Job ID = 1300711 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,046,336 reads read : 27,046,336 reads written : 27,046,336 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: 00:06:46 27046336 reads; of these: 27046336 (100.00%) were unpaired; of these: 9987277 (36.93%) aligned 0 times 13303607 (49.19%) aligned exactly 1 time 3755452 (13.89%) aligned >1 times 63.07% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 8349278 / 17059059 = 0.4894 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 19:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.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 19:39:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:39:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.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 19:39:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:39:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.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 19:39:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:39:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:39:40: 1000000 INFO @ Mon, 03 Jun 2019 19:39:41: 1000000 INFO @ Mon, 03 Jun 2019 19:39:42: 1000000 INFO @ Mon, 03 Jun 2019 19:39:49: 2000000 INFO @ Mon, 03 Jun 2019 19:39:50: 2000000 INFO @ Mon, 03 Jun 2019 19:39:51: 2000000 INFO @ Mon, 03 Jun 2019 19:39:57: 3000000 INFO @ Mon, 03 Jun 2019 19:39:58: 3000000 INFO @ Mon, 03 Jun 2019 19:40:01: 3000000 INFO @ Mon, 03 Jun 2019 19:40:05: 4000000 INFO @ Mon, 03 Jun 2019 19:40:06: 4000000 INFO @ Mon, 03 Jun 2019 19:40:10: 4000000 INFO @ Mon, 03 Jun 2019 19:40:13: 5000000 INFO @ Mon, 03 Jun 2019 19:40:15: 5000000 INFO @ Mon, 03 Jun 2019 19:40:20: 5000000 INFO @ Mon, 03 Jun 2019 19:40:22: 6000000 INFO @ Mon, 03 Jun 2019 19:40:24: 6000000 INFO @ Mon, 03 Jun 2019 19:40:29: 6000000 INFO @ Mon, 03 Jun 2019 19:40:31: 7000000 INFO @ Mon, 03 Jun 2019 19:40:33: 7000000 INFO @ Mon, 03 Jun 2019 19:40:38: 7000000 INFO @ Mon, 03 Jun 2019 19:40:40: 8000000 INFO @ Mon, 03 Jun 2019 19:40:41: 8000000 INFO @ Mon, 03 Jun 2019 19:40:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:40:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:40:46: #1 total tags in treatment: 8709781 INFO @ Mon, 03 Jun 2019 19:40:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:40:46: #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 19:40:46: #1 tags after filtering in treatment: 8709781 INFO @ Mon, 03 Jun 2019 19:40:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:40:46: #1 finished! INFO @ Mon, 03 Jun 2019 19:40:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:40:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:40:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:40:47: #1 total tags in treatment: 8709781 INFO @ Mon, 03 Jun 2019 19:40:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:40:47: #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 19:40:47: #1 tags after filtering in treatment: 8709781 INFO @ Mon, 03 Jun 2019 19:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:40:47: #1 finished! INFO @ Mon, 03 Jun 2019 19:40:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:40:47: #2 number of paired peaks: 5066 INFO @ Mon, 03 Jun 2019 19:40:47: start model_add_line... INFO @ Mon, 03 Jun 2019 19:40:47: start X-correlation... INFO @ Mon, 03 Jun 2019 19:40:47: end of X-cor INFO @ Mon, 03 Jun 2019 19:40:47: #2 finished! INFO @ Mon, 03 Jun 2019 19:40:47: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 19:40:47: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 19:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.10_model.r INFO @ Mon, 03 Jun 2019 19:40:48: 8000000 INFO @ Mon, 03 Jun 2019 19:40:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:40:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:40:48: #2 number of paired peaks: 5066 INFO @ Mon, 03 Jun 2019 19:40:48: start model_add_line... INFO @ Mon, 03 Jun 2019 19:40:48: start X-correlation... INFO @ Mon, 03 Jun 2019 19:40:48: end of X-cor INFO @ Mon, 03 Jun 2019 19:40:48: #2 finished! INFO @ Mon, 03 Jun 2019 19:40:48: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 19:40:48: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 19:40:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.20_model.r INFO @ Mon, 03 Jun 2019 19:40:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:40:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:40:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:40:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:40:54: #1 total tags in treatment: 8709781 INFO @ Mon, 03 Jun 2019 19:40:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:40:54: #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 19:40:54: #1 tags after filtering in treatment: 8709781 INFO @ Mon, 03 Jun 2019 19:40:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:40:54: #1 finished! INFO @ Mon, 03 Jun 2019 19:40:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:40:55: #2 number of paired peaks: 5066 INFO @ Mon, 03 Jun 2019 19:40:55: start model_add_line... INFO @ Mon, 03 Jun 2019 19:40:56: start X-correlation... INFO @ Mon, 03 Jun 2019 19:40:56: end of X-cor INFO @ Mon, 03 Jun 2019 19:40:56: #2 finished! INFO @ Mon, 03 Jun 2019 19:40:56: #2 predicted fragment length is 210 bps INFO @ Mon, 03 Jun 2019 19:40:56: #2 alternative fragment length(s) may be 210 bps INFO @ Mon, 03 Jun 2019 19:40:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.05_model.r INFO @ Mon, 03 Jun 2019 19:40:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:41:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:41:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:41:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.10_summits.bed INFO @ Mon, 03 Jun 2019 19:41:32: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6915 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:41:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:41:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:41:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.20_summits.bed INFO @ Mon, 03 Jun 2019 19:41:34: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5813 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823791/SRX4823791.05_summits.bed INFO @ Mon, 03 Jun 2019 19:41:41: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7859 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。