Job ID = 2640604 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,405,060 reads read : 40,810,120 reads written : 20,405,060 reads 0-length : 20,405,060 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:27 20405060 reads; of these: 20405060 (100.00%) were unpaired; of these: 590358 (2.89%) aligned 0 times 14380852 (70.48%) aligned exactly 1 time 5433850 (26.63%) aligned >1 times 97.11% overall alignment rate Time searching: 00:16:28 Overall time: 00:16:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 12710864 / 19814702 = 0.6415 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:25:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:25:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:25:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:25:14: 1000000 INFO @ Sat, 24 Aug 2019 18:25:20: 2000000 INFO @ Sat, 24 Aug 2019 18:25:27: 3000000 INFO @ Sat, 24 Aug 2019 18:25:33: 4000000 INFO @ Sat, 24 Aug 2019 18:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:25:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:25:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:25:39: 5000000 INFO @ Sat, 24 Aug 2019 18:25:45: 1000000 INFO @ Sat, 24 Aug 2019 18:25:46: 6000000 INFO @ Sat, 24 Aug 2019 18:25:52: 7000000 INFO @ Sat, 24 Aug 2019 18:25:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:25:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:25:53: #1 total tags in treatment: 7103838 INFO @ Sat, 24 Aug 2019 18:25:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:25:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:25:53: 2000000 INFO @ Sat, 24 Aug 2019 18:25:53: #1 tags after filtering in treatment: 7103636 INFO @ Sat, 24 Aug 2019 18:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:25:53: #1 finished! INFO @ Sat, 24 Aug 2019 18:25:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:25:55: #2 number of paired peaks: 28110 INFO @ Sat, 24 Aug 2019 18:25:55: start model_add_line... INFO @ Sat, 24 Aug 2019 18:25:56: start X-correlation... INFO @ Sat, 24 Aug 2019 18:25:56: end of X-cor INFO @ Sat, 24 Aug 2019 18:25:56: #2 finished! INFO @ Sat, 24 Aug 2019 18:25:56: #2 predicted fragment length is 114 bps INFO @ Sat, 24 Aug 2019 18:25:56: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 24 Aug 2019 18:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.05_model.r INFO @ Sat, 24 Aug 2019 18:25:56: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:26:01: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:26:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:26:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:26:09: 4000000 INFO @ Sat, 24 Aug 2019 18:26:13: 1000000 INFO @ Sat, 24 Aug 2019 18:26:16: 5000000 INFO @ Sat, 24 Aug 2019 18:26:18: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:26:20: 2000000 INFO @ Sat, 24 Aug 2019 18:26:24: 6000000 INFO @ Sat, 24 Aug 2019 18:26:26: 3000000 INFO @ Sat, 24 Aug 2019 18:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.05_summits.bed INFO @ Sat, 24 Aug 2019 18:26:29: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (832 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:26:32: 7000000 INFO @ Sat, 24 Aug 2019 18:26:32: 4000000 INFO @ Sat, 24 Aug 2019 18:26:33: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:26:33: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:26:33: #1 total tags in treatment: 7103838 INFO @ Sat, 24 Aug 2019 18:26:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:26:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:26:33: #1 tags after filtering in treatment: 7103636 INFO @ Sat, 24 Aug 2019 18:26:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:26:33: #1 finished! INFO @ Sat, 24 Aug 2019 18:26:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:26:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:26:35: #2 number of paired peaks: 28110 INFO @ Sat, 24 Aug 2019 18:26:35: start model_add_line... INFO @ Sat, 24 Aug 2019 18:26:35: start X-correlation... INFO @ Sat, 24 Aug 2019 18:26:35: end of X-cor INFO @ Sat, 24 Aug 2019 18:26:35: #2 finished! INFO @ Sat, 24 Aug 2019 18:26:35: #2 predicted fragment length is 114 bps INFO @ Sat, 24 Aug 2019 18:26:35: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 24 Aug 2019 18:26:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.10_model.r INFO @ Sat, 24 Aug 2019 18:26:35: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:26:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:26:39: 5000000 INFO @ Sat, 24 Aug 2019 18:26:45: 6000000 INFO @ Sat, 24 Aug 2019 18:26:51: 7000000 INFO @ Sat, 24 Aug 2019 18:26:52: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:26:52: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:26:52: #1 total tags in treatment: 7103838 INFO @ Sat, 24 Aug 2019 18:26:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:26:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:26:52: #1 tags after filtering in treatment: 7103636 INFO @ Sat, 24 Aug 2019 18:26:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:26:52: #1 finished! INFO @ Sat, 24 Aug 2019 18:26:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:26:55: #2 number of paired peaks: 28110 INFO @ Sat, 24 Aug 2019 18:26:55: start model_add_line... INFO @ Sat, 24 Aug 2019 18:26:55: start X-correlation... INFO @ Sat, 24 Aug 2019 18:26:55: end of X-cor INFO @ Sat, 24 Aug 2019 18:26:55: #2 finished! INFO @ Sat, 24 Aug 2019 18:26:55: #2 predicted fragment length is 114 bps INFO @ Sat, 24 Aug 2019 18:26:55: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 24 Aug 2019 18:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.20_model.r INFO @ Sat, 24 Aug 2019 18:26:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:26:58: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:27:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:27:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:27:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.10_summits.bed INFO @ Sat, 24 Aug 2019 18:27:09: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:27:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:27:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:27:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:27:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375033/SRX5375033.20_summits.bed INFO @ Sat, 24 Aug 2019 18:27:28: Done! pass1 - making usageList (21 chroms): 2 millis pass2 - checking and writing primary data (226 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。