Job ID = 2590664 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,725,965 reads read : 51,451,930 reads written : 25,725,965 reads 0-length : 25,725,965 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: 00:09:54 25725965 reads; of these: 25725965 (100.00%) were unpaired; of these: 2047205 (7.96%) aligned 0 times 18415874 (71.58%) aligned exactly 1 time 5262886 (20.46%) aligned >1 times 92.04% overall alignment rate Time searching: 00:09:54 Overall time: 00:09:54 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 12 files... [bam_rmdupse_core] 12084851 / 23678760 = 0.5104 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 23:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.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 23:18:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:18:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:18:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.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 23:18:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:18:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:18:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.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 23:18:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:18:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:18:50: 1000000 INFO @ Mon, 12 Aug 2019 23:18:50: 1000000 INFO @ Mon, 12 Aug 2019 23:18:51: 1000000 INFO @ Mon, 12 Aug 2019 23:18:56: 2000000 INFO @ Mon, 12 Aug 2019 23:18:57: 2000000 INFO @ Mon, 12 Aug 2019 23:18:58: 2000000 INFO @ Mon, 12 Aug 2019 23:19:03: 3000000 INFO @ Mon, 12 Aug 2019 23:19:04: 3000000 INFO @ Mon, 12 Aug 2019 23:19:05: 3000000 INFO @ Mon, 12 Aug 2019 23:19:09: 4000000 INFO @ Mon, 12 Aug 2019 23:19:11: 4000000 INFO @ Mon, 12 Aug 2019 23:19:12: 4000000 INFO @ Mon, 12 Aug 2019 23:19:16: 5000000 INFO @ Mon, 12 Aug 2019 23:19:17: 5000000 INFO @ Mon, 12 Aug 2019 23:19:19: 5000000 INFO @ Mon, 12 Aug 2019 23:19:22: 6000000 INFO @ Mon, 12 Aug 2019 23:19:24: 6000000 INFO @ Mon, 12 Aug 2019 23:19:27: 6000000 INFO @ Mon, 12 Aug 2019 23:19:28: 7000000 INFO @ Mon, 12 Aug 2019 23:19:31: 7000000 INFO @ Mon, 12 Aug 2019 23:19:35: 8000000 INFO @ Mon, 12 Aug 2019 23:19:35: 7000000 INFO @ Mon, 12 Aug 2019 23:19:38: 8000000 INFO @ Mon, 12 Aug 2019 23:19:41: 9000000 INFO @ Mon, 12 Aug 2019 23:19:43: 8000000 INFO @ Mon, 12 Aug 2019 23:19:45: 9000000 INFO @ Mon, 12 Aug 2019 23:19:48: 10000000 INFO @ Mon, 12 Aug 2019 23:19:51: 9000000 INFO @ Mon, 12 Aug 2019 23:19:52: 10000000 INFO @ Mon, 12 Aug 2019 23:19:54: 11000000 INFO @ Mon, 12 Aug 2019 23:19:58: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:19:58: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:19:58: #1 total tags in treatment: 11593909 INFO @ Mon, 12 Aug 2019 23:19:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:19:58: #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 23:19:58: #1 tags after filtering in treatment: 11593909 INFO @ Mon, 12 Aug 2019 23:19:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:19:58: #1 finished! INFO @ Mon, 12 Aug 2019 23:19:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:19:59: 11000000 INFO @ Mon, 12 Aug 2019 23:19:59: 10000000 INFO @ Mon, 12 Aug 2019 23:19:59: #2 number of paired peaks: 3362 INFO @ Mon, 12 Aug 2019 23:19:59: start model_add_line... INFO @ Mon, 12 Aug 2019 23:20:00: start X-correlation... INFO @ Mon, 12 Aug 2019 23:20:00: end of X-cor INFO @ Mon, 12 Aug 2019 23:20:00: #2 finished! INFO @ Mon, 12 Aug 2019 23:20:00: #2 predicted fragment length is 225 bps INFO @ Mon, 12 Aug 2019 23:20:00: #2 alternative fragment length(s) may be 225 bps INFO @ Mon, 12 Aug 2019 23:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.10_model.r INFO @ Mon, 12 Aug 2019 23:20:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:20:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:20:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:20:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:20:03: #1 total tags in treatment: 11593909 INFO @ Mon, 12 Aug 2019 23:20:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:20:03: #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 23:20:04: #1 tags after filtering in treatment: 11593909 INFO @ Mon, 12 Aug 2019 23:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:20:04: #1 finished! INFO @ Mon, 12 Aug 2019 23:20:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:20:05: #2 number of paired peaks: 3362 INFO @ Mon, 12 Aug 2019 23:20:05: start model_add_line... INFO @ Mon, 12 Aug 2019 23:20:05: start X-correlation... INFO @ Mon, 12 Aug 2019 23:20:05: end of X-cor INFO @ Mon, 12 Aug 2019 23:20:05: #2 finished! INFO @ Mon, 12 Aug 2019 23:20:05: #2 predicted fragment length is 225 bps INFO @ Mon, 12 Aug 2019 23:20:05: #2 alternative fragment length(s) may be 225 bps INFO @ Mon, 12 Aug 2019 23:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.05_model.r INFO @ Mon, 12 Aug 2019 23:20:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:20:07: 11000000 INFO @ Mon, 12 Aug 2019 23:20:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:20:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:20:12: #1 total tags in treatment: 11593909 INFO @ Mon, 12 Aug 2019 23:20:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:20:12: #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 23:20:12: #1 tags after filtering in treatment: 11593909 INFO @ Mon, 12 Aug 2019 23:20:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:20:12: #1 finished! INFO @ Mon, 12 Aug 2019 23:20:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:20:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:20:14: #2 number of paired peaks: 3362 INFO @ Mon, 12 Aug 2019 23:20:14: start model_add_line... INFO @ Mon, 12 Aug 2019 23:20:14: start X-correlation... INFO @ Mon, 12 Aug 2019 23:20:14: end of X-cor INFO @ Mon, 12 Aug 2019 23:20:14: #2 finished! INFO @ Mon, 12 Aug 2019 23:20:14: #2 predicted fragment length is 225 bps INFO @ Mon, 12 Aug 2019 23:20:14: #2 alternative fragment length(s) may be 225 bps INFO @ Mon, 12 Aug 2019 23:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.20_model.r INFO @ Mon, 12 Aug 2019 23:20:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:20:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:20:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:20:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:20:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:20:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:20:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.10_summits.bed INFO @ Mon, 12 Aug 2019 23:20:56: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8246 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.05_summits.bed INFO @ Mon, 12 Aug 2019 23:21:02: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (11120 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:21:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:21:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:21:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011013/SRX5011013.20_summits.bed INFO @ Mon, 12 Aug 2019 23:21:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5213 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。