Job ID = 2590682 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 44,458,658 reads read : 88,917,316 reads written : 44,458,658 reads 0-length : 44,458,658 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: 00:17:23 44458658 reads; of these: 44458658 (100.00%) were unpaired; of these: 4121603 (9.27%) aligned 0 times 29619593 (66.62%) aligned exactly 1 time 10717462 (24.11%) aligned >1 times 90.73% overall alignment rate Time searching: 00:17:23 Overall time: 00:17:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 21649495 / 40337055 = 0.5367 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 23:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.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 23:42:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.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 23:42:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.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 23:42:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:40: 1000000 INFO @ Mon, 12 Aug 2019 23:42:41: 1000000 INFO @ Mon, 12 Aug 2019 23:42:43: 1000000 INFO @ Mon, 12 Aug 2019 23:42:49: 2000000 INFO @ Mon, 12 Aug 2019 23:42:50: 2000000 INFO @ Mon, 12 Aug 2019 23:42:52: 2000000 INFO @ Mon, 12 Aug 2019 23:42:57: 3000000 INFO @ Mon, 12 Aug 2019 23:42:58: 3000000 INFO @ Mon, 12 Aug 2019 23:43:01: 3000000 INFO @ Mon, 12 Aug 2019 23:43:06: 4000000 INFO @ Mon, 12 Aug 2019 23:43:07: 4000000 INFO @ Mon, 12 Aug 2019 23:43:10: 4000000 INFO @ Mon, 12 Aug 2019 23:43:15: 5000000 INFO @ Mon, 12 Aug 2019 23:43:16: 5000000 INFO @ Mon, 12 Aug 2019 23:43:20: 5000000 INFO @ Mon, 12 Aug 2019 23:43:23: 6000000 INFO @ Mon, 12 Aug 2019 23:43:25: 6000000 INFO @ Mon, 12 Aug 2019 23:43:29: 6000000 INFO @ Mon, 12 Aug 2019 23:43:32: 7000000 INFO @ Mon, 12 Aug 2019 23:43:34: 7000000 INFO @ Mon, 12 Aug 2019 23:43:38: 7000000 INFO @ Mon, 12 Aug 2019 23:43:42: 8000000 INFO @ Mon, 12 Aug 2019 23:43:43: 8000000 INFO @ Mon, 12 Aug 2019 23:43:48: 8000000 INFO @ Mon, 12 Aug 2019 23:43:51: 9000000 INFO @ Mon, 12 Aug 2019 23:43:52: 9000000 INFO @ Mon, 12 Aug 2019 23:43:58: 9000000 INFO @ Mon, 12 Aug 2019 23:44:01: 10000000 INFO @ Mon, 12 Aug 2019 23:44:02: 10000000 INFO @ Mon, 12 Aug 2019 23:44:08: 10000000 INFO @ Mon, 12 Aug 2019 23:44:10: 11000000 INFO @ Mon, 12 Aug 2019 23:44:11: 11000000 INFO @ Mon, 12 Aug 2019 23:44:18: 11000000 INFO @ Mon, 12 Aug 2019 23:44:19: 12000000 INFO @ Mon, 12 Aug 2019 23:44:21: 12000000 INFO @ Mon, 12 Aug 2019 23:44:28: 12000000 INFO @ Mon, 12 Aug 2019 23:44:29: 13000000 INFO @ Mon, 12 Aug 2019 23:44:30: 13000000 INFO @ Mon, 12 Aug 2019 23:44:38: 14000000 INFO @ Mon, 12 Aug 2019 23:44:38: 13000000 INFO @ Mon, 12 Aug 2019 23:44:39: 14000000 INFO @ Mon, 12 Aug 2019 23:44:47: 15000000 INFO @ Mon, 12 Aug 2019 23:44:48: 14000000 INFO @ Mon, 12 Aug 2019 23:44:48: 15000000 INFO @ Mon, 12 Aug 2019 23:44:56: 16000000 INFO @ Mon, 12 Aug 2019 23:44:57: 16000000 INFO @ Mon, 12 Aug 2019 23:44:57: 15000000 INFO @ Mon, 12 Aug 2019 23:45:05: 17000000 INFO @ Mon, 12 Aug 2019 23:45:06: 17000000 INFO @ Mon, 12 Aug 2019 23:45:07: 16000000 INFO @ Mon, 12 Aug 2019 23:45:14: 18000000 INFO @ Mon, 12 Aug 2019 23:45:15: 18000000 INFO @ Mon, 12 Aug 2019 23:45:17: 17000000 INFO @ Mon, 12 Aug 2019 23:45:20: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:45:20: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:45:20: #1 total tags in treatment: 18687560 INFO @ Mon, 12 Aug 2019 23:45:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:45:20: #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 23:45:21: #1 tags after filtering in treatment: 18687560 INFO @ Mon, 12 Aug 2019 23:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:45:21: #1 finished! INFO @ Mon, 12 Aug 2019 23:45:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:45:21: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:45:21: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:45:21: #1 total tags in treatment: 18687560 INFO @ Mon, 12 Aug 2019 23:45:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:45:21: #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 23:45:22: #1 tags after filtering in treatment: 18687560 INFO @ Mon, 12 Aug 2019 23:45:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:45:22: #1 finished! INFO @ Mon, 12 Aug 2019 23:45:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:45:22: #2 number of paired peaks: 1062 INFO @ Mon, 12 Aug 2019 23:45:22: start model_add_line... INFO @ Mon, 12 Aug 2019 23:45:23: start X-correlation... INFO @ Mon, 12 Aug 2019 23:45:23: end of X-cor INFO @ Mon, 12 Aug 2019 23:45:23: #2 finished! INFO @ Mon, 12 Aug 2019 23:45:23: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 23:45:23: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 23:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.05_model.r INFO @ Mon, 12 Aug 2019 23:45:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:45:23: #2 number of paired peaks: 1062 INFO @ Mon, 12 Aug 2019 23:45:23: start model_add_line... INFO @ Mon, 12 Aug 2019 23:45:24: start X-correlation... INFO @ Mon, 12 Aug 2019 23:45:24: end of X-cor INFO @ Mon, 12 Aug 2019 23:45:24: #2 finished! INFO @ Mon, 12 Aug 2019 23:45:24: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 23:45:24: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 23:45:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.10_model.r INFO @ Mon, 12 Aug 2019 23:45:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:45:26: 18000000 INFO @ Mon, 12 Aug 2019 23:45:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:45:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:45:32: #1 total tags in treatment: 18687560 INFO @ Mon, 12 Aug 2019 23:45:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:45:32: #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 23:45:33: #1 tags after filtering in treatment: 18687560 INFO @ Mon, 12 Aug 2019 23:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:45:33: #1 finished! INFO @ Mon, 12 Aug 2019 23:45:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:45:35: #2 number of paired peaks: 1062 INFO @ Mon, 12 Aug 2019 23:45:35: start model_add_line... INFO @ Mon, 12 Aug 2019 23:45:35: start X-correlation... INFO @ Mon, 12 Aug 2019 23:45:35: end of X-cor INFO @ Mon, 12 Aug 2019 23:45:35: #2 finished! INFO @ Mon, 12 Aug 2019 23:45:35: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 23:45:35: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 23:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.20_model.r INFO @ Mon, 12 Aug 2019 23:45:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:46:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:46:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:46:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:46:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:46:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.05_summits.bed INFO @ Mon, 12 Aug 2019 23:46:40: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12283 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:46:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:46:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:46:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.10_summits.bed INFO @ Mon, 12 Aug 2019 23:46:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7584 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:46:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011028/SRX5011028.20_summits.bed INFO @ Mon, 12 Aug 2019 23:46:52: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3801 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。