ Mon, 03 Jun 2019 04:23:33: #2 predicted fragment length is 113 bps INFO @ Mon, 03 Jun 2019 04:23:33: #2 alternative fragment length(s) may be 113 bps INFO @ Mon, 03 Jun 2019 04:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.10_model.r INFO @ Mon, 03 Jun 2019 04:23:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:24:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:24:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:24:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:24:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.05_summits.bed INFO @ Mon, 03 Jun 2019 04:24:52: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8775 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:24:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:24:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:24:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.20_summits.bed INFO @ Mon, 03 Jun 2019 04:24:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4151 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:24:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:24:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:24:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159174/SRX159174.10_summits.bed INFO @ Mon, 03 Jun 2019 04:24:55: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6265 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。