Job ID = 1294413 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,856,669 reads read : 23,856,669 reads written : 23,856,669 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: 00:09:16 23856669 reads; of these: 23856669 (100.00%) were unpaired; of these: 1558767 (6.53%) aligned 0 times 16771969 (70.30%) aligned exactly 1 time 5525933 (23.16%) aligned >1 times 93.47% overall alignment rate Time searching: 00:09:16 Overall time: 00:09:16 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] 5431294 / 22297902 = 0.2436 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 07:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.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 07:51:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:51:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.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 07:51:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:51:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.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 07:51:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:51:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:51:16: 1000000 INFO @ Mon, 03 Jun 2019 07:51:17: 1000000 INFO @ Mon, 03 Jun 2019 07:51:17: 1000000 INFO @ Mon, 03 Jun 2019 07:51:24: 2000000 INFO @ Mon, 03 Jun 2019 07:51:27: 2000000 INFO @ Mon, 03 Jun 2019 07:51:27: 2000000 INFO @ Mon, 03 Jun 2019 07:51:31: 3000000 INFO @ Mon, 03 Jun 2019 07:51:35: 3000000 INFO @ Mon, 03 Jun 2019 07:51:35: 3000000 INFO @ Mon, 03 Jun 2019 07:51:38: 4000000 INFO @ Mon, 03 Jun 2019 07:51:44: 4000000 INFO @ Mon, 03 Jun 2019 07:51:44: 4000000 INFO @ Mon, 03 Jun 2019 07:51:46: 5000000 INFO @ Mon, 03 Jun 2019 07:51:52: 5000000 INFO @ Mon, 03 Jun 2019 07:51:52: 5000000 INFO @ Mon, 03 Jun 2019 07:51:53: 6000000 INFO @ Mon, 03 Jun 2019 07:51:59: 6000000 INFO @ Mon, 03 Jun 2019 07:52:00: 7000000 INFO @ Mon, 03 Jun 2019 07:52:01: 6000000 INFO @ Mon, 03 Jun 2019 07:52:07: 7000000 INFO @ Mon, 03 Jun 2019 07:52:08: 8000000 INFO @ Mon, 03 Jun 2019 07:52:09: 7000000 INFO @ Mon, 03 Jun 2019 07:52:15: 9000000 INFO @ Mon, 03 Jun 2019 07:52:16: 8000000 INFO @ Mon, 03 Jun 2019 07:52:17: 8000000 INFO @ Mon, 03 Jun 2019 07:52:23: 10000000 INFO @ Mon, 03 Jun 2019 07:52:24: 9000000 INFO @ Mon, 03 Jun 2019 07:52:25: 9000000 INFO @ Mon, 03 Jun 2019 07:52:30: 11000000 INFO @ Mon, 03 Jun 2019 07:52:32: 10000000 INFO @ Mon, 03 Jun 2019 07:52:34: 10000000 INFO @ Mon, 03 Jun 2019 07:52:37: 12000000 INFO @ Mon, 03 Jun 2019 07:52:40: 11000000 INFO @ Mon, 03 Jun 2019 07:52:42: 11000000 INFO @ Mon, 03 Jun 2019 07:52:45: 13000000 INFO @ Mon, 03 Jun 2019 07:52:48: 12000000 INFO @ Mon, 03 Jun 2019 07:52:50: 12000000 INFO @ Mon, 03 Jun 2019 07:52:52: 14000000 INFO @ Mon, 03 Jun 2019 07:52:55: 13000000 INFO @ Mon, 03 Jun 2019 07:52:59: 13000000 INFO @ Mon, 03 Jun 2019 07:52:59: 15000000 INFO @ Mon, 03 Jun 2019 07:53:03: 14000000 INFO @ Mon, 03 Jun 2019 07:53:07: 16000000 INFO @ Mon, 03 Jun 2019 07:53:07: 14000000 INFO @ Mon, 03 Jun 2019 07:53:10: 15000000 INFO @ Mon, 03 Jun 2019 07:53:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:53:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:53:13: #1 total tags in treatment: 16866608 INFO @ Mon, 03 Jun 2019 07:53:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:53:13: #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 07:53:13: #1 tags after filtering in treatment: 16866608 INFO @ Mon, 03 Jun 2019 07:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:53:13: #1 finished! INFO @ Mon, 03 Jun 2019 07:53:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:53:15: #2 number of paired peaks: 1850 INFO @ Mon, 03 Jun 2019 07:53:15: start model_add_line... INFO @ Mon, 03 Jun 2019 07:53:15: start X-correlation... INFO @ Mon, 03 Jun 2019 07:53:15: end of X-cor INFO @ Mon, 03 Jun 2019 07:53:15: #2 finished! INFO @ Mon, 03 Jun 2019 07:53:15: #2 predicted fragment length is 239 bps INFO @ Mon, 03 Jun 2019 07:53:15: #2 alternative fragment length(s) may be 239 bps INFO @ Mon, 03 Jun 2019 07:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.20_model.r INFO @ Mon, 03 Jun 2019 07:53:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:53:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:53:16: 15000000 INFO @ Mon, 03 Jun 2019 07:53:17: 16000000 INFO @ Mon, 03 Jun 2019 07:53:24: 16000000 INFO @ Mon, 03 Jun 2019 07:53:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:53:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:53:24: #1 total tags in treatment: 16866608 INFO @ Mon, 03 Jun 2019 07:53:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:53:24: #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 07:53:24: #1 tags after filtering in treatment: 16866608 INFO @ Mon, 03 Jun 2019 07:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:53:24: #1 finished! INFO @ Mon, 03 Jun 2019 07:53:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:53:26: #2 number of paired peaks: 1850 INFO @ Mon, 03 Jun 2019 07:53:26: start model_add_line... INFO @ Mon, 03 Jun 2019 07:53:26: start X-correlation... INFO @ Mon, 03 Jun 2019 07:53:26: end of X-cor INFO @ Mon, 03 Jun 2019 07:53:26: #2 finished! INFO @ Mon, 03 Jun 2019 07:53:26: #2 predicted fragment length is 239 bps INFO @ Mon, 03 Jun 2019 07:53:26: #2 alternative fragment length(s) may be 239 bps INFO @ Mon, 03 Jun 2019 07:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.05_model.r INFO @ Mon, 03 Jun 2019 07:53:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:53:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:53:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:53:31: #1 total tags in treatment: 16866608 INFO @ Mon, 03 Jun 2019 07:53:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:53:31: #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 07:53:32: #1 tags after filtering in treatment: 16866608 INFO @ Mon, 03 Jun 2019 07:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:53:32: #1 finished! INFO @ Mon, 03 Jun 2019 07:53:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:53:33: #2 number of paired peaks: 1850 INFO @ Mon, 03 Jun 2019 07:53:33: start model_add_line... INFO @ Mon, 03 Jun 2019 07:53:33: start X-correlation... INFO @ Mon, 03 Jun 2019 07:53:33: end of X-cor INFO @ Mon, 03 Jun 2019 07:53:33: #2 finished! INFO @ Mon, 03 Jun 2019 07:53:33: #2 predicted fragment length is 239 bps INFO @ Mon, 03 Jun 2019 07:53:33: #2 alternative fragment length(s) may be 239 bps INFO @ Mon, 03 Jun 2019 07:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.10_model.r INFO @ Mon, 03 Jun 2019 07:53:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:54:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:54:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:54:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:54:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.20_summits.bed INFO @ Mon, 03 Jun 2019 07:54:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4191 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:54:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:54:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:54:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.05_summits.bed INFO @ Mon, 03 Jun 2019 07:54:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7143 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287585/SRX287585.10_summits.bed INFO @ Mon, 03 Jun 2019 07:54:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5314 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。