Job ID = 1301113 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,955,196 reads read : 16,955,196 reads written : 16,955,196 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: 00:06:15 16955196 reads; of these: 16955196 (100.00%) were unpaired; of these: 1790983 (10.56%) aligned 0 times 11443786 (67.49%) aligned exactly 1 time 3720427 (21.94%) aligned >1 times 89.44% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 3027646 / 15164213 = 0.1997 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 19:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.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 19:53:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:53:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.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 19:53:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:53:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.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 19:53:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:53:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:53:24: 1000000 INFO @ Mon, 03 Jun 2019 19:53:25: 1000000 INFO @ Mon, 03 Jun 2019 19:53:27: 1000000 INFO @ Mon, 03 Jun 2019 19:53:31: 2000000 INFO @ Mon, 03 Jun 2019 19:53:33: 2000000 INFO @ Mon, 03 Jun 2019 19:53:37: 2000000 INFO @ Mon, 03 Jun 2019 19:53:39: 3000000 INFO @ Mon, 03 Jun 2019 19:53:40: 3000000 INFO @ Mon, 03 Jun 2019 19:53:46: 4000000 INFO @ Mon, 03 Jun 2019 19:53:47: 3000000 INFO @ Mon, 03 Jun 2019 19:53:48: 4000000 INFO @ Mon, 03 Jun 2019 19:53:54: 5000000 INFO @ Mon, 03 Jun 2019 19:53:56: 5000000 INFO @ Mon, 03 Jun 2019 19:53:57: 4000000 INFO @ Mon, 03 Jun 2019 19:54:01: 6000000 INFO @ Mon, 03 Jun 2019 19:54:04: 6000000 INFO @ Mon, 03 Jun 2019 19:54:07: 5000000 INFO @ Mon, 03 Jun 2019 19:54:08: 7000000 INFO @ Mon, 03 Jun 2019 19:54:12: 7000000 INFO @ Mon, 03 Jun 2019 19:54:15: 8000000 INFO @ Mon, 03 Jun 2019 19:54:17: 6000000 INFO @ Mon, 03 Jun 2019 19:54:19: 8000000 INFO @ Mon, 03 Jun 2019 19:54:22: 9000000 INFO @ Mon, 03 Jun 2019 19:54:26: 7000000 INFO @ Mon, 03 Jun 2019 19:54:27: 9000000 INFO @ Mon, 03 Jun 2019 19:54:30: 10000000 INFO @ Mon, 03 Jun 2019 19:54:35: 10000000 INFO @ Mon, 03 Jun 2019 19:54:35: 8000000 INFO @ Mon, 03 Jun 2019 19:54:37: 11000000 INFO @ Mon, 03 Jun 2019 19:54:43: 11000000 INFO @ Mon, 03 Jun 2019 19:54:44: 12000000 INFO @ Mon, 03 Jun 2019 19:54:44: 9000000 INFO @ Mon, 03 Jun 2019 19:54:45: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 19:54:45: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 19:54:45: #1 total tags in treatment: 12136567 INFO @ Mon, 03 Jun 2019 19:54:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:54:45: #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 19:54:45: #1 tags after filtering in treatment: 12136567 INFO @ Mon, 03 Jun 2019 19:54:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:54:45: #1 finished! INFO @ Mon, 03 Jun 2019 19:54:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:54:46: #2 number of paired peaks: 1351 INFO @ Mon, 03 Jun 2019 19:54:46: start model_add_line... INFO @ Mon, 03 Jun 2019 19:54:46: start X-correlation... INFO @ Mon, 03 Jun 2019 19:54:46: end of X-cor INFO @ Mon, 03 Jun 2019 19:54:46: #2 finished! INFO @ Mon, 03 Jun 2019 19:54:46: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 19:54:46: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 19:54:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.10_model.r INFO @ Mon, 03 Jun 2019 19:54:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:54:50: 12000000 INFO @ Mon, 03 Jun 2019 19:54:52: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 19:54:52: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 19:54:52: #1 total tags in treatment: 12136567 INFO @ Mon, 03 Jun 2019 19:54:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:54:52: #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 19:54:52: #1 tags after filtering in treatment: 12136567 INFO @ Mon, 03 Jun 2019 19:54:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:54:52: #1 finished! INFO @ Mon, 03 Jun 2019 19:54:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:54:53: #2 number of paired peaks: 1351 INFO @ Mon, 03 Jun 2019 19:54:53: start model_add_line... INFO @ Mon, 03 Jun 2019 19:54:53: start X-correlation... INFO @ Mon, 03 Jun 2019 19:54:53: end of X-cor INFO @ Mon, 03 Jun 2019 19:54:53: #2 finished! INFO @ Mon, 03 Jun 2019 19:54:53: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 19:54:53: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 19:54:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.20_model.r INFO @ Mon, 03 Jun 2019 19:54:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:54:53: 10000000 INFO @ Mon, 03 Jun 2019 19:55:02: 11000000 INFO @ Mon, 03 Jun 2019 19:55:11: 12000000 INFO @ Mon, 03 Jun 2019 19:55:12: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 19:55:12: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 19:55:12: #1 total tags in treatment: 12136567 INFO @ Mon, 03 Jun 2019 19:55:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:55:12: #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 19:55:13: #1 tags after filtering in treatment: 12136567 INFO @ Mon, 03 Jun 2019 19:55:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:55:13: #1 finished! INFO @ Mon, 03 Jun 2019 19:55:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:55:14: #2 number of paired peaks: 1351 INFO @ Mon, 03 Jun 2019 19:55:14: start model_add_line... INFO @ Mon, 03 Jun 2019 19:55:14: start X-correlation... INFO @ Mon, 03 Jun 2019 19:55:14: end of X-cor INFO @ Mon, 03 Jun 2019 19:55:14: #2 finished! INFO @ Mon, 03 Jun 2019 19:55:14: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 19:55:14: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 19:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.05_model.r INFO @ Mon, 03 Jun 2019 19:55:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:55:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:55:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:55:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:55:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:55:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:55:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.10_summits.bed INFO @ Mon, 03 Jun 2019 19:55:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7044 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:55:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:55:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:55:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.20_summits.bed INFO @ Mon, 03 Jun 2019 19:55:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3678 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:55:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:56:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:56:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:56:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX482857/SRX482857.05_summits.bed INFO @ Mon, 03 Jun 2019 19:56:07: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (14949 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。