Job ID = 1291532 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,751,200 reads read : 7,751,200 reads written : 7,751,200 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:18 7751200 reads; of these: 7751200 (100.00%) were unpaired; of these: 333069 (4.30%) aligned 0 times 5160433 (66.58%) aligned exactly 1 time 2257698 (29.13%) aligned >1 times 95.70% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 3359457 / 7418131 = 0.4529 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 @ Sun, 02 Jun 2019 16:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.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 @ Sun, 02 Jun 2019 16:03:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.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 @ Sun, 02 Jun 2019 16:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.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 @ Sun, 02 Jun 2019 16:03:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:04:02: 1000000 INFO @ Sun, 02 Jun 2019 16:04:02: 1000000 INFO @ Sun, 02 Jun 2019 16:04:02: 1000000 INFO @ Sun, 02 Jun 2019 16:04:18: 2000000 INFO @ Sun, 02 Jun 2019 16:04:18: 2000000 INFO @ Sun, 02 Jun 2019 16:04:18: 2000000 INFO @ Sun, 02 Jun 2019 16:04:35: 3000000 INFO @ Sun, 02 Jun 2019 16:04:35: 3000000 INFO @ Sun, 02 Jun 2019 16:04:35: 3000000 INFO @ Sun, 02 Jun 2019 16:04:50: 4000000 INFO @ Sun, 02 Jun 2019 16:04:50: 4000000 INFO @ Sun, 02 Jun 2019 16:04:50: 4000000 INFO @ Sun, 02 Jun 2019 16:04:50: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:04:50: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:04:50: #1 total tags in treatment: 4058674 INFO @ Sun, 02 Jun 2019 16:04:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:04:50: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:04:50: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:04:50: #1 total tags in treatment: 4058674 INFO @ Sun, 02 Jun 2019 16:04:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:04:50: #1 tags after filtering in treatment: 4058674 INFO @ Sun, 02 Jun 2019 16:04:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:50: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:51: #1 tags after filtering in treatment: 4058674 INFO @ Sun, 02 Jun 2019 16:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:51: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:51: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:04:51: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:04:51: #1 total tags in treatment: 4058674 INFO @ Sun, 02 Jun 2019 16:04:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:04:51: #1 tags after filtering in treatment: 4058674 INFO @ Sun, 02 Jun 2019 16:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:51: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:52: #2 number of paired peaks: 3635 INFO @ Sun, 02 Jun 2019 16:04:52: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:52: #2 number of paired peaks: 3635 INFO @ Sun, 02 Jun 2019 16:04:52: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:52: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:52: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:52: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:52: #2 predicted fragment length is 180 bps INFO @ Sun, 02 Jun 2019 16:04:52: #2 alternative fragment length(s) may be 1,180 bps INFO @ Sun, 02 Jun 2019 16:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.10_model.r INFO @ Sun, 02 Jun 2019 16:04:52: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:52: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:52: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:52: #2 predicted fragment length is 180 bps INFO @ Sun, 02 Jun 2019 16:04:52: #2 alternative fragment length(s) may be 1,180 bps INFO @ Sun, 02 Jun 2019 16:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.05_model.r INFO @ Sun, 02 Jun 2019 16:04:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:52: #2 number of paired peaks: 3635 INFO @ Sun, 02 Jun 2019 16:04:52: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:52: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:52: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:52: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:52: #2 predicted fragment length is 180 bps INFO @ Sun, 02 Jun 2019 16:04:52: #2 alternative fragment length(s) may be 1,180 bps INFO @ Sun, 02 Jun 2019 16:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.20_model.r INFO @ Sun, 02 Jun 2019 16:04:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:05:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:05:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:05:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.05_summits.bed INFO @ Sun, 02 Jun 2019 16:05:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1437 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:05:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:05:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:05:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.10_summits.bed INFO @ Sun, 02 Jun 2019 16:05:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:05:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:05:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:05:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113621/SRX113621.20_summits.bed INFO @ Sun, 02 Jun 2019 16:05:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。