Job ID = 2589147 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,599,715 reads read : 3,599,715 reads written : 3,599,715 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107348.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: 00:00:40 3599715 reads; of these: 3599715 (100.00%) were unpaired; of these: 978560 (27.18%) aligned 0 times 2337574 (64.94%) aligned exactly 1 time 283581 (7.88%) aligned >1 times 72.82% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 341666 / 2621155 = 0.1303 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 17:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.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 17:01:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:01:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.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 17:01:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:01:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.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 17:01:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:01:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:01:25: 1000000 INFO @ Mon, 12 Aug 2019 17:01:25: 1000000 INFO @ Mon, 12 Aug 2019 17:01:25: 1000000 INFO @ Mon, 12 Aug 2019 17:01:32: 2000000 INFO @ Mon, 12 Aug 2019 17:01:34: 2000000 INFO @ Mon, 12 Aug 2019 17:01:34: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:01:34: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:01:34: #1 total tags in treatment: 2279489 INFO @ Mon, 12 Aug 2019 17:01:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:01:34: #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 17:01:34: #1 tags after filtering in treatment: 2279489 INFO @ Mon, 12 Aug 2019 17:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:01:34: #1 finished! INFO @ Mon, 12 Aug 2019 17:01:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:01:35: #2 number of paired peaks: 3351 INFO @ Mon, 12 Aug 2019 17:01:35: start model_add_line... INFO @ Mon, 12 Aug 2019 17:01:35: start X-correlation... INFO @ Mon, 12 Aug 2019 17:01:35: end of X-cor INFO @ Mon, 12 Aug 2019 17:01:35: #2 finished! INFO @ Mon, 12 Aug 2019 17:01:35: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 17:01:35: #2 alternative fragment length(s) may be 148 bps INFO @ Mon, 12 Aug 2019 17:01:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.20_model.r INFO @ Mon, 12 Aug 2019 17:01:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:01:35: 2000000 INFO @ Mon, 12 Aug 2019 17:01:36: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:01:36: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:01:36: #1 total tags in treatment: 2279489 INFO @ Mon, 12 Aug 2019 17:01:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:01:36: #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 17:01:36: #1 tags after filtering in treatment: 2279489 INFO @ Mon, 12 Aug 2019 17:01:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:01:36: #1 finished! INFO @ Mon, 12 Aug 2019 17:01:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:01:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:01:36: #2 number of paired peaks: 3351 INFO @ Mon, 12 Aug 2019 17:01:36: start model_add_line... INFO @ Mon, 12 Aug 2019 17:01:36: start X-correlation... INFO @ Mon, 12 Aug 2019 17:01:36: end of X-cor INFO @ Mon, 12 Aug 2019 17:01:36: #2 finished! INFO @ Mon, 12 Aug 2019 17:01:36: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 17:01:36: #2 alternative fragment length(s) may be 148 bps INFO @ Mon, 12 Aug 2019 17:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.10_model.r INFO @ Mon, 12 Aug 2019 17:01:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:01:38: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:01:38: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:01:38: #1 total tags in treatment: 2279489 INFO @ Mon, 12 Aug 2019 17:01:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:01:38: #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 17:01:38: #1 tags after filtering in treatment: 2279489 INFO @ Mon, 12 Aug 2019 17:01:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:01:38: #1 finished! INFO @ Mon, 12 Aug 2019 17:01:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:01:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:01:38: #2 number of paired peaks: 3351 INFO @ Mon, 12 Aug 2019 17:01:38: start model_add_line... INFO @ Mon, 12 Aug 2019 17:01:38: start X-correlation... INFO @ Mon, 12 Aug 2019 17:01:38: end of X-cor INFO @ Mon, 12 Aug 2019 17:01:38: #2 finished! INFO @ Mon, 12 Aug 2019 17:01:38: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 17:01:38: #2 alternative fragment length(s) may be 148 bps INFO @ Mon, 12 Aug 2019 17:01:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.05_model.r INFO @ Mon, 12 Aug 2019 17:01:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:01:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:01:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:01:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:01:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.20_summits.bed INFO @ Mon, 12 Aug 2019 17:01:47: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (328 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:01:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:01:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:01:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.10_summits.bed INFO @ Mon, 12 Aug 2019 17:01:48: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1310 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043876/SRX043876.05_summits.bed INFO @ Mon, 12 Aug 2019 17:01:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3195 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。