Job ID = 1293274 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,722,284 reads read : 24,722,284 reads written : 24,722,284 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: 00:07:32 24722284 reads; of these: 24722284 (100.00%) were unpaired; of these: 941755 (3.81%) aligned 0 times 18214178 (73.68%) aligned exactly 1 time 5566351 (22.52%) aligned >1 times 96.19% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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] 13455819 / 23780529 = 0.5658 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 @ Sun, 02 Jun 2019 22:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.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 @ Sun, 02 Jun 2019 22:58:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:58:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.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 @ Sun, 02 Jun 2019 22:58:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:58:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.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 @ Sun, 02 Jun 2019 22:58:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:58:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:58:36: 1000000 INFO @ Sun, 02 Jun 2019 22:58:36: 1000000 INFO @ Sun, 02 Jun 2019 22:58:36: 1000000 INFO @ Sun, 02 Jun 2019 22:58:43: 2000000 INFO @ Sun, 02 Jun 2019 22:58:43: 2000000 INFO @ Sun, 02 Jun 2019 22:58:43: 2000000 INFO @ Sun, 02 Jun 2019 22:58:50: 3000000 INFO @ Sun, 02 Jun 2019 22:58:51: 3000000 INFO @ Sun, 02 Jun 2019 22:58:51: 3000000 INFO @ Sun, 02 Jun 2019 22:58:56: 4000000 INFO @ Sun, 02 Jun 2019 22:58:58: 4000000 INFO @ Sun, 02 Jun 2019 22:58:58: 4000000 INFO @ Sun, 02 Jun 2019 22:59:03: 5000000 INFO @ Sun, 02 Jun 2019 22:59:05: 5000000 INFO @ Sun, 02 Jun 2019 22:59:05: 5000000 INFO @ Sun, 02 Jun 2019 22:59:10: 6000000 INFO @ Sun, 02 Jun 2019 22:59:13: 6000000 INFO @ Sun, 02 Jun 2019 22:59:13: 6000000 INFO @ Sun, 02 Jun 2019 22:59:17: 7000000 INFO @ Sun, 02 Jun 2019 22:59:20: 7000000 INFO @ Sun, 02 Jun 2019 22:59:20: 7000000 INFO @ Sun, 02 Jun 2019 22:59:24: 8000000 INFO @ Sun, 02 Jun 2019 22:59:27: 8000000 INFO @ Sun, 02 Jun 2019 22:59:27: 8000000 INFO @ Sun, 02 Jun 2019 22:59:31: 9000000 INFO @ Sun, 02 Jun 2019 22:59:35: 9000000 INFO @ Sun, 02 Jun 2019 22:59:35: 9000000 INFO @ Sun, 02 Jun 2019 22:59:37: 10000000 INFO @ Sun, 02 Jun 2019 22:59:40: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:59:40: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:59:40: #1 total tags in treatment: 10324710 INFO @ Sun, 02 Jun 2019 22:59:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:59:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:59:40: #1 tags after filtering in treatment: 10324710 INFO @ Sun, 02 Jun 2019 22:59:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:59:40: #1 finished! INFO @ Sun, 02 Jun 2019 22:59:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:59:41: #2 number of paired peaks: 2147 INFO @ Sun, 02 Jun 2019 22:59:41: start model_add_line... INFO @ Sun, 02 Jun 2019 22:59:41: start X-correlation... INFO @ Sun, 02 Jun 2019 22:59:41: end of X-cor INFO @ Sun, 02 Jun 2019 22:59:41: #2 finished! INFO @ Sun, 02 Jun 2019 22:59:41: #2 predicted fragment length is 163 bps INFO @ Sun, 02 Jun 2019 22:59:41: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 02 Jun 2019 22:59:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.20_model.r INFO @ Sun, 02 Jun 2019 22:59:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:59:42: 10000000 INFO @ Sun, 02 Jun 2019 22:59:42: 10000000 INFO @ Sun, 02 Jun 2019 22:59:44: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:59:44: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:59:44: #1 total tags in treatment: 10324710 INFO @ Sun, 02 Jun 2019 22:59:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:59:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:59:44: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:59:44: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:59:44: #1 total tags in treatment: 10324710 INFO @ Sun, 02 Jun 2019 22:59:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:59:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:59:44: #1 tags after filtering in treatment: 10324710 INFO @ Sun, 02 Jun 2019 22:59:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:59:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:59:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:59:45: #1 tags after filtering in treatment: 10324710 INFO @ Sun, 02 Jun 2019 22:59:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:59:45: #1 finished! INFO @ Sun, 02 Jun 2019 22:59:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:59:46: #2 number of paired peaks: 2147 INFO @ Sun, 02 Jun 2019 22:59:46: start model_add_line... INFO @ Sun, 02 Jun 2019 22:59:46: #2 number of paired peaks: 2147 INFO @ Sun, 02 Jun 2019 22:59:46: start model_add_line... INFO @ Sun, 02 Jun 2019 22:59:46: start X-correlation... INFO @ Sun, 02 Jun 2019 22:59:46: end of X-cor INFO @ Sun, 02 Jun 2019 22:59:46: #2 finished! INFO @ Sun, 02 Jun 2019 22:59:46: #2 predicted fragment length is 163 bps INFO @ Sun, 02 Jun 2019 22:59:46: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 02 Jun 2019 22:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.05_model.r INFO @ Sun, 02 Jun 2019 22:59:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:59:46: start X-correlation... INFO @ Sun, 02 Jun 2019 22:59:46: end of X-cor INFO @ Sun, 02 Jun 2019 22:59:46: #2 finished! INFO @ Sun, 02 Jun 2019 22:59:46: #2 predicted fragment length is 163 bps INFO @ Sun, 02 Jun 2019 22:59:46: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 02 Jun 2019 22:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.10_model.r INFO @ Sun, 02 Jun 2019 22:59:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:00:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:00:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:00:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.20_summits.bed INFO @ Sun, 02 Jun 2019 23:00:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4269 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.10_summits.bed INFO @ Sun, 02 Jun 2019 23:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:00:34: Done! INFO @ Sun, 02 Jun 2019 23:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011413/ERX011413.05_summits.bed pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5898 records, 4 fields): 9 millis INFO @ Sun, 02 Jun 2019 23:00:34: Done! CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8035 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。