Job ID = 1295049 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 47,702,706 reads read : 47,702,706 reads written : 47,702,706 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: 00:15:37 47702706 reads; of these: 47702706 (100.00%) were unpaired; of these: 2865665 (6.01%) aligned 0 times 34830242 (73.02%) aligned exactly 1 time 10006799 (20.98%) aligned >1 times 93.99% overall alignment rate Time searching: 00:15:37 Overall time: 00:15:37 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 20 files... [bam_rmdupse_core] 34539002 / 44837041 = 0.7703 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 12:13:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.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 12:13:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:13:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:13:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.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 12:13:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:13:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:13:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.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 12:13:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:13:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:13:31: 1000000 INFO @ Mon, 03 Jun 2019 12:13:32: 1000000 INFO @ Mon, 03 Jun 2019 12:13:32: 1000000 INFO @ Mon, 03 Jun 2019 12:13:38: 2000000 INFO @ Mon, 03 Jun 2019 12:13:40: 2000000 INFO @ Mon, 03 Jun 2019 12:13:40: 2000000 INFO @ Mon, 03 Jun 2019 12:13:45: 3000000 INFO @ Mon, 03 Jun 2019 12:13:47: 3000000 INFO @ Mon, 03 Jun 2019 12:13:48: 3000000 INFO @ Mon, 03 Jun 2019 12:13:52: 4000000 INFO @ Mon, 03 Jun 2019 12:13:55: 4000000 INFO @ Mon, 03 Jun 2019 12:13:55: 4000000 INFO @ Mon, 03 Jun 2019 12:13:59: 5000000 INFO @ Mon, 03 Jun 2019 12:14:03: 5000000 INFO @ Mon, 03 Jun 2019 12:14:04: 5000000 INFO @ Mon, 03 Jun 2019 12:14:06: 6000000 INFO @ Mon, 03 Jun 2019 12:14:12: 6000000 INFO @ Mon, 03 Jun 2019 12:14:13: 6000000 INFO @ Mon, 03 Jun 2019 12:14:13: 7000000 INFO @ Mon, 03 Jun 2019 12:14:20: 8000000 INFO @ Mon, 03 Jun 2019 12:14:20: 7000000 INFO @ Mon, 03 Jun 2019 12:14:21: 7000000 INFO @ Mon, 03 Jun 2019 12:14:27: 9000000 INFO @ Mon, 03 Jun 2019 12:14:29: 8000000 INFO @ Mon, 03 Jun 2019 12:14:29: 8000000 INFO @ Mon, 03 Jun 2019 12:14:34: 10000000 INFO @ Mon, 03 Jun 2019 12:14:36: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:14:36: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:14:36: #1 total tags in treatment: 10298039 INFO @ Mon, 03 Jun 2019 12:14:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:14:36: #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 12:14:36: #1 tags after filtering in treatment: 10298039 INFO @ Mon, 03 Jun 2019 12:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:14:36: #1 finished! INFO @ Mon, 03 Jun 2019 12:14:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:14:37: 9000000 INFO @ Mon, 03 Jun 2019 12:14:37: #2 number of paired peaks: 2491 INFO @ Mon, 03 Jun 2019 12:14:37: start model_add_line... INFO @ Mon, 03 Jun 2019 12:14:37: start X-correlation... INFO @ Mon, 03 Jun 2019 12:14:37: end of X-cor INFO @ Mon, 03 Jun 2019 12:14:37: #2 finished! INFO @ Mon, 03 Jun 2019 12:14:37: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 12:14:37: #2 alternative fragment length(s) may be 103 bps INFO @ Mon, 03 Jun 2019 12:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.05_model.r INFO @ Mon, 03 Jun 2019 12:14:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:14:38: 9000000 INFO @ Mon, 03 Jun 2019 12:14:45: 10000000 INFO @ Mon, 03 Jun 2019 12:14:46: 10000000 INFO @ Mon, 03 Jun 2019 12:14:47: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:14:47: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:14:47: #1 total tags in treatment: 10298039 INFO @ Mon, 03 Jun 2019 12:14:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:14:47: #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 12:14:48: #1 tags after filtering in treatment: 10298039 INFO @ Mon, 03 Jun 2019 12:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:14:48: #1 finished! INFO @ Mon, 03 Jun 2019 12:14:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:14:48: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 12:14:48: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 12:14:48: #1 total tags in treatment: 10298039 INFO @ Mon, 03 Jun 2019 12:14:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:14:48: #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 12:14:48: #1 tags after filtering in treatment: 10298039 INFO @ Mon, 03 Jun 2019 12:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:14:48: #1 finished! INFO @ Mon, 03 Jun 2019 12:14:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:14:49: #2 number of paired peaks: 2491 INFO @ Mon, 03 Jun 2019 12:14:49: start model_add_line... INFO @ Mon, 03 Jun 2019 12:14:49: start X-correlation... INFO @ Mon, 03 Jun 2019 12:14:49: end of X-cor INFO @ Mon, 03 Jun 2019 12:14:49: #2 finished! INFO @ Mon, 03 Jun 2019 12:14:49: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 12:14:49: #2 alternative fragment length(s) may be 103 bps INFO @ Mon, 03 Jun 2019 12:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.10_model.r INFO @ Mon, 03 Jun 2019 12:14:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:14:49: #2 number of paired peaks: 2491 INFO @ Mon, 03 Jun 2019 12:14:49: start model_add_line... INFO @ Mon, 03 Jun 2019 12:14:50: start X-correlation... INFO @ Mon, 03 Jun 2019 12:14:50: end of X-cor INFO @ Mon, 03 Jun 2019 12:14:50: #2 finished! INFO @ Mon, 03 Jun 2019 12:14:50: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 12:14:50: #2 alternative fragment length(s) may be 103 bps INFO @ Mon, 03 Jun 2019 12:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.20_model.r INFO @ Mon, 03 Jun 2019 12:14:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:15:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:15:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:15:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:15:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:15:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.05_summits.bed INFO @ Mon, 03 Jun 2019 12:15:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5975 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:15:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.10_summits.bed INFO @ Mon, 03 Jun 2019 12:15:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3301 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:15:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167244/SRX3167244.20_summits.bed INFO @ Mon, 03 Jun 2019 12:15:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1584 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。