Job ID = 2589694 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,199,430 reads read : 7,199,430 reads written : 7,199,430 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947294.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: 00:01:09 7199430 reads; of these: 7199430 (100.00%) were unpaired; of these: 1005134 (13.96%) aligned 0 times 5316193 (73.84%) aligned exactly 1 time 878103 (12.20%) aligned >1 times 86.04% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 775857 / 6194296 = 0.1253 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 18:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.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 18:17:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:17:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:17:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.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 18:17:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:17:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.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 18:17:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:17:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:17:51: 1000000 INFO @ Mon, 12 Aug 2019 18:17:52: 1000000 INFO @ Mon, 12 Aug 2019 18:17:53: 1000000 INFO @ Mon, 12 Aug 2019 18:17:58: 2000000 INFO @ Mon, 12 Aug 2019 18:17:59: 2000000 INFO @ Mon, 12 Aug 2019 18:18:01: 2000000 INFO @ Mon, 12 Aug 2019 18:18:05: 3000000 INFO @ Mon, 12 Aug 2019 18:18:06: 3000000 INFO @ Mon, 12 Aug 2019 18:18:10: 3000000 INFO @ Mon, 12 Aug 2019 18:18:12: 4000000 INFO @ Mon, 12 Aug 2019 18:18:16: 4000000 INFO @ Mon, 12 Aug 2019 18:18:19: 4000000 INFO @ Mon, 12 Aug 2019 18:18:19: 5000000 INFO @ Mon, 12 Aug 2019 18:18:22: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:18:22: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:18:22: #1 total tags in treatment: 5418439 INFO @ Mon, 12 Aug 2019 18:18:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:18:22: #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 18:18:22: #1 tags after filtering in treatment: 5418439 INFO @ Mon, 12 Aug 2019 18:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:18:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:18:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:18:22: #2 number of paired peaks: 1114 INFO @ Mon, 12 Aug 2019 18:18:22: start model_add_line... INFO @ Mon, 12 Aug 2019 18:18:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:18:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:18:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:18:23: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 18:18:23: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 12 Aug 2019 18:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.20_model.r INFO @ Mon, 12 Aug 2019 18:18:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:18:23: 5000000 INFO @ Mon, 12 Aug 2019 18:18:25: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:18:25: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:18:25: #1 total tags in treatment: 5418439 INFO @ Mon, 12 Aug 2019 18:18:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:18:25: #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 18:18:26: #1 tags after filtering in treatment: 5418439 INFO @ Mon, 12 Aug 2019 18:18:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:18:26: #1 finished! INFO @ Mon, 12 Aug 2019 18:18:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:18:26: #2 number of paired peaks: 1114 INFO @ Mon, 12 Aug 2019 18:18:26: start model_add_line... INFO @ Mon, 12 Aug 2019 18:18:26: start X-correlation... INFO @ Mon, 12 Aug 2019 18:18:26: end of X-cor INFO @ Mon, 12 Aug 2019 18:18:26: #2 finished! INFO @ Mon, 12 Aug 2019 18:18:26: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 18:18:26: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 12 Aug 2019 18:18:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.05_model.r INFO @ Mon, 12 Aug 2019 18:18:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:18:27: 5000000 INFO @ Mon, 12 Aug 2019 18:18:30: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:18:30: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:18:30: #1 total tags in treatment: 5418439 INFO @ Mon, 12 Aug 2019 18:18:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:18:30: #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 18:18:30: #1 tags after filtering in treatment: 5418439 INFO @ Mon, 12 Aug 2019 18:18:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:18:30: #1 finished! INFO @ Mon, 12 Aug 2019 18:18:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:18:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:18:31: #2 number of paired peaks: 1114 INFO @ Mon, 12 Aug 2019 18:18:31: start model_add_line... INFO @ Mon, 12 Aug 2019 18:18:31: start X-correlation... INFO @ Mon, 12 Aug 2019 18:18:31: end of X-cor INFO @ Mon, 12 Aug 2019 18:18:31: #2 finished! INFO @ Mon, 12 Aug 2019 18:18:31: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 18:18:31: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 12 Aug 2019 18:18:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.10_model.r INFO @ Mon, 12 Aug 2019 18:18:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:18:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:18:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:18:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.20_summits.bed INFO @ Mon, 12 Aug 2019 18:18:47: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1693 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:18:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:18:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:18:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:18:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.05_summits.bed INFO @ Mon, 12 Aug 2019 18:18:51: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5055 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:18:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:18:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331070/SRX331070.10_summits.bed INFO @ Mon, 12 Aug 2019 18:18:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3275 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。