Job ID = 2590302 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,636,737 reads read : 23,636,737 reads written : 23,636,737 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: 00:06:59 23636737 reads; of these: 23636737 (100.00%) were unpaired; of these: 3629461 (15.36%) aligned 0 times 15737388 (66.58%) aligned exactly 1 time 4269888 (18.06%) aligned >1 times 84.64% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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] 7180943 / 20007276 = 0.3589 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 20:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.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 20:57:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:57:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:57:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.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 20:57:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:57:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.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 20:57:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:57:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:57:58: 1000000 INFO @ Mon, 12 Aug 2019 20:58:01: 1000000 INFO @ Mon, 12 Aug 2019 20:58:01: 1000000 INFO @ Mon, 12 Aug 2019 20:58:07: 2000000 INFO @ Mon, 12 Aug 2019 20:58:09: 2000000 INFO @ Mon, 12 Aug 2019 20:58:11: 2000000 INFO @ Mon, 12 Aug 2019 20:58:15: 3000000 INFO @ Mon, 12 Aug 2019 20:58:18: 3000000 INFO @ Mon, 12 Aug 2019 20:58:22: 3000000 INFO @ Mon, 12 Aug 2019 20:58:27: 4000000 INFO @ Mon, 12 Aug 2019 20:58:27: 4000000 INFO @ Mon, 12 Aug 2019 20:58:34: 4000000 INFO @ Mon, 12 Aug 2019 20:58:35: 5000000 INFO @ Mon, 12 Aug 2019 20:58:38: 5000000 INFO @ Mon, 12 Aug 2019 20:58:44: 6000000 INFO @ Mon, 12 Aug 2019 20:58:45: 5000000 INFO @ Mon, 12 Aug 2019 20:58:50: 6000000 INFO @ Mon, 12 Aug 2019 20:58:52: 7000000 INFO @ Mon, 12 Aug 2019 20:58:57: 6000000 INFO @ Mon, 12 Aug 2019 20:59:01: 8000000 INFO @ Mon, 12 Aug 2019 20:59:02: 7000000 INFO @ Mon, 12 Aug 2019 20:59:09: 7000000 INFO @ Mon, 12 Aug 2019 20:59:09: 9000000 INFO @ Mon, 12 Aug 2019 20:59:13: 8000000 INFO @ Mon, 12 Aug 2019 20:59:18: 10000000 INFO @ Mon, 12 Aug 2019 20:59:20: 8000000 INFO @ Mon, 12 Aug 2019 20:59:25: 9000000 INFO @ Mon, 12 Aug 2019 20:59:26: 11000000 INFO @ Mon, 12 Aug 2019 20:59:32: 9000000 INFO @ Mon, 12 Aug 2019 20:59:35: 12000000 INFO @ Mon, 12 Aug 2019 20:59:36: 10000000 INFO @ Mon, 12 Aug 2019 20:59:42: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:59:42: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:59:42: #1 total tags in treatment: 12826333 INFO @ Mon, 12 Aug 2019 20:59:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:59:42: #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 20:59:42: #1 tags after filtering in treatment: 12826333 INFO @ Mon, 12 Aug 2019 20:59:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:59:42: #1 finished! INFO @ Mon, 12 Aug 2019 20:59:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:59:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:59:43: 10000000 INFO @ Mon, 12 Aug 2019 20:59:44: #2 number of paired peaks: 9208 INFO @ Mon, 12 Aug 2019 20:59:44: start model_add_line... INFO @ Mon, 12 Aug 2019 20:59:44: start X-correlation... INFO @ Mon, 12 Aug 2019 20:59:44: end of X-cor INFO @ Mon, 12 Aug 2019 20:59:44: #2 finished! INFO @ Mon, 12 Aug 2019 20:59:44: #2 predicted fragment length is 226 bps INFO @ Mon, 12 Aug 2019 20:59:44: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 12 Aug 2019 20:59:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.20_model.r INFO @ Mon, 12 Aug 2019 20:59:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:59:48: 11000000 INFO @ Mon, 12 Aug 2019 20:59:55: 11000000 INFO @ Mon, 12 Aug 2019 20:59:59: 12000000 INFO @ Mon, 12 Aug 2019 21:00:06: 12000000 INFO @ Mon, 12 Aug 2019 21:00:09: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:00:09: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:00:09: #1 total tags in treatment: 12826333 INFO @ Mon, 12 Aug 2019 21:00:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:09: #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 21:00:09: #1 tags after filtering in treatment: 12826333 INFO @ Mon, 12 Aug 2019 21:00:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:09: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:11: #2 number of paired peaks: 9208 INFO @ Mon, 12 Aug 2019 21:00:11: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:12: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:12: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:12: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:12: #2 predicted fragment length is 226 bps INFO @ Mon, 12 Aug 2019 21:00:12: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 12 Aug 2019 21:00:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.05_model.r INFO @ Mon, 12 Aug 2019 21:00:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:00:14: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:00:14: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:00:14: #1 total tags in treatment: 12826333 INFO @ Mon, 12 Aug 2019 21:00:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:14: #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 21:00:15: #1 tags after filtering in treatment: 12826333 INFO @ Mon, 12 Aug 2019 21:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:15: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:17: #2 number of paired peaks: 9208 INFO @ Mon, 12 Aug 2019 21:00:17: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:17: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:17: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:17: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:17: #2 predicted fragment length is 226 bps INFO @ Mon, 12 Aug 2019 21:00:17: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 12 Aug 2019 21:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.10_model.r INFO @ Mon, 12 Aug 2019 21:00:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:00:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:00:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:00:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:00:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.20_summits.bed INFO @ Mon, 12 Aug 2019 21:00:55: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7314 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:01:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:01:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:01:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:01:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.05_summits.bed INFO @ Mon, 12 Aug 2019 21:01:28: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10047 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:01:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:01:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318797/SRX318797.10_summits.bed INFO @ Mon, 12 Aug 2019 21:01:29: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8800 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。