Job ID = 2590850 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,305,535 reads read : 23,305,535 reads written : 23,305,535 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: 00:08:49 23305535 reads; of these: 23305535 (100.00%) were unpaired; of these: 4615436 (19.80%) aligned 0 times 14045056 (60.26%) aligned exactly 1 time 4645043 (19.93%) aligned >1 times 80.20% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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] 9314780 / 18690099 = 0.4984 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 23:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.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 23:56:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.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 23:56:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.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 23:56:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:30: 1000000 INFO @ Mon, 12 Aug 2019 23:56:31: 1000000 INFO @ Mon, 12 Aug 2019 23:56:32: 1000000 INFO @ Mon, 12 Aug 2019 23:56:39: 2000000 INFO @ Mon, 12 Aug 2019 23:56:40: 2000000 INFO @ Mon, 12 Aug 2019 23:56:42: 2000000 INFO @ Mon, 12 Aug 2019 23:56:49: 3000000 INFO @ Mon, 12 Aug 2019 23:56:50: 3000000 INFO @ Mon, 12 Aug 2019 23:56:52: 3000000 INFO @ Mon, 12 Aug 2019 23:56:58: 4000000 INFO @ Mon, 12 Aug 2019 23:56:59: 4000000 INFO @ Mon, 12 Aug 2019 23:57:01: 4000000 INFO @ Mon, 12 Aug 2019 23:57:07: 5000000 INFO @ Mon, 12 Aug 2019 23:57:08: 5000000 INFO @ Mon, 12 Aug 2019 23:57:11: 5000000 INFO @ Mon, 12 Aug 2019 23:57:16: 6000000 INFO @ Mon, 12 Aug 2019 23:57:17: 6000000 INFO @ Mon, 12 Aug 2019 23:57:21: 6000000 INFO @ Mon, 12 Aug 2019 23:57:26: 7000000 INFO @ Mon, 12 Aug 2019 23:57:27: 7000000 INFO @ Mon, 12 Aug 2019 23:57:30: 7000000 INFO @ Mon, 12 Aug 2019 23:57:35: 8000000 INFO @ Mon, 12 Aug 2019 23:57:36: 8000000 INFO @ Mon, 12 Aug 2019 23:57:40: 8000000 INFO @ Mon, 12 Aug 2019 23:57:44: 9000000 INFO @ Mon, 12 Aug 2019 23:57:45: 9000000 INFO @ Mon, 12 Aug 2019 23:57:48: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:57:48: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:57:48: #1 total tags in treatment: 9375319 INFO @ Mon, 12 Aug 2019 23:57:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:57:48: #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 23:57:48: #1 tags after filtering in treatment: 9375319 INFO @ Mon, 12 Aug 2019 23:57:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:57:48: #1 finished! INFO @ Mon, 12 Aug 2019 23:57:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:57:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:57:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:57:49: #1 total tags in treatment: 9375319 INFO @ Mon, 12 Aug 2019 23:57:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:57:49: #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 23:57:49: #1 tags after filtering in treatment: 9375319 INFO @ Mon, 12 Aug 2019 23:57:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:57:49: #1 finished! INFO @ Mon, 12 Aug 2019 23:57:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:57:49: #2 number of paired peaks: 2556 INFO @ Mon, 12 Aug 2019 23:57:49: start model_add_line... INFO @ Mon, 12 Aug 2019 23:57:49: start X-correlation... INFO @ Mon, 12 Aug 2019 23:57:49: end of X-cor INFO @ Mon, 12 Aug 2019 23:57:49: #2 finished! INFO @ Mon, 12 Aug 2019 23:57:49: #2 predicted fragment length is 120 bps INFO @ Mon, 12 Aug 2019 23:57:49: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 12 Aug 2019 23:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.05_model.r INFO @ Mon, 12 Aug 2019 23:57:50: 9000000 INFO @ Mon, 12 Aug 2019 23:57:50: #2 number of paired peaks: 2556 INFO @ Mon, 12 Aug 2019 23:57:50: start model_add_line... INFO @ Mon, 12 Aug 2019 23:57:50: start X-correlation... INFO @ Mon, 12 Aug 2019 23:57:50: end of X-cor INFO @ Mon, 12 Aug 2019 23:57:50: #2 finished! INFO @ Mon, 12 Aug 2019 23:57:50: #2 predicted fragment length is 120 bps INFO @ Mon, 12 Aug 2019 23:57:50: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 12 Aug 2019 23:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.10_model.r INFO @ Mon, 12 Aug 2019 23:57:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:57:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:57:53: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:57:53: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:57:53: #1 total tags in treatment: 9375319 INFO @ Mon, 12 Aug 2019 23:57:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:57:53: #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 23:57:53: #1 tags after filtering in treatment: 9375319 INFO @ Mon, 12 Aug 2019 23:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:57:53: #1 finished! INFO @ Mon, 12 Aug 2019 23:57:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:57:54: #2 number of paired peaks: 2556 INFO @ Mon, 12 Aug 2019 23:57:54: start model_add_line... INFO @ Mon, 12 Aug 2019 23:57:54: start X-correlation... INFO @ Mon, 12 Aug 2019 23:57:54: end of X-cor INFO @ Mon, 12 Aug 2019 23:57:54: #2 finished! INFO @ Mon, 12 Aug 2019 23:57:54: #2 predicted fragment length is 120 bps INFO @ Mon, 12 Aug 2019 23:57:54: #2 alternative fragment length(s) may be 120 bps INFO @ Mon, 12 Aug 2019 23:57:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.20_model.r INFO @ Mon, 12 Aug 2019 23:57:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:57:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:58:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:58:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:58:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:58:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:58:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:58:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:58:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.05_summits.bed INFO @ Mon, 12 Aug 2019 23:58:33: Done! INFO @ Mon, 12 Aug 2019 23:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.10_summits.bed INFO @ Mon, 12 Aug 2019 23:58:34: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9348 records, 4 fields): 19 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5889 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011084/SRX5011084.20_summits.bed INFO @ Mon, 12 Aug 2019 23:58:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3244 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。