Job ID = 2589542 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,751,348 reads read : 2,751,348 reads written : 2,751,348 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR701518.sra.cache’: 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: 00:00:18 2751348 reads; of these: 2751348 (100.00%) were unpaired; of these: 1704647 (61.96%) aligned 0 times 888115 (32.28%) aligned exactly 1 time 158586 (5.76%) aligned >1 times 38.04% overall alignment rate Time searching: 00:00:18 Overall time: 00:00:18 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] 70741 / 1046701 = 0.0676 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 @ Mon, 12 Aug 2019 17:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.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 @ Mon, 12 Aug 2019 17:54:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:54:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.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 @ Mon, 12 Aug 2019 17:54:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:54:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.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 @ Mon, 12 Aug 2019 17:54:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:54:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:54:43: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:43: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:43: #1 total tags in treatment: 975960 INFO @ Mon, 12 Aug 2019 17:54:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:54:43: #1 tags after filtering in treatment: 975960 INFO @ Mon, 12 Aug 2019 17:54:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:43: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:43: #2 number of paired peaks: 1882 INFO @ Mon, 12 Aug 2019 17:54:43: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:43: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:43: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:43: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:43: #2 predicted fragment length is 142 bps INFO @ Mon, 12 Aug 2019 17:54:43: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 12 Aug 2019 17:54:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.05_model.r INFO @ Mon, 12 Aug 2019 17:54:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:43: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:43: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:43: #1 total tags in treatment: 975960 INFO @ Mon, 12 Aug 2019 17:54:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:54:43: #1 tags after filtering in treatment: 975960 INFO @ Mon, 12 Aug 2019 17:54:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:43: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:44: #2 number of paired peaks: 1882 INFO @ Mon, 12 Aug 2019 17:54:44: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:44: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:44: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:44: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:44: #2 predicted fragment length is 142 bps INFO @ Mon, 12 Aug 2019 17:54:44: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 12 Aug 2019 17:54:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.10_model.r INFO @ Mon, 12 Aug 2019 17:54:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:44: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:54:44: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:54:44: #1 total tags in treatment: 975960 INFO @ Mon, 12 Aug 2019 17:54:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:54:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:54:44: #1 tags after filtering in treatment: 975960 INFO @ Mon, 12 Aug 2019 17:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:54:44: #1 finished! INFO @ Mon, 12 Aug 2019 17:54:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:54:45: #2 number of paired peaks: 1882 INFO @ Mon, 12 Aug 2019 17:54:45: start model_add_line... INFO @ Mon, 12 Aug 2019 17:54:45: start X-correlation... INFO @ Mon, 12 Aug 2019 17:54:45: end of X-cor INFO @ Mon, 12 Aug 2019 17:54:45: #2 finished! INFO @ Mon, 12 Aug 2019 17:54:45: #2 predicted fragment length is 142 bps INFO @ Mon, 12 Aug 2019 17:54:45: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 12 Aug 2019 17:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.20_model.r INFO @ Mon, 12 Aug 2019 17:54:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:54:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.05_summits.bed INFO @ Mon, 12 Aug 2019 17:54:48: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2006 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:54:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.10_summits.bed INFO @ Mon, 12 Aug 2019 17:54:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (999 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233462/SRX233462.20_summits.bed INFO @ Mon, 12 Aug 2019 17:54:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (428 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。