Job ID = 1294544 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,579,648 reads read : 16,579,648 reads written : 16,579,648 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:55 16579648 reads; of these: 16579648 (100.00%) were unpaired; of these: 1004331 (6.06%) aligned 0 times 14635196 (88.27%) aligned exactly 1 time 940121 (5.67%) aligned >1 times 93.94% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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 8 files... [bam_rmdupse_core] 3131434 / 15575317 = 0.2011 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, 03 Jun 2019 09:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.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, 03 Jun 2019 09:01:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:01:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.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, 03 Jun 2019 09:01:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:01:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.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, 03 Jun 2019 09:01:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:01:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:01:47: 1000000 INFO @ Mon, 03 Jun 2019 09:01:47: 1000000 INFO @ Mon, 03 Jun 2019 09:01:47: 1000000 INFO @ Mon, 03 Jun 2019 09:01:55: 2000000 INFO @ Mon, 03 Jun 2019 09:01:55: 2000000 INFO @ Mon, 03 Jun 2019 09:01:55: 2000000 INFO @ Mon, 03 Jun 2019 09:02:03: 3000000 INFO @ Mon, 03 Jun 2019 09:02:04: 3000000 INFO @ Mon, 03 Jun 2019 09:02:04: 3000000 INFO @ Mon, 03 Jun 2019 09:02:11: 4000000 INFO @ Mon, 03 Jun 2019 09:02:12: 4000000 INFO @ Mon, 03 Jun 2019 09:02:12: 4000000 INFO @ Mon, 03 Jun 2019 09:02:19: 5000000 INFO @ Mon, 03 Jun 2019 09:02:21: 5000000 INFO @ Mon, 03 Jun 2019 09:02:21: 5000000 INFO @ Mon, 03 Jun 2019 09:02:27: 6000000 INFO @ Mon, 03 Jun 2019 09:02:30: 6000000 INFO @ Mon, 03 Jun 2019 09:02:30: 6000000 INFO @ Mon, 03 Jun 2019 09:02:36: 7000000 INFO @ Mon, 03 Jun 2019 09:02:38: 7000000 INFO @ Mon, 03 Jun 2019 09:02:38: 7000000 INFO @ Mon, 03 Jun 2019 09:02:44: 8000000 INFO @ Mon, 03 Jun 2019 09:02:47: 8000000 INFO @ Mon, 03 Jun 2019 09:02:47: 8000000 INFO @ Mon, 03 Jun 2019 09:02:52: 9000000 INFO @ Mon, 03 Jun 2019 09:02:56: 9000000 INFO @ Mon, 03 Jun 2019 09:02:56: 9000000 INFO @ Mon, 03 Jun 2019 09:03:00: 10000000 INFO @ Mon, 03 Jun 2019 09:03:04: 10000000 INFO @ Mon, 03 Jun 2019 09:03:04: 10000000 INFO @ Mon, 03 Jun 2019 09:03:08: 11000000 INFO @ Mon, 03 Jun 2019 09:03:13: 11000000 INFO @ Mon, 03 Jun 2019 09:03:13: 11000000 INFO @ Mon, 03 Jun 2019 09:03:16: 12000000 INFO @ Mon, 03 Jun 2019 09:03:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:03:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:03:20: #1 total tags in treatment: 12443883 INFO @ Mon, 03 Jun 2019 09:03:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:03:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:03:20: #1 tags after filtering in treatment: 12443883 INFO @ Mon, 03 Jun 2019 09:03:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:03:20: #1 finished! INFO @ Mon, 03 Jun 2019 09:03:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:03:21: 12000000 INFO @ Mon, 03 Jun 2019 09:03:21: 12000000 INFO @ Mon, 03 Jun 2019 09:03:22: #2 number of paired peaks: 11778 INFO @ Mon, 03 Jun 2019 09:03:22: start model_add_line... INFO @ Mon, 03 Jun 2019 09:03:23: start X-correlation... INFO @ Mon, 03 Jun 2019 09:03:23: end of X-cor INFO @ Mon, 03 Jun 2019 09:03:23: #2 finished! INFO @ Mon, 03 Jun 2019 09:03:23: #2 predicted fragment length is 196 bps INFO @ Mon, 03 Jun 2019 09:03:23: #2 alternative fragment length(s) may be 196 bps INFO @ Mon, 03 Jun 2019 09:03:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.10_model.r INFO @ Mon, 03 Jun 2019 09:03:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:03:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:03:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:03:25: #1 total tags in treatment: 12443883 INFO @ Mon, 03 Jun 2019 09:03:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:03:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:03:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:03:25: #1 total tags in treatment: 12443883 INFO @ Mon, 03 Jun 2019 09:03:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 09:03:25: #1 tags after filtering in treatment: 12443883 INFO @ Mon, 03 Jun 2019 09:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:03:25: #1 finished! INFO @ Mon, 03 Jun 2019 09:03:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:03:25: #1 tags after filtering in treatment: 12443883 INFO @ Mon, 03 Jun 2019 09:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:03:25: #1 finished! INFO @ Mon, 03 Jun 2019 09:03:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:03:28: #2 number of paired peaks: 11778 INFO @ Mon, 03 Jun 2019 09:03:28: start model_add_line... INFO @ Mon, 03 Jun 2019 09:03:28: #2 number of paired peaks: 11778 INFO @ Mon, 03 Jun 2019 09:03:28: start model_add_line... INFO @ Mon, 03 Jun 2019 09:03:28: start X-correlation... INFO @ Mon, 03 Jun 2019 09:03:28: end of X-cor INFO @ Mon, 03 Jun 2019 09:03:28: #2 finished! INFO @ Mon, 03 Jun 2019 09:03:28: #2 predicted fragment length is 196 bps INFO @ Mon, 03 Jun 2019 09:03:28: #2 alternative fragment length(s) may be 196 bps INFO @ Mon, 03 Jun 2019 09:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.05_model.r INFO @ Mon, 03 Jun 2019 09:03:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:03:28: start X-correlation... INFO @ Mon, 03 Jun 2019 09:03:28: end of X-cor INFO @ Mon, 03 Jun 2019 09:03:28: #2 finished! INFO @ Mon, 03 Jun 2019 09:03:28: #2 predicted fragment length is 196 bps INFO @ Mon, 03 Jun 2019 09:03:28: #2 alternative fragment length(s) may be 196 bps INFO @ Mon, 03 Jun 2019 09:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.20_model.r INFO @ Mon, 03 Jun 2019 09:03:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:04:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:04:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:04:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:04:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:04:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:04:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.10_summits.bed INFO @ Mon, 03 Jun 2019 09:04:22: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8161 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:04:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.20_summits.bed INFO @ Mon, 03 Jun 2019 09:04:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:04:27: Done! INFO @ Mon, 03 Jun 2019 09:04:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287731/SRX287731.05_summits.bed INFO @ Mon, 03 Jun 2019 09:04:27: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (6828 records, 4 fields): 13 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9013 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。