Job ID = 2589302 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,518,274 reads read : 6,518,274 reads written : 6,518,274 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217384.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: 00:01:04 6518274 reads; of these: 6518274 (100.00%) were unpaired; of these: 1880220 (28.85%) aligned 0 times 3968441 (60.88%) aligned exactly 1 time 669613 (10.27%) aligned >1 times 71.15% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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] 1068937 / 4638054 = 0.2305 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 17:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.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 17:23:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:23:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:23:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.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 17:23:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:23:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.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 17:23:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:23:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:23:27: 1000000 INFO @ Mon, 12 Aug 2019 17:23:28: 1000000 INFO @ Mon, 12 Aug 2019 17:23:30: 1000000 INFO @ Mon, 12 Aug 2019 17:23:35: 2000000 INFO @ Mon, 12 Aug 2019 17:23:37: 2000000 INFO @ Mon, 12 Aug 2019 17:23:40: 2000000 INFO @ Mon, 12 Aug 2019 17:23:42: 3000000 INFO @ Mon, 12 Aug 2019 17:23:46: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:23:46: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:23:46: #1 total tags in treatment: 3569117 INFO @ Mon, 12 Aug 2019 17:23:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:23:46: #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 17:23:46: #1 tags after filtering in treatment: 3569117 INFO @ Mon, 12 Aug 2019 17:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:23:46: #1 finished! INFO @ Mon, 12 Aug 2019 17:23:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:23:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:23:46: #2 number of paired peaks: 1798 INFO @ Mon, 12 Aug 2019 17:23:46: start model_add_line... INFO @ Mon, 12 Aug 2019 17:23:47: start X-correlation... INFO @ Mon, 12 Aug 2019 17:23:47: end of X-cor INFO @ Mon, 12 Aug 2019 17:23:47: #2 finished! INFO @ Mon, 12 Aug 2019 17:23:47: #2 predicted fragment length is 147 bps INFO @ Mon, 12 Aug 2019 17:23:47: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 12 Aug 2019 17:23:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.05_model.r INFO @ Mon, 12 Aug 2019 17:23:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:23:47: 3000000 INFO @ Mon, 12 Aug 2019 17:23:50: 3000000 INFO @ Mon, 12 Aug 2019 17:23:51: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:23:51: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:23:51: #1 total tags in treatment: 3569117 INFO @ Mon, 12 Aug 2019 17:23:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:23:51: #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 17:23:51: #1 tags after filtering in treatment: 3569117 INFO @ Mon, 12 Aug 2019 17:23:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:23:51: #1 finished! INFO @ Mon, 12 Aug 2019 17:23:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:23:52: #2 number of paired peaks: 1798 INFO @ Mon, 12 Aug 2019 17:23:52: start model_add_line... INFO @ Mon, 12 Aug 2019 17:23:52: start X-correlation... INFO @ Mon, 12 Aug 2019 17:23:52: end of X-cor INFO @ Mon, 12 Aug 2019 17:23:52: #2 finished! INFO @ Mon, 12 Aug 2019 17:23:52: #2 predicted fragment length is 147 bps INFO @ Mon, 12 Aug 2019 17:23:52: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 12 Aug 2019 17:23:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.10_model.r INFO @ Mon, 12 Aug 2019 17:23:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:23:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:23:55: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:23:55: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:23:55: #1 total tags in treatment: 3569117 INFO @ Mon, 12 Aug 2019 17:23:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:23:55: #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 17:23:55: #1 tags after filtering in treatment: 3569117 INFO @ Mon, 12 Aug 2019 17:23:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:23:55: #1 finished! INFO @ Mon, 12 Aug 2019 17:23:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:23:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:23:56: #2 number of paired peaks: 1798 INFO @ Mon, 12 Aug 2019 17:23:56: start model_add_line... INFO @ Mon, 12 Aug 2019 17:23:56: start X-correlation... INFO @ Mon, 12 Aug 2019 17:23:56: end of X-cor INFO @ Mon, 12 Aug 2019 17:23:56: #2 finished! INFO @ Mon, 12 Aug 2019 17:23:56: #2 predicted fragment length is 147 bps INFO @ Mon, 12 Aug 2019 17:23:56: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 12 Aug 2019 17:23:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.20_model.r INFO @ Mon, 12 Aug 2019 17:23:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:23:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:23:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:24:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:24:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.05_summits.bed INFO @ Mon, 12 Aug 2019 17:24:06: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4727 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:24:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:24:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.10_summits.bed INFO @ Mon, 12 Aug 2019 17:24:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2820 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:24:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:24:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:24:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065678/SRX065678.20_summits.bed INFO @ Mon, 12 Aug 2019 17:24:14: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1548 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。