Job ID = 2589561 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,275,526 reads read : 6,275,526 reads written : 6,275,526 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR707568.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: 00:01:13 6275526 reads; of these: 6275526 (100.00%) were unpaired; of these: 474343 (7.56%) aligned 0 times 4929329 (78.55%) aligned exactly 1 time 871854 (13.89%) aligned >1 times 92.44% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 796354 / 5801183 = 0.1373 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 17:59:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.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 17:59:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:59:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.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 17:59:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:59:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:59:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.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 17:59:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:59:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:59:47: 1000000 INFO @ Mon, 12 Aug 2019 17:59:50: 1000000 INFO @ Mon, 12 Aug 2019 17:59:50: 1000000 INFO @ Mon, 12 Aug 2019 17:59:53: 2000000 INFO @ Mon, 12 Aug 2019 17:59:58: 2000000 INFO @ Mon, 12 Aug 2019 17:59:59: 2000000 INFO @ Mon, 12 Aug 2019 18:00:00: 3000000 INFO @ Mon, 12 Aug 2019 18:00:05: 3000000 INFO @ Mon, 12 Aug 2019 18:00:07: 4000000 INFO @ Mon, 12 Aug 2019 18:00:08: 3000000 INFO @ Mon, 12 Aug 2019 18:00:13: 4000000 INFO @ Mon, 12 Aug 2019 18:00:14: 5000000 INFO @ Mon, 12 Aug 2019 18:00:14: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:00:14: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:00:14: #1 total tags in treatment: 5004829 INFO @ Mon, 12 Aug 2019 18:00:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:00:14: #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 18:00:14: #1 tags after filtering in treatment: 5004829 INFO @ Mon, 12 Aug 2019 18:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:00:14: #1 finished! INFO @ Mon, 12 Aug 2019 18:00:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:00:15: #2 number of paired peaks: 1186 INFO @ Mon, 12 Aug 2019 18:00:15: start model_add_line... INFO @ Mon, 12 Aug 2019 18:00:15: start X-correlation... INFO @ Mon, 12 Aug 2019 18:00:15: end of X-cor INFO @ Mon, 12 Aug 2019 18:00:15: #2 finished! INFO @ Mon, 12 Aug 2019 18:00:15: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 18:00:15: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 18:00:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.05_model.r INFO @ Mon, 12 Aug 2019 18:00:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:00:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:00:16: 4000000 INFO @ Mon, 12 Aug 2019 18:00:20: 5000000 INFO @ Mon, 12 Aug 2019 18:00:20: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:00:20: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:00:20: #1 total tags in treatment: 5004829 INFO @ Mon, 12 Aug 2019 18:00:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:00:20: #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 18:00:20: #1 tags after filtering in treatment: 5004829 INFO @ Mon, 12 Aug 2019 18:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:00:20: #1 finished! INFO @ Mon, 12 Aug 2019 18:00:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:00:21: #2 number of paired peaks: 1186 INFO @ Mon, 12 Aug 2019 18:00:21: start model_add_line... INFO @ Mon, 12 Aug 2019 18:00:21: start X-correlation... INFO @ Mon, 12 Aug 2019 18:00:21: end of X-cor INFO @ Mon, 12 Aug 2019 18:00:21: #2 finished! INFO @ Mon, 12 Aug 2019 18:00:21: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 18:00:21: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 18:00:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.20_model.r INFO @ Mon, 12 Aug 2019 18:00:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:00:25: 5000000 INFO @ Mon, 12 Aug 2019 18:00:25: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:00:25: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:00:25: #1 total tags in treatment: 5004829 INFO @ Mon, 12 Aug 2019 18:00:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:00:25: #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 18:00:25: #1 tags after filtering in treatment: 5004829 INFO @ Mon, 12 Aug 2019 18:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:00:25: #1 finished! INFO @ Mon, 12 Aug 2019 18:00:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:00:26: #2 number of paired peaks: 1186 INFO @ Mon, 12 Aug 2019 18:00:26: start model_add_line... INFO @ Mon, 12 Aug 2019 18:00:26: start X-correlation... INFO @ Mon, 12 Aug 2019 18:00:26: end of X-cor INFO @ Mon, 12 Aug 2019 18:00:26: #2 finished! INFO @ Mon, 12 Aug 2019 18:00:26: #2 predicted fragment length is 140 bps INFO @ Mon, 12 Aug 2019 18:00:26: #2 alternative fragment length(s) may be 140 bps INFO @ Mon, 12 Aug 2019 18:00:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.10_model.r INFO @ Mon, 12 Aug 2019 18:00:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:00:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:00:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:00:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:00:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:00:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:00:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.05_summits.bed INFO @ Mon, 12 Aug 2019 18:00:38: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4594 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:00:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.20_summits.bed INFO @ Mon, 12 Aug 2019 18:00:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1270 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:00:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:00:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:00:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX234924/SRX234924.10_summits.bed INFO @ Mon, 12 Aug 2019 18:00:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2834 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。