Job ID = 1291654 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,470,371 reads read : 3,470,371 reads written : 3,470,371 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:55 3470371 reads; of these: 3470371 (100.00%) were unpaired; of these: 667625 (19.24%) aligned 0 times 2363587 (68.11%) aligned exactly 1 time 439159 (12.65%) aligned >1 times 80.76% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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] 950163 / 2802746 = 0.3390 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 16:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.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 16:12:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:12:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.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 16:12:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:12:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.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 16:12:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:12:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:12:13: 1000000 INFO @ Sun, 02 Jun 2019 16:12:14: 1000000 INFO @ Sun, 02 Jun 2019 16:12:14: 1000000 INFO @ Sun, 02 Jun 2019 16:12:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:12:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:12:21: #1 total tags in treatment: 1852583 INFO @ Sun, 02 Jun 2019 16:12:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:12:21: #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 16:12:21: #1 tags after filtering in treatment: 1852583 INFO @ Sun, 02 Jun 2019 16:12:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:12:21: #1 finished! INFO @ Sun, 02 Jun 2019 16:12:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:12:21: #2 number of paired peaks: 1193 INFO @ Sun, 02 Jun 2019 16:12:21: start model_add_line... INFO @ Sun, 02 Jun 2019 16:12:21: start X-correlation... INFO @ Sun, 02 Jun 2019 16:12:21: end of X-cor INFO @ Sun, 02 Jun 2019 16:12:21: #2 finished! INFO @ Sun, 02 Jun 2019 16:12:21: #2 predicted fragment length is 211 bps INFO @ Sun, 02 Jun 2019 16:12:21: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 02 Jun 2019 16:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.05_model.r INFO @ Sun, 02 Jun 2019 16:12:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:12:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:12:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:12:23: #1 total tags in treatment: 1852583 INFO @ Sun, 02 Jun 2019 16:12:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:12:23: #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 16:12:23: #1 tags after filtering in treatment: 1852583 INFO @ Sun, 02 Jun 2019 16:12:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:12:23: #1 finished! INFO @ Sun, 02 Jun 2019 16:12:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:12:23: #2 number of paired peaks: 1193 INFO @ Sun, 02 Jun 2019 16:12:23: start model_add_line... INFO @ Sun, 02 Jun 2019 16:12:23: start X-correlation... INFO @ Sun, 02 Jun 2019 16:12:23: end of X-cor INFO @ Sun, 02 Jun 2019 16:12:23: #2 finished! INFO @ Sun, 02 Jun 2019 16:12:23: #2 predicted fragment length is 211 bps INFO @ Sun, 02 Jun 2019 16:12:23: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 02 Jun 2019 16:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.10_model.r INFO @ Sun, 02 Jun 2019 16:12:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:12:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:12:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:12:23: #1 total tags in treatment: 1852583 INFO @ Sun, 02 Jun 2019 16:12:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:12:23: #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 16:12:23: #1 tags after filtering in treatment: 1852583 INFO @ Sun, 02 Jun 2019 16:12:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:12:23: #1 finished! INFO @ Sun, 02 Jun 2019 16:12:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:12:24: #2 number of paired peaks: 1193 INFO @ Sun, 02 Jun 2019 16:12:24: start model_add_line... INFO @ Sun, 02 Jun 2019 16:12:24: start X-correlation... INFO @ Sun, 02 Jun 2019 16:12:24: end of X-cor INFO @ Sun, 02 Jun 2019 16:12:24: #2 finished! INFO @ Sun, 02 Jun 2019 16:12:24: #2 predicted fragment length is 211 bps INFO @ Sun, 02 Jun 2019 16:12:24: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 02 Jun 2019 16:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.20_model.r INFO @ Sun, 02 Jun 2019 16:12:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:12:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:12:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:12:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:12:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:12:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:12:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.05_summits.bed INFO @ Sun, 02 Jun 2019 16:12:31: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1425 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.10_summits.bed INFO @ Sun, 02 Jun 2019 16:12:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (804 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769982/SRX1769982.20_summits.bed INFO @ Sun, 02 Jun 2019 16:12:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (409 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。