Job ID = 1294104 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,654,302 reads read : 11,654,302 reads written : 11,654,302 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: 00:03:07 11654302 reads; of these: 11654302 (100.00%) were unpaired; of these: 2347951 (20.15%) aligned 0 times 6884770 (59.07%) aligned exactly 1 time 2421581 (20.78%) aligned >1 times 79.85% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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_rmdupse_core] 4483828 / 9306351 = 0.4818 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 04:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.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 04:59:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.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 04:59:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.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 04:59:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:59:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:59:23: 1000000 INFO @ Mon, 03 Jun 2019 04:59:23: 1000000 INFO @ Mon, 03 Jun 2019 04:59:25: 1000000 INFO @ Mon, 03 Jun 2019 04:59:29: 2000000 INFO @ Mon, 03 Jun 2019 04:59:30: 2000000 INFO @ Mon, 03 Jun 2019 04:59:33: 2000000 INFO @ Mon, 03 Jun 2019 04:59:36: 3000000 INFO @ Mon, 03 Jun 2019 04:59:37: 3000000 INFO @ Mon, 03 Jun 2019 04:59:41: 3000000 INFO @ Mon, 03 Jun 2019 04:59:42: 4000000 INFO @ Mon, 03 Jun 2019 04:59:44: 4000000 INFO @ Mon, 03 Jun 2019 04:59:47: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:59:47: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:59:47: #1 total tags in treatment: 4822523 INFO @ Mon, 03 Jun 2019 04:59:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:59:47: #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 04:59:47: #1 tags after filtering in treatment: 4822523 INFO @ Mon, 03 Jun 2019 04:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:59:47: #1 finished! INFO @ Mon, 03 Jun 2019 04:59:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:59:48: #2 number of paired peaks: 1520 INFO @ Mon, 03 Jun 2019 04:59:48: start model_add_line... INFO @ Mon, 03 Jun 2019 04:59:48: start X-correlation... INFO @ Mon, 03 Jun 2019 04:59:48: end of X-cor INFO @ Mon, 03 Jun 2019 04:59:48: #2 finished! INFO @ Mon, 03 Jun 2019 04:59:48: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 04:59:48: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 04:59:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.20_model.r INFO @ Mon, 03 Jun 2019 04:59:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:59:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:59:49: 4000000 INFO @ Mon, 03 Jun 2019 04:59:49: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:59:49: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:59:49: #1 total tags in treatment: 4822523 INFO @ Mon, 03 Jun 2019 04:59:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:59:49: #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 04:59:49: #1 tags after filtering in treatment: 4822523 INFO @ Mon, 03 Jun 2019 04:59:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:59:49: #1 finished! INFO @ Mon, 03 Jun 2019 04:59:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:59:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:59:50: #2 number of paired peaks: 1520 INFO @ Mon, 03 Jun 2019 04:59:50: start model_add_line... INFO @ Mon, 03 Jun 2019 04:59:50: start X-correlation... INFO @ Mon, 03 Jun 2019 04:59:50: end of X-cor INFO @ Mon, 03 Jun 2019 04:59:50: #2 finished! INFO @ Mon, 03 Jun 2019 04:59:50: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 04:59:50: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 04:59:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.05_model.r INFO @ Mon, 03 Jun 2019 04:59:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:59:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:59:55: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:59:55: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:59:55: #1 total tags in treatment: 4822523 INFO @ Mon, 03 Jun 2019 04:59:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:59:55: #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 04:59:56: #1 tags after filtering in treatment: 4822523 INFO @ Mon, 03 Jun 2019 04:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:59:56: #1 finished! INFO @ Mon, 03 Jun 2019 04:59:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:59:56: #2 number of paired peaks: 1520 INFO @ Mon, 03 Jun 2019 04:59:56: start model_add_line... INFO @ Mon, 03 Jun 2019 04:59:56: start X-correlation... INFO @ Mon, 03 Jun 2019 04:59:56: end of X-cor INFO @ Mon, 03 Jun 2019 04:59:56: #2 finished! INFO @ Mon, 03 Jun 2019 04:59:56: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 04:59:56: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 04:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.10_model.r INFO @ Mon, 03 Jun 2019 04:59:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:00:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.20_summits.bed INFO @ Mon, 03 Jun 2019 05:00:10: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2125 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:00:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:00:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.05_summits.bed INFO @ Mon, 03 Jun 2019 05:00:12: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4334 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:00:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX186109/SRX186109.10_summits.bed INFO @ Mon, 03 Jun 2019 05:00:18: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3109 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。