Job ID = 1294989 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,086,246 reads read : 17,086,246 reads written : 17,086,246 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: 00:04:43 17086246 reads; of these: 17086246 (100.00%) were unpaired; of these: 806830 (4.72%) aligned 0 times 13808267 (80.82%) aligned exactly 1 time 2471149 (14.46%) aligned >1 times 95.28% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 2431958 / 16279416 = 0.1494 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 11:21:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.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 11:21:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:21:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:21:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.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 11:21:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:21:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:21:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.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 11:21:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:21:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:22:05: 1000000 INFO @ Mon, 03 Jun 2019 11:22:05: 1000000 INFO @ Mon, 03 Jun 2019 11:22:07: 1000000 INFO @ Mon, 03 Jun 2019 11:22:12: 2000000 INFO @ Mon, 03 Jun 2019 11:22:13: 2000000 INFO @ Mon, 03 Jun 2019 11:22:17: 2000000 INFO @ Mon, 03 Jun 2019 11:22:19: 3000000 INFO @ Mon, 03 Jun 2019 11:22:21: 3000000 INFO @ Mon, 03 Jun 2019 11:22:27: 4000000 INFO @ Mon, 03 Jun 2019 11:22:28: 3000000 INFO @ Mon, 03 Jun 2019 11:22:30: 4000000 INFO @ Mon, 03 Jun 2019 11:22:35: 5000000 INFO @ Mon, 03 Jun 2019 11:22:38: 5000000 INFO @ Mon, 03 Jun 2019 11:22:39: 4000000 INFO @ Mon, 03 Jun 2019 11:22:42: 6000000 INFO @ Mon, 03 Jun 2019 11:22:45: 6000000 INFO @ Mon, 03 Jun 2019 11:22:49: 7000000 INFO @ Mon, 03 Jun 2019 11:22:51: 5000000 INFO @ Mon, 03 Jun 2019 11:22:55: 7000000 INFO @ Mon, 03 Jun 2019 11:22:56: 8000000 INFO @ Mon, 03 Jun 2019 11:23:01: 6000000 INFO @ Mon, 03 Jun 2019 11:23:03: 8000000 INFO @ Mon, 03 Jun 2019 11:23:03: 9000000 INFO @ Mon, 03 Jun 2019 11:23:10: 10000000 INFO @ Mon, 03 Jun 2019 11:23:10: 9000000 INFO @ Mon, 03 Jun 2019 11:23:11: 7000000 INFO @ Mon, 03 Jun 2019 11:23:17: 11000000 INFO @ Mon, 03 Jun 2019 11:23:19: 10000000 INFO @ Mon, 03 Jun 2019 11:23:21: 8000000 INFO @ Mon, 03 Jun 2019 11:23:24: 12000000 INFO @ Mon, 03 Jun 2019 11:23:27: 11000000 INFO @ Mon, 03 Jun 2019 11:23:31: 13000000 INFO @ Mon, 03 Jun 2019 11:23:31: 9000000 INFO @ Mon, 03 Jun 2019 11:23:34: 12000000 INFO @ Mon, 03 Jun 2019 11:23:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:23:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:23:38: #1 total tags in treatment: 13847458 INFO @ Mon, 03 Jun 2019 11:23:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:23:38: #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 11:23:38: #1 tags after filtering in treatment: 13847458 INFO @ Mon, 03 Jun 2019 11:23:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:23:38: #1 finished! INFO @ Mon, 03 Jun 2019 11:23:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:23:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:23:39: #2 number of paired peaks: 3377 INFO @ Mon, 03 Jun 2019 11:23:39: start model_add_line... INFO @ Mon, 03 Jun 2019 11:23:40: start X-correlation... INFO @ Mon, 03 Jun 2019 11:23:40: end of X-cor INFO @ Mon, 03 Jun 2019 11:23:40: #2 finished! INFO @ Mon, 03 Jun 2019 11:23:40: #2 predicted fragment length is 203 bps INFO @ Mon, 03 Jun 2019 11:23:40: #2 alternative fragment length(s) may be 2,187,203 bps INFO @ Mon, 03 Jun 2019 11:23:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.20_model.r INFO @ Mon, 03 Jun 2019 11:23:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:23:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:23:42: 10000000 INFO @ Mon, 03 Jun 2019 11:23:42: 13000000 INFO @ Mon, 03 Jun 2019 11:23:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:23:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:23:49: #1 total tags in treatment: 13847458 INFO @ Mon, 03 Jun 2019 11:23:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:23:49: #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 11:23:49: #1 tags after filtering in treatment: 13847458 INFO @ Mon, 03 Jun 2019 11:23:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:23:49: #1 finished! INFO @ Mon, 03 Jun 2019 11:23:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:23:51: #2 number of paired peaks: 3377 INFO @ Mon, 03 Jun 2019 11:23:51: start model_add_line... INFO @ Mon, 03 Jun 2019 11:23:51: start X-correlation... INFO @ Mon, 03 Jun 2019 11:23:51: end of X-cor INFO @ Mon, 03 Jun 2019 11:23:51: #2 finished! INFO @ Mon, 03 Jun 2019 11:23:51: #2 predicted fragment length is 203 bps INFO @ Mon, 03 Jun 2019 11:23:51: #2 alternative fragment length(s) may be 2,187,203 bps INFO @ Mon, 03 Jun 2019 11:23:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.10_model.r INFO @ Mon, 03 Jun 2019 11:23:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:23:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:23:52: 11000000 INFO @ Mon, 03 Jun 2019 11:24:02: 12000000 INFO @ Mon, 03 Jun 2019 11:24:12: 13000000 INFO @ Mon, 03 Jun 2019 11:24:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:24:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:24:21: #1 total tags in treatment: 13847458 INFO @ Mon, 03 Jun 2019 11:24:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:24:21: #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 11:24:21: #1 tags after filtering in treatment: 13847458 INFO @ Mon, 03 Jun 2019 11:24:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:24:21: #1 finished! INFO @ Mon, 03 Jun 2019 11:24:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:24:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:24:23: #2 number of paired peaks: 3377 INFO @ Mon, 03 Jun 2019 11:24:23: start model_add_line... INFO @ Mon, 03 Jun 2019 11:24:23: start X-correlation... INFO @ Mon, 03 Jun 2019 11:24:23: end of X-cor INFO @ Mon, 03 Jun 2019 11:24:23: #2 finished! INFO @ Mon, 03 Jun 2019 11:24:23: #2 predicted fragment length is 203 bps INFO @ Mon, 03 Jun 2019 11:24:23: #2 alternative fragment length(s) may be 2,187,203 bps INFO @ Mon, 03 Jun 2019 11:24:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.05_model.r INFO @ Mon, 03 Jun 2019 11:24:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:24:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:24:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:24:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.20_summits.bed INFO @ Mon, 03 Jun 2019 11:24:47: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1408 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.10_summits.bed INFO @ Mon, 03 Jun 2019 11:25:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4818 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:25:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:25:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:25:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:25:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288045/SRX288045.05_summits.bed INFO @ Mon, 03 Jun 2019 11:25:33: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9354 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。