Job ID = 1293926 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,521,365 reads read : 27,521,365 reads written : 27,521,365 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: 00:08:18 27521365 reads; of these: 27521365 (100.00%) were unpaired; of these: 7605907 (27.64%) aligned 0 times 13823667 (50.23%) aligned exactly 1 time 6091791 (22.13%) aligned >1 times 72.36% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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] 5894693 / 19915458 = 0.2960 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 03:29:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.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 03:29:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:29:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.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 03:29:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:29:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.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 03:29:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:29:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:29:21: 1000000 INFO @ Mon, 03 Jun 2019 03:29:22: 1000000 INFO @ Mon, 03 Jun 2019 03:29:22: 1000000 INFO @ Mon, 03 Jun 2019 03:29:30: 2000000 INFO @ Mon, 03 Jun 2019 03:29:32: 2000000 INFO @ Mon, 03 Jun 2019 03:29:33: 2000000 INFO @ Mon, 03 Jun 2019 03:29:40: 3000000 INFO @ Mon, 03 Jun 2019 03:29:43: 3000000 INFO @ Mon, 03 Jun 2019 03:29:44: 3000000 INFO @ Mon, 03 Jun 2019 03:29:49: 4000000 INFO @ Mon, 03 Jun 2019 03:29:53: 4000000 INFO @ Mon, 03 Jun 2019 03:29:54: 4000000 INFO @ Mon, 03 Jun 2019 03:29:58: 5000000 INFO @ Mon, 03 Jun 2019 03:30:03: 5000000 INFO @ Mon, 03 Jun 2019 03:30:05: 5000000 INFO @ Mon, 03 Jun 2019 03:30:07: 6000000 INFO @ Mon, 03 Jun 2019 03:30:13: 6000000 INFO @ Mon, 03 Jun 2019 03:30:15: 6000000 INFO @ Mon, 03 Jun 2019 03:30:17: 7000000 INFO @ Mon, 03 Jun 2019 03:30:23: 7000000 INFO @ Mon, 03 Jun 2019 03:30:25: 7000000 INFO @ Mon, 03 Jun 2019 03:30:26: 8000000 INFO @ Mon, 03 Jun 2019 03:30:32: 8000000 INFO @ Mon, 03 Jun 2019 03:30:34: 8000000 INFO @ Mon, 03 Jun 2019 03:30:35: 9000000 INFO @ Mon, 03 Jun 2019 03:30:42: 9000000 INFO @ Mon, 03 Jun 2019 03:30:44: 10000000 INFO @ Mon, 03 Jun 2019 03:30:44: 9000000 INFO @ Mon, 03 Jun 2019 03:30:52: 10000000 INFO @ Mon, 03 Jun 2019 03:30:53: 11000000 INFO @ Mon, 03 Jun 2019 03:30:54: 10000000 INFO @ Mon, 03 Jun 2019 03:31:02: 11000000 INFO @ Mon, 03 Jun 2019 03:31:02: 12000000 INFO @ Mon, 03 Jun 2019 03:31:04: 11000000 INFO @ Mon, 03 Jun 2019 03:31:11: 12000000 INFO @ Mon, 03 Jun 2019 03:31:11: 13000000 INFO @ Mon, 03 Jun 2019 03:31:14: 12000000 INFO @ Mon, 03 Jun 2019 03:31:20: 14000000 INFO @ Mon, 03 Jun 2019 03:31:21: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:31:21: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:31:21: #1 total tags in treatment: 14020765 INFO @ Mon, 03 Jun 2019 03:31:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:31:21: #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 03:31:21: #1 tags after filtering in treatment: 14020765 INFO @ Mon, 03 Jun 2019 03:31:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:31:21: #1 finished! INFO @ Mon, 03 Jun 2019 03:31:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:31:21: 13000000 INFO @ Mon, 03 Jun 2019 03:31:22: #2 number of paired peaks: 1597 INFO @ Mon, 03 Jun 2019 03:31:22: start model_add_line... INFO @ Mon, 03 Jun 2019 03:31:23: start X-correlation... INFO @ Mon, 03 Jun 2019 03:31:23: end of X-cor INFO @ Mon, 03 Jun 2019 03:31:23: #2 finished! INFO @ Mon, 03 Jun 2019 03:31:23: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 03:31:23: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 03:31:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.05_model.r INFO @ Mon, 03 Jun 2019 03:31:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:31:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:31:24: 13000000 INFO @ Mon, 03 Jun 2019 03:31:31: 14000000 INFO @ Mon, 03 Jun 2019 03:31:31: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:31:31: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:31:31: #1 total tags in treatment: 14020765 INFO @ Mon, 03 Jun 2019 03:31:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:31:31: #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 03:31:31: #1 tags after filtering in treatment: 14020765 INFO @ Mon, 03 Jun 2019 03:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:31:31: #1 finished! INFO @ Mon, 03 Jun 2019 03:31:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:31:33: #2 number of paired peaks: 1597 INFO @ Mon, 03 Jun 2019 03:31:33: start model_add_line... INFO @ Mon, 03 Jun 2019 03:31:33: start X-correlation... INFO @ Mon, 03 Jun 2019 03:31:33: end of X-cor INFO @ Mon, 03 Jun 2019 03:31:33: #2 finished! INFO @ Mon, 03 Jun 2019 03:31:33: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 03:31:33: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 03:31:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.20_model.r INFO @ Mon, 03 Jun 2019 03:31:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:31:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:31:33: 14000000 INFO @ Mon, 03 Jun 2019 03:31:34: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:31:34: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:31:34: #1 total tags in treatment: 14020765 INFO @ Mon, 03 Jun 2019 03:31:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:31:34: #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 03:31:34: #1 tags after filtering in treatment: 14020765 INFO @ Mon, 03 Jun 2019 03:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:31:34: #1 finished! INFO @ Mon, 03 Jun 2019 03:31:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:31:36: #2 number of paired peaks: 1597 INFO @ Mon, 03 Jun 2019 03:31:36: start model_add_line... INFO @ Mon, 03 Jun 2019 03:31:36: start X-correlation... INFO @ Mon, 03 Jun 2019 03:31:36: end of X-cor INFO @ Mon, 03 Jun 2019 03:31:36: #2 finished! INFO @ Mon, 03 Jun 2019 03:31:36: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 03:31:36: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 03:31:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.10_model.r INFO @ Mon, 03 Jun 2019 03:31:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:31:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:32:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:32:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:32:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:32:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:32:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:32:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.05_summits.bed INFO @ Mon, 03 Jun 2019 03:32:23: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12019 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:32:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.20_summits.bed INFO @ Mon, 03 Jun 2019 03:32:32: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3604 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:32:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:32:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:32:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149198/SRX149198.10_summits.bed INFO @ Mon, 03 Jun 2019 03:32:35: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7531 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。