Job ID = 2589760 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,294,213 reads read : 4,294,213 reads written : 4,294,213 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947365.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: 00:00:29 4294213 reads; of these: 4294213 (100.00%) were unpaired; of these: 2575936 (59.99%) aligned 0 times 1530406 (35.64%) aligned exactly 1 time 187871 (4.37%) aligned >1 times 40.01% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 475632 / 1718277 = 0.2768 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 18:24:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.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 18:24:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:24:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.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 18:24:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:24:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.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 18:24:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:24:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:24:39: 1000000 INFO @ Mon, 12 Aug 2019 18:24:40: 1000000 INFO @ Mon, 12 Aug 2019 18:24:41: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:24:41: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:24:41: #1 total tags in treatment: 1242645 INFO @ Mon, 12 Aug 2019 18:24:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:24:41: #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 18:24:41: #1 tags after filtering in treatment: 1242645 INFO @ Mon, 12 Aug 2019 18:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:24:41: #1 finished! INFO @ Mon, 12 Aug 2019 18:24:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:24:41: 1000000 INFO @ Mon, 12 Aug 2019 18:24:41: #2 number of paired peaks: 3641 INFO @ Mon, 12 Aug 2019 18:24:41: start model_add_line... INFO @ Mon, 12 Aug 2019 18:24:41: start X-correlation... INFO @ Mon, 12 Aug 2019 18:24:41: end of X-cor INFO @ Mon, 12 Aug 2019 18:24:41: #2 finished! INFO @ Mon, 12 Aug 2019 18:24:41: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 18:24:41: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 18:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.05_model.r INFO @ Mon, 12 Aug 2019 18:24:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:24:42: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:24:42: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:24:42: #1 total tags in treatment: 1242645 INFO @ Mon, 12 Aug 2019 18:24:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:24:42: #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 18:24:42: #1 tags after filtering in treatment: 1242645 INFO @ Mon, 12 Aug 2019 18:24:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:24:42: #1 finished! INFO @ Mon, 12 Aug 2019 18:24:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:24:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:24:43: #2 number of paired peaks: 3641 INFO @ Mon, 12 Aug 2019 18:24:43: start model_add_line... INFO @ Mon, 12 Aug 2019 18:24:43: start X-correlation... INFO @ Mon, 12 Aug 2019 18:24:43: end of X-cor INFO @ Mon, 12 Aug 2019 18:24:43: #2 finished! INFO @ Mon, 12 Aug 2019 18:24:43: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 18:24:43: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 18:24:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.10_model.r INFO @ Mon, 12 Aug 2019 18:24:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:24:43: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:24:43: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:24:43: #1 total tags in treatment: 1242645 INFO @ Mon, 12 Aug 2019 18:24:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:24:43: #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 18:24:43: #1 tags after filtering in treatment: 1242645 INFO @ Mon, 12 Aug 2019 18:24:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:24:43: #1 finished! INFO @ Mon, 12 Aug 2019 18:24:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:24:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:24:43: #2 number of paired peaks: 3641 INFO @ Mon, 12 Aug 2019 18:24:43: start model_add_line... INFO @ Mon, 12 Aug 2019 18:24:43: start X-correlation... INFO @ Mon, 12 Aug 2019 18:24:43: end of X-cor INFO @ Mon, 12 Aug 2019 18:24:43: #2 finished! INFO @ Mon, 12 Aug 2019 18:24:43: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 18:24:43: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 18:24:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.20_model.r INFO @ Mon, 12 Aug 2019 18:24:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:24:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:24:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:24:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:24:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:24:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:24:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.05_summits.bed INFO @ Mon, 12 Aug 2019 18:24:48: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4028 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.10_summits.bed INFO @ Mon, 12 Aug 2019 18:24:49: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2086 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331134/SRX331134.20_summits.bed INFO @ Mon, 12 Aug 2019 18:24:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (700 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。