Job ID = 1292015 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,877,608 reads read : 59,755,216 reads written : 29,877,608 reads 0-length : 29,877,608 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: 00:04:32 29877608 reads; of these: 29877608 (100.00%) were unpaired; of these: 20961734 (70.16%) aligned 0 times 7645715 (25.59%) aligned exactly 1 time 1270159 (4.25%) aligned >1 times 29.84% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 2736372 / 8915874 = 0.3069 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 17:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.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 17:23:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:23:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.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 17:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.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 17:23:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:23:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:23:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:23:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:23:17: 1000000 INFO @ Sun, 02 Jun 2019 17:23:17: 1000000 INFO @ Sun, 02 Jun 2019 17:23:17: 1000000 INFO @ Sun, 02 Jun 2019 17:23:27: 2000000 INFO @ Sun, 02 Jun 2019 17:23:27: 2000000 INFO @ Sun, 02 Jun 2019 17:23:27: 2000000 INFO @ Sun, 02 Jun 2019 17:23:37: 3000000 INFO @ Sun, 02 Jun 2019 17:23:37: 3000000 INFO @ Sun, 02 Jun 2019 17:23:37: 3000000 INFO @ Sun, 02 Jun 2019 17:23:47: 4000000 INFO @ Sun, 02 Jun 2019 17:23:47: 4000000 INFO @ Sun, 02 Jun 2019 17:23:47: 4000000 INFO @ Sun, 02 Jun 2019 17:23:57: 5000000 INFO @ Sun, 02 Jun 2019 17:23:58: 5000000 INFO @ Sun, 02 Jun 2019 17:23:58: 5000000 INFO @ Sun, 02 Jun 2019 17:24:08: 6000000 INFO @ Sun, 02 Jun 2019 17:24:08: 6000000 INFO @ Sun, 02 Jun 2019 17:24:08: 6000000 INFO @ Sun, 02 Jun 2019 17:24:10: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:24:10: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:24:10: #1 total tags in treatment: 6179502 INFO @ Sun, 02 Jun 2019 17:24:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:24:10: #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 17:24:10: #1 tags after filtering in treatment: 6179502 INFO @ Sun, 02 Jun 2019 17:24:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:24:10: #1 finished! INFO @ Sun, 02 Jun 2019 17:24:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:24:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:24:10: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:24:10: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:24:10: #1 total tags in treatment: 6179502 INFO @ Sun, 02 Jun 2019 17:24:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:24:10: #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 17:24:10: #1 tags after filtering in treatment: 6179502 INFO @ Sun, 02 Jun 2019 17:24:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:24:10: #1 finished! INFO @ Sun, 02 Jun 2019 17:24:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:24:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:24:10: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:24:10: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:24:10: #1 total tags in treatment: 6179502 INFO @ Sun, 02 Jun 2019 17:24:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:24:10: #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 17:24:10: #1 tags after filtering in treatment: 6179502 INFO @ Sun, 02 Jun 2019 17:24:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:24:10: #1 finished! INFO @ Sun, 02 Jun 2019 17:24:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:24:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:24:10: #2 number of paired peaks: 1510 INFO @ Sun, 02 Jun 2019 17:24:10: start model_add_line... INFO @ Sun, 02 Jun 2019 17:24:10: start X-correlation... INFO @ Sun, 02 Jun 2019 17:24:10: end of X-cor INFO @ Sun, 02 Jun 2019 17:24:10: #2 finished! INFO @ Sun, 02 Jun 2019 17:24:10: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 17:24:10: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 02 Jun 2019 17:24:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.10_model.r INFO @ Sun, 02 Jun 2019 17:24:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:24:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:24:10: #2 number of paired peaks: 1510 INFO @ Sun, 02 Jun 2019 17:24:10: start model_add_line... INFO @ Sun, 02 Jun 2019 17:24:11: start X-correlation... INFO @ Sun, 02 Jun 2019 17:24:11: end of X-cor INFO @ Sun, 02 Jun 2019 17:24:11: #2 finished! INFO @ Sun, 02 Jun 2019 17:24:11: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 17:24:11: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 02 Jun 2019 17:24:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.05_model.r INFO @ Sun, 02 Jun 2019 17:24:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:24:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:24:11: #2 number of paired peaks: 1510 INFO @ Sun, 02 Jun 2019 17:24:11: start model_add_line... INFO @ Sun, 02 Jun 2019 17:24:11: start X-correlation... INFO @ Sun, 02 Jun 2019 17:24:11: end of X-cor INFO @ Sun, 02 Jun 2019 17:24:11: #2 finished! INFO @ Sun, 02 Jun 2019 17:24:11: #2 predicted fragment length is 192 bps INFO @ Sun, 02 Jun 2019 17:24:11: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 02 Jun 2019 17:24:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.20_model.r INFO @ Sun, 02 Jun 2019 17:24:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:24:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:24:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:24:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:24:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.05_summits.bed INFO @ Sun, 02 Jun 2019 17:24:41: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3710 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:24:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:24:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:24:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.20_summits.bed INFO @ Sun, 02 Jun 2019 17:24:42: Done! INFO @ Sun, 02 Jun 2019 17:24:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:24:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:24:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3104605/SRX3104605.10_summits.bed pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (933 records, 4 fields): 4 millis INFO @ Sun, 02 Jun 2019 17:24:42: Done! CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2053 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。