Job ID = 2590675 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,836,429 reads read : 67,672,858 reads written : 33,836,429 reads 0-length : 33,836,429 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:50 33836429 reads; of these: 33836429 (100.00%) were unpaired; of these: 2903790 (8.58%) aligned 0 times 22431570 (66.29%) aligned exactly 1 time 8501069 (25.12%) aligned >1 times 91.42% overall alignment rate Time searching: 00:12:50 Overall time: 00:12:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 16658177 / 30932639 = 0.5385 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 23:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.bam'] # control file = None # effective genome size = 1.20e+08 # 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 23:29:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:29:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.bam'] # control file = None # effective genome size = 1.20e+08 # 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 23:29:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:29:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.bam'] # control file = None # effective genome size = 1.20e+08 # 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 23:29:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:29:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:14: 1000000 INFO @ Mon, 12 Aug 2019 23:29:15: 1000000 INFO @ Mon, 12 Aug 2019 23:29:17: 1000000 INFO @ Mon, 12 Aug 2019 23:29:22: 2000000 INFO @ Mon, 12 Aug 2019 23:29:23: 2000000 INFO @ Mon, 12 Aug 2019 23:29:25: 2000000 INFO @ Mon, 12 Aug 2019 23:29:29: 3000000 INFO @ Mon, 12 Aug 2019 23:29:30: 3000000 INFO @ Mon, 12 Aug 2019 23:29:33: 3000000 INFO @ Mon, 12 Aug 2019 23:29:37: 4000000 INFO @ Mon, 12 Aug 2019 23:29:37: 4000000 INFO @ Mon, 12 Aug 2019 23:29:40: 4000000 INFO @ Mon, 12 Aug 2019 23:29:44: 5000000 INFO @ Mon, 12 Aug 2019 23:29:45: 5000000 INFO @ Mon, 12 Aug 2019 23:29:47: 5000000 INFO @ Mon, 12 Aug 2019 23:29:51: 6000000 INFO @ Mon, 12 Aug 2019 23:29:52: 6000000 INFO @ Mon, 12 Aug 2019 23:29:54: 6000000 INFO @ Mon, 12 Aug 2019 23:29:59: 7000000 INFO @ Mon, 12 Aug 2019 23:29:59: 7000000 INFO @ Mon, 12 Aug 2019 23:30:01: 7000000 INFO @ Mon, 12 Aug 2019 23:30:06: 8000000 INFO @ Mon, 12 Aug 2019 23:30:06: 8000000 INFO @ Mon, 12 Aug 2019 23:30:09: 8000000 INFO @ Mon, 12 Aug 2019 23:30:13: 9000000 INFO @ Mon, 12 Aug 2019 23:30:13: 9000000 INFO @ Mon, 12 Aug 2019 23:30:16: 9000000 INFO @ Mon, 12 Aug 2019 23:30:21: 10000000 INFO @ Mon, 12 Aug 2019 23:30:21: 10000000 INFO @ Mon, 12 Aug 2019 23:30:23: 10000000 INFO @ Mon, 12 Aug 2019 23:30:28: 11000000 INFO @ Mon, 12 Aug 2019 23:30:29: 11000000 INFO @ Mon, 12 Aug 2019 23:30:31: 11000000 INFO @ Mon, 12 Aug 2019 23:30:36: 12000000 INFO @ Mon, 12 Aug 2019 23:30:36: 12000000 INFO @ Mon, 12 Aug 2019 23:30:38: 12000000 INFO @ Mon, 12 Aug 2019 23:30:44: 13000000 INFO @ Mon, 12 Aug 2019 23:30:44: 13000000 INFO @ Mon, 12 Aug 2019 23:30:46: 13000000 INFO @ Mon, 12 Aug 2019 23:30:51: 14000000 INFO @ Mon, 12 Aug 2019 23:30:52: 14000000 INFO @ Mon, 12 Aug 2019 23:30:53: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:30:53: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:30:53: #1 total tags in treatment: 14274462 INFO @ Mon, 12 Aug 2019 23:30:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:30:53: #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 23:30:53: 14000000 INFO @ Mon, 12 Aug 2019 23:30:54: #1 tags after filtering in treatment: 14274462 INFO @ Mon, 12 Aug 2019 23:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:30:54: #1 finished! INFO @ Mon, 12 Aug 2019 23:30:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:30:54: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:30:54: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:30:54: #1 total tags in treatment: 14274462 INFO @ Mon, 12 Aug 2019 23:30:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:30:54: #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 23:30:54: #1 tags after filtering in treatment: 14274462 INFO @ Mon, 12 Aug 2019 23:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:30:54: #1 finished! INFO @ Mon, 12 Aug 2019 23:30:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:30:55: #2 number of paired peaks: 1322 INFO @ Mon, 12 Aug 2019 23:30:55: start model_add_line... INFO @ Mon, 12 Aug 2019 23:30:55: start X-correlation... INFO @ Mon, 12 Aug 2019 23:30:55: end of X-cor INFO @ Mon, 12 Aug 2019 23:30:55: #2 finished! INFO @ Mon, 12 Aug 2019 23:30:55: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 23:30:55: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 23:30:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.10_model.r INFO @ Mon, 12 Aug 2019 23:30:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:30:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:30:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:30:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:30:55: #1 total tags in treatment: 14274462 INFO @ Mon, 12 Aug 2019 23:30:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:30:55: #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 23:30:55: #2 number of paired peaks: 1322 INFO @ Mon, 12 Aug 2019 23:30:55: start model_add_line... INFO @ Mon, 12 Aug 2019 23:30:56: #1 tags after filtering in treatment: 14274462 INFO @ Mon, 12 Aug 2019 23:30:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:30:56: #1 finished! INFO @ Mon, 12 Aug 2019 23:30:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:30:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:30:56: start X-correlation... INFO @ Mon, 12 Aug 2019 23:30:56: end of X-cor INFO @ Mon, 12 Aug 2019 23:30:56: #2 finished! INFO @ Mon, 12 Aug 2019 23:30:56: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 23:30:56: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 23:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.05_model.r INFO @ Mon, 12 Aug 2019 23:30:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:30:57: #2 number of paired peaks: 1322 INFO @ Mon, 12 Aug 2019 23:30:57: start model_add_line... INFO @ Mon, 12 Aug 2019 23:30:57: start X-correlation... INFO @ Mon, 12 Aug 2019 23:30:57: end of X-cor INFO @ Mon, 12 Aug 2019 23:30:57: #2 finished! INFO @ Mon, 12 Aug 2019 23:30:57: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 23:30:57: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 23:30:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.20_model.r INFO @ Mon, 12 Aug 2019 23:30:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:31:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:31:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:31:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:31:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:31:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:31:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:31:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.10_summits.bed INFO @ Mon, 12 Aug 2019 23:31:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:31:57: Done! INFO @ Mon, 12 Aug 2019 23:31:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.05_summits.bed INFO @ Mon, 12 Aug 2019 23:31:57: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4471 records, 4 fields): 10 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8325 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011022/SRX5011022.20_summits.bed INFO @ Mon, 12 Aug 2019 23:31:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2047 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。