Job ID = 2589685 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,030,633 reads read : 3,030,633 reads written : 3,030,633 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947286.sra.cache’: 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: 00:00:12 3030633 reads; of these: 3030633 (100.00%) were unpaired; of these: 2767617 (91.32%) aligned 0 times 207451 (6.85%) aligned exactly 1 time 55565 (1.83%) aligned >1 times 8.68% overall alignment rate Time searching: 00:00:12 Overall time: 00:00:12 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_rmdupse_core] 14533 / 263016 = 0.0553 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 18:14:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.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 18:14:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:14:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.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 18:14:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:14:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:14:03: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:03: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:03: #1 total tags in treatment: 248483 INFO @ Mon, 12 Aug 2019 18:14:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:03: #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 18:14:03: #1 tags after filtering in treatment: 248483 INFO @ Mon, 12 Aug 2019 18:14:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:03: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.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 18:14:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:14:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:14:03: #2 number of paired peaks: 1941 INFO @ Mon, 12 Aug 2019 18:14:03: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:03: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:03: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:03: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:03: #2 predicted fragment length is 129 bps INFO @ Mon, 12 Aug 2019 18:14:03: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 12 Aug 2019 18:14:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.05_model.r INFO @ Mon, 12 Aug 2019 18:14:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:04: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:04: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:04: #1 total tags in treatment: 248483 INFO @ Mon, 12 Aug 2019 18:14:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:04: #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 18:14:04: #1 tags after filtering in treatment: 248483 INFO @ Mon, 12 Aug 2019 18:14:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:04: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:04: #2 number of paired peaks: 1941 INFO @ Mon, 12 Aug 2019 18:14:04: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:04: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:04: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:04: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:04: #2 predicted fragment length is 129 bps INFO @ Mon, 12 Aug 2019 18:14:04: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 12 Aug 2019 18:14:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.10_model.r INFO @ Mon, 12 Aug 2019 18:14:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.05_summits.bed INFO @ Mon, 12 Aug 2019 18:14:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:14:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:05: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:05: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:05: #1 total tags in treatment: 248483 INFO @ Mon, 12 Aug 2019 18:14:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:05: #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 18:14:05: #1 tags after filtering in treatment: 248483 INFO @ Mon, 12 Aug 2019 18:14:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:05: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:05: #2 number of paired peaks: 1941 INFO @ Mon, 12 Aug 2019 18:14:05: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:05: start X-correlation... BedGraph に変換しました。 INFO @ Mon, 12 Aug 2019 18:14:05: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:05: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:05: #2 predicted fragment length is 129 bps INFO @ Mon, 12 Aug 2019 18:14:05: #2 alternative fragment length(s) may be 129 bps INFO @ Mon, 12 Aug 2019 18:14:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.20_model.r BigWig に変換中... INFO @ Mon, 12 Aug 2019 18:14:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.10_summits.bed INFO @ Mon, 12 Aug 2019 18:14:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 18:14:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331062/SRX331062.20_summits.bed INFO @ Mon, 12 Aug 2019 18:14:06: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (74 records, 4 fields): 6 millis CompletedMACS2peakCalling