Job ID = 1292344 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,309,088 reads read : 10,309,088 reads written : 10,309,088 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: 00:01:48 10309088 reads; of these: 10309088 (100.00%) were unpaired; of these: 182537 (1.77%) aligned 0 times 8816332 (85.52%) aligned exactly 1 time 1310219 (12.71%) aligned >1 times 98.23% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 2387196 / 10126551 = 0.2357 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 18:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.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 18:01:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.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 18:01:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.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 18:01:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:11: 1000000 INFO @ Sun, 02 Jun 2019 18:01:12: 1000000 INFO @ Sun, 02 Jun 2019 18:01:12: 1000000 INFO @ Sun, 02 Jun 2019 18:01:18: 2000000 INFO @ Sun, 02 Jun 2019 18:01:20: 2000000 INFO @ Sun, 02 Jun 2019 18:01:20: 2000000 INFO @ Sun, 02 Jun 2019 18:01:25: 3000000 INFO @ Sun, 02 Jun 2019 18:01:28: 3000000 INFO @ Sun, 02 Jun 2019 18:01:28: 3000000 INFO @ Sun, 02 Jun 2019 18:01:31: 4000000 INFO @ Sun, 02 Jun 2019 18:01:35: 4000000 INFO @ Sun, 02 Jun 2019 18:01:35: 4000000 INFO @ Sun, 02 Jun 2019 18:01:38: 5000000 INFO @ Sun, 02 Jun 2019 18:01:42: 5000000 INFO @ Sun, 02 Jun 2019 18:01:42: 5000000 INFO @ Sun, 02 Jun 2019 18:01:44: 6000000 INFO @ Sun, 02 Jun 2019 18:01:50: 6000000 INFO @ Sun, 02 Jun 2019 18:01:50: 6000000 INFO @ Sun, 02 Jun 2019 18:01:51: 7000000 INFO @ Sun, 02 Jun 2019 18:01:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:01:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:01:56: #1 total tags in treatment: 7739355 INFO @ Sun, 02 Jun 2019 18:01:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:01:56: #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 18:01:56: #1 tags after filtering in treatment: 7739355 INFO @ Sun, 02 Jun 2019 18:01:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:01:56: #1 finished! INFO @ Sun, 02 Jun 2019 18:01:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:01:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:01:57: #2 number of paired peaks: 4240 INFO @ Sun, 02 Jun 2019 18:01:57: start model_add_line... INFO @ Sun, 02 Jun 2019 18:01:57: 7000000 INFO @ Sun, 02 Jun 2019 18:01:57: 7000000 INFO @ Sun, 02 Jun 2019 18:01:57: start X-correlation... INFO @ Sun, 02 Jun 2019 18:01:57: end of X-cor INFO @ Sun, 02 Jun 2019 18:01:57: #2 finished! INFO @ Sun, 02 Jun 2019 18:01:57: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 18:01:57: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 02 Jun 2019 18:01:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.10_model.r INFO @ Sun, 02 Jun 2019 18:01:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:01:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:02:03: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:02:03: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:02:03: #1 total tags in treatment: 7739355 INFO @ Sun, 02 Jun 2019 18:02:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:02:03: #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 18:02:03: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:02:03: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:02:03: #1 total tags in treatment: 7739355 INFO @ Sun, 02 Jun 2019 18:02:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:02:03: #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 18:02:03: #1 tags after filtering in treatment: 7739355 INFO @ Sun, 02 Jun 2019 18:02:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:02:03: #1 finished! INFO @ Sun, 02 Jun 2019 18:02:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:02:03: #1 tags after filtering in treatment: 7739355 INFO @ Sun, 02 Jun 2019 18:02:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:02:03: #1 finished! INFO @ Sun, 02 Jun 2019 18:02:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:02:04: #2 number of paired peaks: 4240 INFO @ Sun, 02 Jun 2019 18:02:04: start model_add_line... INFO @ Sun, 02 Jun 2019 18:02:04: #2 number of paired peaks: 4240 INFO @ Sun, 02 Jun 2019 18:02:04: start model_add_line... INFO @ Sun, 02 Jun 2019 18:02:04: start X-correlation... INFO @ Sun, 02 Jun 2019 18:02:04: start X-correlation... INFO @ Sun, 02 Jun 2019 18:02:04: end of X-cor INFO @ Sun, 02 Jun 2019 18:02:04: #2 finished! INFO @ Sun, 02 Jun 2019 18:02:04: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 18:02:04: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 02 Jun 2019 18:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.05_model.r INFO @ Sun, 02 Jun 2019 18:02:04: end of X-cor INFO @ Sun, 02 Jun 2019 18:02:04: #2 finished! INFO @ Sun, 02 Jun 2019 18:02:04: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 18:02:04: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 02 Jun 2019 18:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.20_model.r INFO @ Sun, 02 Jun 2019 18:02:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:02:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:02:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:02:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:02:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:02:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:02:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:02:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.10_summits.bed INFO @ Sun, 02 Jun 2019 18:02:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5068 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:02:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:02:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:02:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.05_summits.bed INFO @ Sun, 02 Jun 2019 18:02:40: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6162 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:02:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:02:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:02:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX335104/SRX335104.20_summits.bed INFO @ Sun, 02 Jun 2019 18:02:41: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4006 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。