Job ID = 1306937 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,341,191 reads read : 10,341,191 reads written : 10,341,191 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:41 10341191 reads; of these: 10341191 (100.00%) were unpaired; of these: 315131 (3.05%) aligned 0 times 6854473 (66.28%) aligned exactly 1 time 3171587 (30.67%) aligned >1 times 96.95% overall alignment rate Time searching: 00:04:42 Overall time: 00:04:42 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] 1484697 / 10026060 = 0.1481 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 22:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.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 22:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.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 22:14:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:14:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:14:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:14:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.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 22:14:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:14:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:14:23: 1000000 INFO @ Mon, 03 Jun 2019 22:14:23: 1000000 INFO @ Mon, 03 Jun 2019 22:14:24: 1000000 INFO @ Mon, 03 Jun 2019 22:14:30: 2000000 INFO @ Mon, 03 Jun 2019 22:14:30: 2000000 INFO @ Mon, 03 Jun 2019 22:14:33: 2000000 INFO @ Mon, 03 Jun 2019 22:14:38: 3000000 INFO @ Mon, 03 Jun 2019 22:14:38: 3000000 INFO @ Mon, 03 Jun 2019 22:14:42: 3000000 INFO @ Mon, 03 Jun 2019 22:14:46: 4000000 INFO @ Mon, 03 Jun 2019 22:14:46: 4000000 INFO @ Mon, 03 Jun 2019 22:14:50: 4000000 INFO @ Mon, 03 Jun 2019 22:14:53: 5000000 INFO @ Mon, 03 Jun 2019 22:14:53: 5000000 INFO @ Mon, 03 Jun 2019 22:14:58: 5000000 INFO @ Mon, 03 Jun 2019 22:15:01: 6000000 INFO @ Mon, 03 Jun 2019 22:15:01: 6000000 INFO @ Mon, 03 Jun 2019 22:15:07: 6000000 INFO @ Mon, 03 Jun 2019 22:15:08: 7000000 INFO @ Mon, 03 Jun 2019 22:15:08: 7000000 INFO @ Mon, 03 Jun 2019 22:15:15: 7000000 INFO @ Mon, 03 Jun 2019 22:15:15: 8000000 INFO @ Mon, 03 Jun 2019 22:15:15: 8000000 INFO @ Mon, 03 Jun 2019 22:15:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:15:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:15:19: #1 total tags in treatment: 8541363 INFO @ Mon, 03 Jun 2019 22:15:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:19: #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 22:15:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:15:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:15:19: #1 total tags in treatment: 8541363 INFO @ Mon, 03 Jun 2019 22:15:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:19: #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 22:15:19: #1 tags after filtering in treatment: 8541363 INFO @ Mon, 03 Jun 2019 22:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:19: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:19: #1 tags after filtering in treatment: 8541363 INFO @ Mon, 03 Jun 2019 22:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:19: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:20: #2 number of paired peaks: 4150 INFO @ Mon, 03 Jun 2019 22:15:20: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:20: #2 number of paired peaks: 4150 INFO @ Mon, 03 Jun 2019 22:15:20: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:21: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:21: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:21: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:21: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:21: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:21: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 22:15:21: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:21: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 22:15:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.05_model.r INFO @ Mon, 03 Jun 2019 22:15:21: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 22:15:21: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 22:15:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.20_model.r INFO @ Mon, 03 Jun 2019 22:15:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:23: 8000000 INFO @ Mon, 03 Jun 2019 22:15:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 22:15:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 22:15:27: #1 total tags in treatment: 8541363 INFO @ Mon, 03 Jun 2019 22:15:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:15:27: #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 22:15:27: #1 tags after filtering in treatment: 8541363 INFO @ Mon, 03 Jun 2019 22:15:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:15:27: #1 finished! INFO @ Mon, 03 Jun 2019 22:15:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:15:28: #2 number of paired peaks: 4150 INFO @ Mon, 03 Jun 2019 22:15:28: start model_add_line... INFO @ Mon, 03 Jun 2019 22:15:29: start X-correlation... INFO @ Mon, 03 Jun 2019 22:15:29: end of X-cor INFO @ Mon, 03 Jun 2019 22:15:29: #2 finished! INFO @ Mon, 03 Jun 2019 22:15:29: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 22:15:29: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 22:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.10_model.r INFO @ Mon, 03 Jun 2019 22:15:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:15:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:15:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:15:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.20_summits.bed INFO @ Mon, 03 Jun 2019 22:16:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4042 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.05_summits.bed INFO @ Mon, 03 Jun 2019 22:16:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6791 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:16:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:16:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:16:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511131/SRX511131.10_summits.bed INFO @ Mon, 03 Jun 2019 22:16:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5314 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。