Job ID = 2590801 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,857,352 reads read : 73,714,704 reads written : 36,857,352 reads 0-length : 36,857,352 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: 00:12:13 36857352 reads; of these: 36857352 (100.00%) were unpaired; of these: 2820067 (7.65%) aligned 0 times 26780930 (72.66%) aligned exactly 1 time 7256355 (19.69%) aligned >1 times 92.35% overall alignment rate Time searching: 00:12:13 Overall time: 00:12:13 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] 19227694 / 34037285 = 0.5649 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 23:41:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.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 23:41:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:41:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:41:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.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 23:41:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:41:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:41:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.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 23:41:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:41:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:41:15: 1000000 INFO @ Mon, 12 Aug 2019 23:41:17: 1000000 INFO @ Mon, 12 Aug 2019 23:41:19: 1000000 INFO @ Mon, 12 Aug 2019 23:41:22: 2000000 INFO @ Mon, 12 Aug 2019 23:41:24: 2000000 INFO @ Mon, 12 Aug 2019 23:41:28: 2000000 INFO @ Mon, 12 Aug 2019 23:41:28: 3000000 INFO @ Mon, 12 Aug 2019 23:41:31: 3000000 INFO @ Mon, 12 Aug 2019 23:41:35: 4000000 INFO @ Mon, 12 Aug 2019 23:41:36: 3000000 INFO @ Mon, 12 Aug 2019 23:41:38: 4000000 INFO @ Mon, 12 Aug 2019 23:41:41: 5000000 INFO @ Mon, 12 Aug 2019 23:41:45: 4000000 INFO @ Mon, 12 Aug 2019 23:41:45: 5000000 INFO @ Mon, 12 Aug 2019 23:41:48: 6000000 INFO @ Mon, 12 Aug 2019 23:41:52: 6000000 INFO @ Mon, 12 Aug 2019 23:41:53: 5000000 INFO @ Mon, 12 Aug 2019 23:41:54: 7000000 INFO @ Mon, 12 Aug 2019 23:41:59: 7000000 INFO @ Mon, 12 Aug 2019 23:42:01: 8000000 INFO @ Mon, 12 Aug 2019 23:42:01: 6000000 INFO @ Mon, 12 Aug 2019 23:42:06: 8000000 INFO @ Mon, 12 Aug 2019 23:42:07: 9000000 INFO @ Mon, 12 Aug 2019 23:42:10: 7000000 INFO @ Mon, 12 Aug 2019 23:42:13: 9000000 INFO @ Mon, 12 Aug 2019 23:42:14: 10000000 INFO @ Mon, 12 Aug 2019 23:42:18: 8000000 INFO @ Mon, 12 Aug 2019 23:42:20: 10000000 INFO @ Mon, 12 Aug 2019 23:42:20: 11000000 INFO @ Mon, 12 Aug 2019 23:42:26: 12000000 INFO @ Mon, 12 Aug 2019 23:42:27: 11000000 INFO @ Mon, 12 Aug 2019 23:42:27: 9000000 INFO @ Mon, 12 Aug 2019 23:42:33: 13000000 INFO @ Mon, 12 Aug 2019 23:42:34: 12000000 INFO @ Mon, 12 Aug 2019 23:42:35: 10000000 INFO @ Mon, 12 Aug 2019 23:42:39: 14000000 INFO @ Mon, 12 Aug 2019 23:42:40: 13000000 INFO @ Mon, 12 Aug 2019 23:42:43: 11000000 INFO @ Mon, 12 Aug 2019 23:42:44: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:42:44: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:42:44: #1 total tags in treatment: 14809591 INFO @ Mon, 12 Aug 2019 23:42:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:42:44: #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 23:42:45: #1 tags after filtering in treatment: 14809591 INFO @ Mon, 12 Aug 2019 23:42:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:42:45: #1 finished! INFO @ Mon, 12 Aug 2019 23:42:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:42:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:42:46: #2 number of paired peaks: 4738 INFO @ Mon, 12 Aug 2019 23:42:46: start model_add_line... INFO @ Mon, 12 Aug 2019 23:42:47: start X-correlation... INFO @ Mon, 12 Aug 2019 23:42:47: end of X-cor INFO @ Mon, 12 Aug 2019 23:42:47: #2 finished! INFO @ Mon, 12 Aug 2019 23:42:47: #2 predicted fragment length is 245 bps INFO @ Mon, 12 Aug 2019 23:42:47: #2 alternative fragment length(s) may be 245 bps INFO @ Mon, 12 Aug 2019 23:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.05_model.r INFO @ Mon, 12 Aug 2019 23:42:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:42:47: 14000000 INFO @ Mon, 12 Aug 2019 23:42:51: 12000000 INFO @ Mon, 12 Aug 2019 23:42:53: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:42:53: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:42:53: #1 total tags in treatment: 14809591 INFO @ Mon, 12 Aug 2019 23:42:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:42:53: #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 23:42:53: #1 tags after filtering in treatment: 14809591 INFO @ Mon, 12 Aug 2019 23:42:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:42:53: #1 finished! INFO @ Mon, 12 Aug 2019 23:42:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:42:55: #2 number of paired peaks: 4738 INFO @ Mon, 12 Aug 2019 23:42:55: start model_add_line... INFO @ Mon, 12 Aug 2019 23:42:55: start X-correlation... INFO @ Mon, 12 Aug 2019 23:42:55: end of X-cor INFO @ Mon, 12 Aug 2019 23:42:55: #2 finished! INFO @ Mon, 12 Aug 2019 23:42:55: #2 predicted fragment length is 245 bps INFO @ Mon, 12 Aug 2019 23:42:55: #2 alternative fragment length(s) may be 245 bps INFO @ Mon, 12 Aug 2019 23:42:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.10_model.r INFO @ Mon, 12 Aug 2019 23:42:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:42:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:42:59: 13000000 INFO @ Mon, 12 Aug 2019 23:43:07: 14000000 INFO @ Mon, 12 Aug 2019 23:43:14: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:14: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:14: #1 total tags in treatment: 14809591 INFO @ Mon, 12 Aug 2019 23:43:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:14: #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 23:43:14: #1 tags after filtering in treatment: 14809591 INFO @ Mon, 12 Aug 2019 23:43:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:14: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:16: #2 number of paired peaks: 4738 INFO @ Mon, 12 Aug 2019 23:43:16: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:16: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:16: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:16: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:16: #2 predicted fragment length is 245 bps INFO @ Mon, 12 Aug 2019 23:43:16: #2 alternative fragment length(s) may be 245 bps INFO @ Mon, 12 Aug 2019 23:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.20_model.r INFO @ Mon, 12 Aug 2019 23:43:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:43:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:43:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:44:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:44:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:44:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.05_summits.bed INFO @ Mon, 12 Aug 2019 23:44:05: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (11247 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:44:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:44:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:44:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:44:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.10_summits.bed INFO @ Mon, 12 Aug 2019 23:44:12: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9182 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011043/SRX5011043.20_summits.bed INFO @ Mon, 12 Aug 2019 23:44:33: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6775 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。