Job ID = 1295098 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,115,118 reads read : 21,115,118 reads written : 21,115,118 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: 00:08:30 21115118 reads; of these: 21115118 (100.00%) were unpaired; of these: 1590438 (7.53%) aligned 0 times 14799791 (70.09%) aligned exactly 1 time 4724889 (22.38%) aligned >1 times 92.47% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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] 3130669 / 19524680 = 0.1603 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 12:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.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 12:04:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:04:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.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 12:04:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:04:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.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 12:04:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:04:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:04:11: 1000000 INFO @ Mon, 03 Jun 2019 12:04:12: 1000000 INFO @ Mon, 03 Jun 2019 12:04:13: 1000000 INFO @ Mon, 03 Jun 2019 12:04:21: 2000000 INFO @ Mon, 03 Jun 2019 12:04:22: 2000000 INFO @ Mon, 03 Jun 2019 12:04:26: 2000000 INFO @ Mon, 03 Jun 2019 12:04:32: 3000000 INFO @ Mon, 03 Jun 2019 12:04:32: 3000000 INFO @ Mon, 03 Jun 2019 12:04:38: 3000000 INFO @ Mon, 03 Jun 2019 12:04:41: 4000000 INFO @ Mon, 03 Jun 2019 12:04:43: 4000000 INFO @ Mon, 03 Jun 2019 12:04:50: 4000000 INFO @ Mon, 03 Jun 2019 12:04:51: 5000000 INFO @ Mon, 03 Jun 2019 12:04:52: 5000000 INFO @ Mon, 03 Jun 2019 12:05:01: 6000000 INFO @ Mon, 03 Jun 2019 12:05:01: 5000000 INFO @ Mon, 03 Jun 2019 12:05:03: 6000000 INFO @ Mon, 03 Jun 2019 12:05:10: 7000000 INFO @ Mon, 03 Jun 2019 12:05:12: 6000000 INFO @ Mon, 03 Jun 2019 12:05:13: 7000000 INFO @ Mon, 03 Jun 2019 12:05:20: 8000000 INFO @ Mon, 03 Jun 2019 12:05:23: 8000000 INFO @ Mon, 03 Jun 2019 12:05:24: 7000000 INFO @ Mon, 03 Jun 2019 12:05:30: 9000000 INFO @ Mon, 03 Jun 2019 12:05:32: 9000000 INFO @ Mon, 03 Jun 2019 12:05:35: 8000000 INFO @ Mon, 03 Jun 2019 12:05:39: 10000000 INFO @ Mon, 03 Jun 2019 12:05:42: 10000000 INFO @ Mon, 03 Jun 2019 12:05:47: 9000000 INFO @ Mon, 03 Jun 2019 12:05:49: 11000000 INFO @ Mon, 03 Jun 2019 12:05:52: 11000000 INFO @ Mon, 03 Jun 2019 12:05:58: 10000000 INFO @ Mon, 03 Jun 2019 12:05:58: 12000000 INFO @ Mon, 03 Jun 2019 12:06:02: 12000000 INFO @ Mon, 03 Jun 2019 12:06:08: 13000000 INFO @ Mon, 03 Jun 2019 12:06:09: 11000000 INFO @ Mon, 03 Jun 2019 12:06:12: 13000000 INFO @ Mon, 03 Jun 2019 12:06:17: 14000000 INFO @ Mon, 03 Jun 2019 12:06:20: 12000000 INFO @ Mon, 03 Jun 2019 12:06:22: 14000000 INFO @ Mon, 03 Jun 2019 12:06:27: 15000000 INFO @ Mon, 03 Jun 2019 12:06:31: 13000000 INFO @ Mon, 03 Jun 2019 12:06:31: 15000000 INFO @ Mon, 03 Jun 2019 12:06:36: 16000000 INFO @ Mon, 03 Jun 2019 12:06:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:06:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:06:40: #1 total tags in treatment: 16394011 INFO @ Mon, 03 Jun 2019 12:06:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:06:40: #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 12:06:40: #1 tags after filtering in treatment: 16394011 INFO @ Mon, 03 Jun 2019 12:06:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:06:40: #1 finished! INFO @ Mon, 03 Jun 2019 12:06:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:06:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:06:41: 16000000 INFO @ Mon, 03 Jun 2019 12:06:42: #2 number of paired peaks: 1475 INFO @ Mon, 03 Jun 2019 12:06:42: start model_add_line... INFO @ Mon, 03 Jun 2019 12:06:42: start X-correlation... INFO @ Mon, 03 Jun 2019 12:06:42: end of X-cor INFO @ Mon, 03 Jun 2019 12:06:42: #2 finished! INFO @ Mon, 03 Jun 2019 12:06:42: #2 predicted fragment length is 214 bps INFO @ Mon, 03 Jun 2019 12:06:42: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 03 Jun 2019 12:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.20_model.r INFO @ Mon, 03 Jun 2019 12:06:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:06:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:06:42: 14000000 INFO @ Mon, 03 Jun 2019 12:06:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:06:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:06:45: #1 total tags in treatment: 16394011 INFO @ Mon, 03 Jun 2019 12:06:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:06:45: #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 12:06:45: #1 tags after filtering in treatment: 16394011 INFO @ Mon, 03 Jun 2019 12:06:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:06:45: #1 finished! INFO @ Mon, 03 Jun 2019 12:06:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:06:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:06:47: #2 number of paired peaks: 1475 INFO @ Mon, 03 Jun 2019 12:06:47: start model_add_line... INFO @ Mon, 03 Jun 2019 12:06:47: start X-correlation... INFO @ Mon, 03 Jun 2019 12:06:47: end of X-cor INFO @ Mon, 03 Jun 2019 12:06:47: #2 finished! INFO @ Mon, 03 Jun 2019 12:06:47: #2 predicted fragment length is 214 bps INFO @ Mon, 03 Jun 2019 12:06:47: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 03 Jun 2019 12:06:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.05_model.r INFO @ Mon, 03 Jun 2019 12:06:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:06:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:06:54: 15000000 INFO @ Mon, 03 Jun 2019 12:07:05: 16000000 INFO @ Mon, 03 Jun 2019 12:07:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:07:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:07:09: #1 total tags in treatment: 16394011 INFO @ Mon, 03 Jun 2019 12:07:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:07:09: #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 12:07:09: #1 tags after filtering in treatment: 16394011 INFO @ Mon, 03 Jun 2019 12:07:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:07:09: #1 finished! INFO @ Mon, 03 Jun 2019 12:07:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:07:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:07:11: #2 number of paired peaks: 1475 INFO @ Mon, 03 Jun 2019 12:07:11: start model_add_line... INFO @ Mon, 03 Jun 2019 12:07:11: start X-correlation... INFO @ Mon, 03 Jun 2019 12:07:11: end of X-cor INFO @ Mon, 03 Jun 2019 12:07:11: #2 finished! INFO @ Mon, 03 Jun 2019 12:07:11: #2 predicted fragment length is 214 bps INFO @ Mon, 03 Jun 2019 12:07:11: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 03 Jun 2019 12:07:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.10_model.r INFO @ Mon, 03 Jun 2019 12:07:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:07:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:07:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:07:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:07:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:07:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.20_summits.bed INFO @ Mon, 03 Jun 2019 12:07:57: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4858 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:08:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:08:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.05_summits.bed INFO @ Mon, 03 Jun 2019 12:08:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9381 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:08:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:08:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318793/SRX318793.10_summits.bed INFO @ Mon, 03 Jun 2019 12:08:25: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7245 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。