Job ID = 2590040 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,576,402 reads read : 37,576,402 reads written : 37,576,402 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: 00:09:21 37576402 reads; of these: 37576402 (100.00%) were unpaired; of these: 5674608 (15.10%) aligned 0 times 26140646 (69.57%) aligned exactly 1 time 5761148 (15.33%) aligned >1 times 84.90% overall alignment rate Time searching: 00:09:21 Overall time: 00:09:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 25937133 / 31901794 = 0.8130 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 19:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.bam'] # control file = None # effective genome size = 9.00e+07 # 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 19:45:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:45:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.bam'] # control file = None # effective genome size = 9.00e+07 # 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 19:45:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:45:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.bam'] # control file = None # effective genome size = 9.00e+07 # 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 19:45:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:45:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:45:40: 1000000 INFO @ Mon, 12 Aug 2019 19:45:41: 1000000 INFO @ Mon, 12 Aug 2019 19:45:42: 1000000 INFO @ Mon, 12 Aug 2019 19:45:47: 2000000 INFO @ Mon, 12 Aug 2019 19:45:48: 2000000 INFO @ Mon, 12 Aug 2019 19:45:49: 2000000 INFO @ Mon, 12 Aug 2019 19:45:54: 3000000 INFO @ Mon, 12 Aug 2019 19:45:55: 3000000 INFO @ Mon, 12 Aug 2019 19:45:56: 3000000 INFO @ Mon, 12 Aug 2019 19:46:01: 4000000 INFO @ Mon, 12 Aug 2019 19:46:02: 4000000 INFO @ Mon, 12 Aug 2019 19:46:03: 4000000 INFO @ Mon, 12 Aug 2019 19:46:08: 5000000 INFO @ Mon, 12 Aug 2019 19:46:09: 5000000 INFO @ Mon, 12 Aug 2019 19:46:10: 5000000 INFO @ Mon, 12 Aug 2019 19:46:15: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:46:15: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:46:15: #1 total tags in treatment: 5964661 INFO @ Mon, 12 Aug 2019 19:46:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:46:15: #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 19:46:15: #1 tags after filtering in treatment: 5964661 INFO @ Mon, 12 Aug 2019 19:46:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:46:15: #1 finished! INFO @ Mon, 12 Aug 2019 19:46:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:46:16: #2 number of paired peaks: 1486 INFO @ Mon, 12 Aug 2019 19:46:16: start model_add_line... INFO @ Mon, 12 Aug 2019 19:46:16: start X-correlation... INFO @ Mon, 12 Aug 2019 19:46:16: end of X-cor INFO @ Mon, 12 Aug 2019 19:46:16: #2 finished! INFO @ Mon, 12 Aug 2019 19:46:16: #2 predicted fragment length is 106 bps INFO @ Mon, 12 Aug 2019 19:46:16: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 12 Aug 2019 19:46:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.05_model.r INFO @ Mon, 12 Aug 2019 19:46:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:46:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:46:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:46:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:46:16: #1 total tags in treatment: 5964661 INFO @ Mon, 12 Aug 2019 19:46:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:46:16: #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 19:46:16: #1 tags after filtering in treatment: 5964661 INFO @ Mon, 12 Aug 2019 19:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:46:16: #1 finished! INFO @ Mon, 12 Aug 2019 19:46:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:46:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:46:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:46:17: #1 total tags in treatment: 5964661 INFO @ Mon, 12 Aug 2019 19:46:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:46:17: #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 19:46:17: #1 tags after filtering in treatment: 5964661 INFO @ Mon, 12 Aug 2019 19:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:46:17: #1 finished! INFO @ Mon, 12 Aug 2019 19:46:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:46:17: #2 number of paired peaks: 1486 INFO @ Mon, 12 Aug 2019 19:46:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:46:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:46:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:46:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:46:17: #2 predicted fragment length is 106 bps INFO @ Mon, 12 Aug 2019 19:46:17: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 12 Aug 2019 19:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.10_model.r INFO @ Mon, 12 Aug 2019 19:46:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:46:18: #2 number of paired peaks: 1486 INFO @ Mon, 12 Aug 2019 19:46:18: start model_add_line... INFO @ Mon, 12 Aug 2019 19:46:18: start X-correlation... INFO @ Mon, 12 Aug 2019 19:46:18: end of X-cor INFO @ Mon, 12 Aug 2019 19:46:18: #2 finished! INFO @ Mon, 12 Aug 2019 19:46:18: #2 predicted fragment length is 106 bps INFO @ Mon, 12 Aug 2019 19:46:18: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 12 Aug 2019 19:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.20_model.r INFO @ Mon, 12 Aug 2019 19:46:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:46:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:46:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:46:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.05_summits.bed INFO @ Mon, 12 Aug 2019 19:46:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4836 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.10_summits.bed INFO @ Mon, 12 Aug 2019 19:46:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2785 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:46:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:46:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:46:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494884/SRX494884.20_summits.bed INFO @ Mon, 12 Aug 2019 19:46:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1352 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。