Job ID = 2640580 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,117,182 reads read : 10,234,364 reads written : 5,117,182 reads 0-length : 5,117,182 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:48 5117182 reads; of these: 5117182 (100.00%) were unpaired; of these: 486444 (9.51%) aligned 0 times 3444005 (67.30%) aligned exactly 1 time 1186733 (23.19%) aligned >1 times 90.49% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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_rmdupse_core] 158712 / 4630738 = 0.0343 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.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 17:58:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:58:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:58:47: 1000000 INFO @ Sat, 24 Aug 2019 17:58:54: 2000000 INFO @ Sat, 24 Aug 2019 17:59:01: 3000000 INFO @ Sat, 24 Aug 2019 17:59:08: 4000000 INFO @ Sat, 24 Aug 2019 17:59:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.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 17:59:10: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:59:10: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:59:11: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:59:11: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:59:11: #1 total tags in treatment: 4472026 INFO @ Sat, 24 Aug 2019 17:59:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:59:11: #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 17:59:11: #1 tags after filtering in treatment: 4471752 INFO @ Sat, 24 Aug 2019 17:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:59:11: #1 finished! INFO @ Sat, 24 Aug 2019 17:59:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:59:14: #2 number of paired peaks: 36606 INFO @ Sat, 24 Aug 2019 17:59:14: start model_add_line... INFO @ Sat, 24 Aug 2019 17:59:14: start X-correlation... INFO @ Sat, 24 Aug 2019 17:59:14: end of X-cor INFO @ Sat, 24 Aug 2019 17:59:14: #2 finished! INFO @ Sat, 24 Aug 2019 17:59:14: #2 predicted fragment length is 232 bps INFO @ Sat, 24 Aug 2019 17:59:14: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 24 Aug 2019 17:59:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.05_model.r INFO @ Sat, 24 Aug 2019 17:59:14: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:59:19: 1000000 INFO @ Sat, 24 Aug 2019 17:59:27: 2000000 INFO @ Sat, 24 Aug 2019 17:59:29: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:59:35: 3000000 INFO @ Sat, 24 Aug 2019 17:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.05_summits.bed INFO @ Sat, 24 Aug 2019 17:59:36: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (1168 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:59:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.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 17:59:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:59:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:59:42: 4000000 INFO @ Sat, 24 Aug 2019 17:59:45: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:59:45: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:59:45: #1 total tags in treatment: 4472026 INFO @ Sat, 24 Aug 2019 17:59:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:59:45: #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 17:59:45: #1 tags after filtering in treatment: 4471752 INFO @ Sat, 24 Aug 2019 17:59:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:59:45: #1 finished! INFO @ Sat, 24 Aug 2019 17:59:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:59:48: 1000000 INFO @ Sat, 24 Aug 2019 17:59:48: #2 number of paired peaks: 36606 INFO @ Sat, 24 Aug 2019 17:59:48: start model_add_line... INFO @ Sat, 24 Aug 2019 17:59:49: start X-correlation... INFO @ Sat, 24 Aug 2019 17:59:49: end of X-cor INFO @ Sat, 24 Aug 2019 17:59:49: #2 finished! INFO @ Sat, 24 Aug 2019 17:59:49: #2 predicted fragment length is 232 bps INFO @ Sat, 24 Aug 2019 17:59:49: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 24 Aug 2019 17:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.10_model.r INFO @ Sat, 24 Aug 2019 17:59:49: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:59:57: 2000000 INFO @ Sat, 24 Aug 2019 18:00:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:00:06: 3000000 INFO @ Sat, 24 Aug 2019 18:00:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:00:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:00:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.10_summits.bed INFO @ Sat, 24 Aug 2019 18:00:11: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:00:14: 4000000 INFO @ Sat, 24 Aug 2019 18:00:18: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:00:18: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:00:18: #1 total tags in treatment: 4472026 INFO @ Sat, 24 Aug 2019 18:00:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:00:18: #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 18:00:18: #1 tags after filtering in treatment: 4471752 INFO @ Sat, 24 Aug 2019 18:00:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:00:18: #1 finished! INFO @ Sat, 24 Aug 2019 18:00:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:00:22: #2 number of paired peaks: 36606 INFO @ Sat, 24 Aug 2019 18:00:22: start model_add_line... INFO @ Sat, 24 Aug 2019 18:00:22: start X-correlation... INFO @ Sat, 24 Aug 2019 18:00:22: end of X-cor INFO @ Sat, 24 Aug 2019 18:00:22: #2 finished! INFO @ Sat, 24 Aug 2019 18:00:22: #2 predicted fragment length is 232 bps INFO @ Sat, 24 Aug 2019 18:00:22: #2 alternative fragment length(s) may be 232 bps INFO @ Sat, 24 Aug 2019 18:00:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.20_model.r INFO @ Sat, 24 Aug 2019 18:00:22: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:00:36: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:00:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:00:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:00:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375021/SRX5375021.20_summits.bed INFO @ Sat, 24 Aug 2019 18:00:43: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (76 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。