Job ID = 1293290 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,692,804 reads read : 33,692,804 reads written : 33,692,804 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: 00:11:32 33692804 reads; of these: 33692804 (100.00%) were unpaired; of these: 4616575 (13.70%) aligned 0 times 19199466 (56.98%) aligned exactly 1 time 9876763 (29.31%) aligned >1 times 86.30% overall alignment rate Time searching: 00:11:32 Overall time: 00:11:32 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] 14610300 / 29076229 = 0.5025 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 23:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.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 23:08:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:08:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.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 23:08:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:08:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.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 23:08:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:08:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:08:16: 1000000 INFO @ Sun, 02 Jun 2019 23:08:19: 1000000 INFO @ Sun, 02 Jun 2019 23:08:19: 1000000 INFO @ Sun, 02 Jun 2019 23:08:24: 2000000 INFO @ Sun, 02 Jun 2019 23:08:28: 2000000 INFO @ Sun, 02 Jun 2019 23:08:29: 2000000 INFO @ Sun, 02 Jun 2019 23:08:31: 3000000 INFO @ Sun, 02 Jun 2019 23:08:36: 3000000 INFO @ Sun, 02 Jun 2019 23:08:37: 4000000 INFO @ Sun, 02 Jun 2019 23:08:38: 3000000 INFO @ Sun, 02 Jun 2019 23:08:44: 5000000 INFO @ Sun, 02 Jun 2019 23:08:45: 4000000 INFO @ Sun, 02 Jun 2019 23:08:47: 4000000 INFO @ Sun, 02 Jun 2019 23:08:51: 6000000 INFO @ Sun, 02 Jun 2019 23:08:54: 5000000 INFO @ Sun, 02 Jun 2019 23:08:56: 5000000 INFO @ Sun, 02 Jun 2019 23:08:58: 7000000 INFO @ Sun, 02 Jun 2019 23:09:03: 6000000 INFO @ Sun, 02 Jun 2019 23:09:04: 8000000 INFO @ Sun, 02 Jun 2019 23:09:05: 6000000 INFO @ Sun, 02 Jun 2019 23:09:11: 9000000 INFO @ Sun, 02 Jun 2019 23:09:11: 7000000 INFO @ Sun, 02 Jun 2019 23:09:14: 7000000 INFO @ Sun, 02 Jun 2019 23:09:18: 10000000 INFO @ Sun, 02 Jun 2019 23:09:20: 8000000 INFO @ Sun, 02 Jun 2019 23:09:23: 8000000 INFO @ Sun, 02 Jun 2019 23:09:25: 11000000 INFO @ Sun, 02 Jun 2019 23:09:29: 9000000 INFO @ Sun, 02 Jun 2019 23:09:32: 12000000 INFO @ Sun, 02 Jun 2019 23:09:32: 9000000 INFO @ Sun, 02 Jun 2019 23:09:38: 10000000 INFO @ Sun, 02 Jun 2019 23:09:38: 13000000 INFO @ Sun, 02 Jun 2019 23:09:42: 10000000 INFO @ Sun, 02 Jun 2019 23:09:45: 14000000 INFO @ Sun, 02 Jun 2019 23:09:46: 11000000 INFO @ Sun, 02 Jun 2019 23:09:48: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:09:48: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:09:48: #1 total tags in treatment: 14465929 INFO @ Sun, 02 Jun 2019 23:09:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:09:48: #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 23:09:49: #1 tags after filtering in treatment: 14465929 INFO @ Sun, 02 Jun 2019 23:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:09:49: #1 finished! INFO @ Sun, 02 Jun 2019 23:09:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:09:50: #2 number of paired peaks: 2489 INFO @ Sun, 02 Jun 2019 23:09:50: start model_add_line... INFO @ Sun, 02 Jun 2019 23:09:51: start X-correlation... INFO @ Sun, 02 Jun 2019 23:09:51: end of X-cor INFO @ Sun, 02 Jun 2019 23:09:51: #2 finished! INFO @ Sun, 02 Jun 2019 23:09:51: #2 predicted fragment length is 80 bps INFO @ Sun, 02 Jun 2019 23:09:51: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 02 Jun 2019 23:09:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.20_model.r INFO @ Sun, 02 Jun 2019 23:09:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:09:51: 11000000 INFO @ Sun, 02 Jun 2019 23:09:55: 12000000 INFO @ Sun, 02 Jun 2019 23:10:00: 12000000 INFO @ Sun, 02 Jun 2019 23:10:04: 13000000 INFO @ Sun, 02 Jun 2019 23:10:09: 13000000 INFO @ Sun, 02 Jun 2019 23:10:12: 14000000 INFO @ Sun, 02 Jun 2019 23:10:16: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:10:16: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:10:16: #1 total tags in treatment: 14465929 INFO @ Sun, 02 Jun 2019 23:10:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:10:16: #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 23:10:17: #1 tags after filtering in treatment: 14465929 INFO @ Sun, 02 Jun 2019 23:10:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:10:17: #1 finished! INFO @ Sun, 02 Jun 2019 23:10:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:10:18: 14000000 INFO @ Sun, 02 Jun 2019 23:10:18: #2 number of paired peaks: 2489 INFO @ Sun, 02 Jun 2019 23:10:18: start model_add_line... INFO @ Sun, 02 Jun 2019 23:10:18: start X-correlation... INFO @ Sun, 02 Jun 2019 23:10:18: end of X-cor INFO @ Sun, 02 Jun 2019 23:10:18: #2 finished! INFO @ Sun, 02 Jun 2019 23:10:18: #2 predicted fragment length is 80 bps INFO @ Sun, 02 Jun 2019 23:10:18: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 02 Jun 2019 23:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.05_model.r INFO @ Sun, 02 Jun 2019 23:10:18: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:10:22: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:10:22: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:10:22: #1 total tags in treatment: 14465929 INFO @ Sun, 02 Jun 2019 23:10:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:10:22: #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 23:10:22: #1 tags after filtering in treatment: 14465929 INFO @ Sun, 02 Jun 2019 23:10:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:10:22: #1 finished! INFO @ Sun, 02 Jun 2019 23:10:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:10:24: #2 number of paired peaks: 2489 INFO @ Sun, 02 Jun 2019 23:10:24: start model_add_line... INFO @ Sun, 02 Jun 2019 23:10:24: start X-correlation... INFO @ Sun, 02 Jun 2019 23:10:24: end of X-cor INFO @ Sun, 02 Jun 2019 23:10:24: #2 finished! INFO @ Sun, 02 Jun 2019 23:10:24: #2 predicted fragment length is 80 bps INFO @ Sun, 02 Jun 2019 23:10:24: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 02 Jun 2019 23:10:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.10_model.r INFO @ Sun, 02 Jun 2019 23:10:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:10:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:10:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:10:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.20_summits.bed INFO @ Sun, 02 Jun 2019 23:10:51: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6436 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:10:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:11:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.05_summits.bed INFO @ Sun, 02 Jun 2019 23:11:19: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (18732 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:11:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX032305/ERX032305.10_summits.bed INFO @ Sun, 02 Jun 2019 23:11:27: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (13486 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。