Job ID = 1293276 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,316,923 reads read : 22,316,923 reads written : 22,316,923 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: 00:03:24 22316923 reads; of these: 22316923 (100.00%) were unpaired; of these: 812633 (3.64%) aligned 0 times 20140426 (90.25%) aligned exactly 1 time 1363864 (6.11%) aligned >1 times 96.36% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 7569999 / 21504290 = 0.3520 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 22:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.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 22:51:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:51:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.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 22:51:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:51:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.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 22:51:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:51:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:52:04: 1000000 INFO @ Sun, 02 Jun 2019 22:52:04: 1000000 INFO @ Sun, 02 Jun 2019 22:52:05: 1000000 INFO @ Sun, 02 Jun 2019 22:52:12: 2000000 INFO @ Sun, 02 Jun 2019 22:52:12: 2000000 INFO @ Sun, 02 Jun 2019 22:52:13: 2000000 INFO @ Sun, 02 Jun 2019 22:52:19: 3000000 INFO @ Sun, 02 Jun 2019 22:52:19: 3000000 INFO @ Sun, 02 Jun 2019 22:52:21: 3000000 INFO @ Sun, 02 Jun 2019 22:52:27: 4000000 INFO @ Sun, 02 Jun 2019 22:52:27: 4000000 INFO @ Sun, 02 Jun 2019 22:52:28: 4000000 INFO @ Sun, 02 Jun 2019 22:52:34: 5000000 INFO @ Sun, 02 Jun 2019 22:52:34: 5000000 INFO @ Sun, 02 Jun 2019 22:52:36: 5000000 INFO @ Sun, 02 Jun 2019 22:52:42: 6000000 INFO @ Sun, 02 Jun 2019 22:52:42: 6000000 INFO @ Sun, 02 Jun 2019 22:52:44: 6000000 INFO @ Sun, 02 Jun 2019 22:52:49: 7000000 INFO @ Sun, 02 Jun 2019 22:52:49: 7000000 INFO @ Sun, 02 Jun 2019 22:52:51: 7000000 INFO @ Sun, 02 Jun 2019 22:52:57: 8000000 INFO @ Sun, 02 Jun 2019 22:52:57: 8000000 INFO @ Sun, 02 Jun 2019 22:52:59: 8000000 INFO @ Sun, 02 Jun 2019 22:53:05: 9000000 INFO @ Sun, 02 Jun 2019 22:53:05: 9000000 INFO @ Sun, 02 Jun 2019 22:53:07: 9000000 INFO @ Sun, 02 Jun 2019 22:53:12: 10000000 INFO @ Sun, 02 Jun 2019 22:53:13: 10000000 INFO @ Sun, 02 Jun 2019 22:53:15: 10000000 INFO @ Sun, 02 Jun 2019 22:53:21: 11000000 INFO @ Sun, 02 Jun 2019 22:53:21: 11000000 INFO @ Sun, 02 Jun 2019 22:53:23: 11000000 INFO @ Sun, 02 Jun 2019 22:53:29: 12000000 INFO @ Sun, 02 Jun 2019 22:53:29: 12000000 INFO @ Sun, 02 Jun 2019 22:53:32: 12000000 INFO @ Sun, 02 Jun 2019 22:53:37: 13000000 INFO @ Sun, 02 Jun 2019 22:53:37: 13000000 INFO @ Sun, 02 Jun 2019 22:53:39: 13000000 INFO @ Sun, 02 Jun 2019 22:53:44: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:53:44: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:53:44: #1 total tags in treatment: 13934291 INFO @ Sun, 02 Jun 2019 22:53:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:53:44: #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 22:53:44: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:53:44: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:53:44: #1 total tags in treatment: 13934291 INFO @ Sun, 02 Jun 2019 22:53:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:53:44: #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 22:53:44: #1 tags after filtering in treatment: 13934291 INFO @ Sun, 02 Jun 2019 22:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:53:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:53:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:53:44: #1 tags after filtering in treatment: 13934291 INFO @ Sun, 02 Jun 2019 22:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:53:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:53:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:53:46: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:53:46: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:53:46: #1 total tags in treatment: 13934291 INFO @ Sun, 02 Jun 2019 22:53:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:53:46: #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 22:53:47: #1 tags after filtering in treatment: 13934291 INFO @ Sun, 02 Jun 2019 22:53:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:53:47: #1 finished! INFO @ Sun, 02 Jun 2019 22:53:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:53:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:53:47: #2 number of paired peaks: 15870 INFO @ Sun, 02 Jun 2019 22:53:47: start model_add_line... INFO @ Sun, 02 Jun 2019 22:53:47: #2 number of paired peaks: 15870 INFO @ Sun, 02 Jun 2019 22:53:47: start model_add_line... INFO @ Sun, 02 Jun 2019 22:53:47: start X-correlation... INFO @ Sun, 02 Jun 2019 22:53:47: end of X-cor INFO @ Sun, 02 Jun 2019 22:53:47: #2 finished! INFO @ Sun, 02 Jun 2019 22:53:47: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 22:53:47: #2 alternative fragment length(s) may be 4,167 bps INFO @ Sun, 02 Jun 2019 22:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.20_model.r INFO @ Sun, 02 Jun 2019 22:53:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:53:48: start X-correlation... INFO @ Sun, 02 Jun 2019 22:53:48: end of X-cor INFO @ Sun, 02 Jun 2019 22:53:48: #2 finished! INFO @ Sun, 02 Jun 2019 22:53:48: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 22:53:48: #2 alternative fragment length(s) may be 4,167 bps INFO @ Sun, 02 Jun 2019 22:53:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.10_model.r INFO @ Sun, 02 Jun 2019 22:53:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:53:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:53:50: #2 number of paired peaks: 15870 INFO @ Sun, 02 Jun 2019 22:53:50: start model_add_line... INFO @ Sun, 02 Jun 2019 22:53:50: start X-correlation... INFO @ Sun, 02 Jun 2019 22:53:50: end of X-cor INFO @ Sun, 02 Jun 2019 22:53:50: #2 finished! INFO @ Sun, 02 Jun 2019 22:53:50: #2 predicted fragment length is 167 bps INFO @ Sun, 02 Jun 2019 22:53:50: #2 alternative fragment length(s) may be 4,167 bps INFO @ Sun, 02 Jun 2019 22:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.05_model.r INFO @ Sun, 02 Jun 2019 22:53:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:54:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:54:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:54:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:54:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:54:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.20_summits.bed INFO @ Sun, 02 Jun 2019 22:54:50: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4887 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.10_summits.bed INFO @ Sun, 02 Jun 2019 22:54:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8274 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:54:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:54:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:54:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011415/ERX011415.05_summits.bed BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 22:54:53: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10406 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。