Job ID = 2589728 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,220,288 reads read : 8,220,288 reads written : 8,220,288 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947330.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: 00:01:23 8220288 reads; of these: 8220288 (100.00%) were unpaired; of these: 964275 (11.73%) aligned 0 times 6175804 (75.13%) aligned exactly 1 time 1080209 (13.14%) aligned >1 times 88.27% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 901833 / 7256013 = 0.1243 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 18:22:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.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 18:22:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:22:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.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 18:22:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:22:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.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 18:22:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:22:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:22:53: 1000000 INFO @ Mon, 12 Aug 2019 18:22:55: 1000000 INFO @ Mon, 12 Aug 2019 18:22:56: 1000000 INFO @ Mon, 12 Aug 2019 18:23:00: 2000000 INFO @ Mon, 12 Aug 2019 18:23:04: 2000000 INFO @ Mon, 12 Aug 2019 18:23:04: 2000000 INFO @ Mon, 12 Aug 2019 18:23:07: 3000000 INFO @ Mon, 12 Aug 2019 18:23:12: 3000000 INFO @ Mon, 12 Aug 2019 18:23:14: 4000000 INFO @ Mon, 12 Aug 2019 18:23:16: 3000000 INFO @ Mon, 12 Aug 2019 18:23:20: 4000000 INFO @ Mon, 12 Aug 2019 18:23:21: 5000000 INFO @ Mon, 12 Aug 2019 18:23:27: 4000000 INFO @ Mon, 12 Aug 2019 18:23:28: 5000000 INFO @ Mon, 12 Aug 2019 18:23:28: 6000000 INFO @ Mon, 12 Aug 2019 18:23:31: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:23:31: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:23:31: #1 total tags in treatment: 6354180 INFO @ Mon, 12 Aug 2019 18:23:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:23:31: #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 18:23:31: #1 tags after filtering in treatment: 6354180 INFO @ Mon, 12 Aug 2019 18:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:23:31: #1 finished! INFO @ Mon, 12 Aug 2019 18:23:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:23:32: #2 number of paired peaks: 1059 INFO @ Mon, 12 Aug 2019 18:23:32: start model_add_line... INFO @ Mon, 12 Aug 2019 18:23:32: start X-correlation... INFO @ Mon, 12 Aug 2019 18:23:32: end of X-cor INFO @ Mon, 12 Aug 2019 18:23:32: #2 finished! INFO @ Mon, 12 Aug 2019 18:23:32: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 18:23:32: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 18:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.05_model.r INFO @ Mon, 12 Aug 2019 18:23:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:23:35: 6000000 INFO @ Mon, 12 Aug 2019 18:23:37: 5000000 INFO @ Mon, 12 Aug 2019 18:23:38: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:23:38: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:23:38: #1 total tags in treatment: 6354180 INFO @ Mon, 12 Aug 2019 18:23:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:23:38: #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 18:23:38: #1 tags after filtering in treatment: 6354180 INFO @ Mon, 12 Aug 2019 18:23:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:23:38: #1 finished! INFO @ Mon, 12 Aug 2019 18:23:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:23:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:23:39: #2 number of paired peaks: 1059 INFO @ Mon, 12 Aug 2019 18:23:39: start model_add_line... INFO @ Mon, 12 Aug 2019 18:23:39: start X-correlation... INFO @ Mon, 12 Aug 2019 18:23:39: end of X-cor INFO @ Mon, 12 Aug 2019 18:23:39: #2 finished! INFO @ Mon, 12 Aug 2019 18:23:39: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 18:23:39: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 18:23:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.10_model.r INFO @ Mon, 12 Aug 2019 18:23:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:23:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:23:46: 6000000 INFO @ Mon, 12 Aug 2019 18:23:49: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:23:49: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:23:49: #1 total tags in treatment: 6354180 INFO @ Mon, 12 Aug 2019 18:23:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:23:49: #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 18:23:49: #1 tags after filtering in treatment: 6354180 INFO @ Mon, 12 Aug 2019 18:23:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:23:49: #1 finished! INFO @ Mon, 12 Aug 2019 18:23:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:23:50: #2 number of paired peaks: 1059 INFO @ Mon, 12 Aug 2019 18:23:50: start model_add_line... INFO @ Mon, 12 Aug 2019 18:23:50: start X-correlation... INFO @ Mon, 12 Aug 2019 18:23:50: end of X-cor INFO @ Mon, 12 Aug 2019 18:23:50: #2 finished! INFO @ Mon, 12 Aug 2019 18:23:50: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 18:23:50: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 18:23:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.20_model.r INFO @ Mon, 12 Aug 2019 18:23:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:23:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:23:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:23:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:24:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:24:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:24:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.05_summits.bed INFO @ Mon, 12 Aug 2019 18:24:02: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (5491 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:24:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.10_summits.bed INFO @ Mon, 12 Aug 2019 18:24:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3504 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:24:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:24:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:24:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:24:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331100/SRX331100.20_summits.bed INFO @ Mon, 12 Aug 2019 18:24:20: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1736 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。