Job ID = 1291531 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,873,247 reads read : 6,873,247 reads written : 6,873,247 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: 00:02:06 6873247 reads; of these: 6873247 (100.00%) were unpaired; of these: 270670 (3.94%) aligned 0 times 4498691 (65.45%) aligned exactly 1 time 2103886 (30.61%) aligned >1 times 96.06% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 2286304 / 6602577 = 0.3463 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 16:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.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 16:00:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:00:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.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 16:00:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:00:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.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 16:00:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:00:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:00:43: 1000000 INFO @ Sun, 02 Jun 2019 16:00:43: 1000000 INFO @ Sun, 02 Jun 2019 16:00:45: 1000000 INFO @ Sun, 02 Jun 2019 16:00:49: 2000000 INFO @ Sun, 02 Jun 2019 16:00:50: 2000000 INFO @ Sun, 02 Jun 2019 16:00:54: 2000000 INFO @ Sun, 02 Jun 2019 16:00:56: 3000000 INFO @ Sun, 02 Jun 2019 16:00:58: 3000000 INFO @ Sun, 02 Jun 2019 16:01:02: 4000000 INFO @ Sun, 02 Jun 2019 16:01:03: 3000000 INFO @ Sun, 02 Jun 2019 16:01:05: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:01:05: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:01:05: #1 total tags in treatment: 4316273 INFO @ Sun, 02 Jun 2019 16:01:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:01:05: #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 16:01:05: #1 tags after filtering in treatment: 4316273 INFO @ Sun, 02 Jun 2019 16:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:01:05: #1 finished! INFO @ Sun, 02 Jun 2019 16:01:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:01:05: 4000000 INFO @ Sun, 02 Jun 2019 16:01:05: #2 number of paired peaks: 4049 INFO @ Sun, 02 Jun 2019 16:01:05: start model_add_line... INFO @ Sun, 02 Jun 2019 16:01:05: start X-correlation... INFO @ Sun, 02 Jun 2019 16:01:05: end of X-cor INFO @ Sun, 02 Jun 2019 16:01:05: #2 finished! INFO @ Sun, 02 Jun 2019 16:01:05: #2 predicted fragment length is 159 bps INFO @ Sun, 02 Jun 2019 16:01:05: #2 alternative fragment length(s) may be 1,159 bps INFO @ Sun, 02 Jun 2019 16:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.05_model.r INFO @ Sun, 02 Jun 2019 16:01:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:01:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:01:07: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:01:07: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:01:07: #1 total tags in treatment: 4316273 INFO @ Sun, 02 Jun 2019 16:01:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:01:07: #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 16:01:07: #1 tags after filtering in treatment: 4316273 INFO @ Sun, 02 Jun 2019 16:01:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:01:07: #1 finished! INFO @ Sun, 02 Jun 2019 16:01:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:01:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:01:08: #2 number of paired peaks: 4049 INFO @ Sun, 02 Jun 2019 16:01:08: start model_add_line... INFO @ Sun, 02 Jun 2019 16:01:08: start X-correlation... INFO @ Sun, 02 Jun 2019 16:01:08: end of X-cor INFO @ Sun, 02 Jun 2019 16:01:08: #2 finished! INFO @ Sun, 02 Jun 2019 16:01:08: #2 predicted fragment length is 159 bps INFO @ Sun, 02 Jun 2019 16:01:08: #2 alternative fragment length(s) may be 1,159 bps INFO @ Sun, 02 Jun 2019 16:01:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.20_model.r INFO @ Sun, 02 Jun 2019 16:01:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:01:12: 4000000 INFO @ Sun, 02 Jun 2019 16:01:14: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:01:14: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:01:14: #1 total tags in treatment: 4316273 INFO @ Sun, 02 Jun 2019 16:01:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:01:14: #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 16:01:14: #1 tags after filtering in treatment: 4316273 INFO @ Sun, 02 Jun 2019 16:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:01:14: #1 finished! INFO @ Sun, 02 Jun 2019 16:01:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:01:15: #2 number of paired peaks: 4049 INFO @ Sun, 02 Jun 2019 16:01:15: start model_add_line... INFO @ Sun, 02 Jun 2019 16:01:15: start X-correlation... INFO @ Sun, 02 Jun 2019 16:01:15: end of X-cor INFO @ Sun, 02 Jun 2019 16:01:15: #2 finished! INFO @ Sun, 02 Jun 2019 16:01:15: #2 predicted fragment length is 159 bps INFO @ Sun, 02 Jun 2019 16:01:15: #2 alternative fragment length(s) may be 1,159 bps INFO @ Sun, 02 Jun 2019 16:01:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.10_model.r INFO @ Sun, 02 Jun 2019 16:01:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:01:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:01:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.05_summits.bed INFO @ Sun, 02 Jun 2019 16:01:27: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1076 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:01:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:01:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.20_summits.bed INFO @ Sun, 02 Jun 2019 16:01:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:01:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:01:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:01:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:01:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113620/SRX113620.10_summits.bed INFO @ Sun, 02 Jun 2019 16:01:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (354 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。