Job ID = 1294119 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,815,444 reads read : 12,815,444 reads written : 12,815,444 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: 00:02:50 12815444 reads; of these: 12815444 (100.00%) were unpaired; of these: 3348060 (26.13%) aligned 0 times 7871654 (61.42%) aligned exactly 1 time 1595730 (12.45%) aligned >1 times 73.87% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 3665524 / 9467384 = 0.3872 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 05:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.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 05:08:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:08:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.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 05:08:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:08:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.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 05:08:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:08:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:08:39: 1000000 INFO @ Mon, 03 Jun 2019 05:08:41: 1000000 INFO @ Mon, 03 Jun 2019 05:08:41: 1000000 INFO @ Mon, 03 Jun 2019 05:08:48: 2000000 INFO @ Mon, 03 Jun 2019 05:08:51: 2000000 INFO @ Mon, 03 Jun 2019 05:08:52: 2000000 INFO @ Mon, 03 Jun 2019 05:08:56: 3000000 INFO @ Mon, 03 Jun 2019 05:09:02: 3000000 INFO @ Mon, 03 Jun 2019 05:09:02: 3000000 INFO @ Mon, 03 Jun 2019 05:09:04: 4000000 INFO @ Mon, 03 Jun 2019 05:09:12: 4000000 INFO @ Mon, 03 Jun 2019 05:09:12: 5000000 INFO @ Mon, 03 Jun 2019 05:09:13: 4000000 INFO @ Mon, 03 Jun 2019 05:09:19: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:09:19: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:09:19: #1 total tags in treatment: 5801860 INFO @ Mon, 03 Jun 2019 05:09:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:09:19: #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 05:09:19: #1 tags after filtering in treatment: 5801860 INFO @ Mon, 03 Jun 2019 05:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:09:19: #1 finished! INFO @ Mon, 03 Jun 2019 05:09:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:09:20: #2 number of paired peaks: 4169 INFO @ Mon, 03 Jun 2019 05:09:20: start model_add_line... INFO @ Mon, 03 Jun 2019 05:09:20: start X-correlation... INFO @ Mon, 03 Jun 2019 05:09:20: end of X-cor INFO @ Mon, 03 Jun 2019 05:09:20: #2 finished! INFO @ Mon, 03 Jun 2019 05:09:20: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 05:09:20: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 03 Jun 2019 05:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.05_model.r INFO @ Mon, 03 Jun 2019 05:09:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:09:23: 5000000 INFO @ Mon, 03 Jun 2019 05:09:25: 5000000 INFO @ Mon, 03 Jun 2019 05:09:31: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:09:31: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:09:31: #1 total tags in treatment: 5801860 INFO @ Mon, 03 Jun 2019 05:09:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:09:31: #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 05:09:31: #1 tags after filtering in treatment: 5801860 INFO @ Mon, 03 Jun 2019 05:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:09:31: #1 finished! INFO @ Mon, 03 Jun 2019 05:09:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:09:32: #2 number of paired peaks: 4169 INFO @ Mon, 03 Jun 2019 05:09:32: start model_add_line... INFO @ Mon, 03 Jun 2019 05:09:32: start X-correlation... INFO @ Mon, 03 Jun 2019 05:09:32: end of X-cor INFO @ Mon, 03 Jun 2019 05:09:32: #2 finished! INFO @ Mon, 03 Jun 2019 05:09:32: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 05:09:32: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 03 Jun 2019 05:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.10_model.r INFO @ Mon, 03 Jun 2019 05:09:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:09:33: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:09:33: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:09:33: #1 total tags in treatment: 5801860 INFO @ Mon, 03 Jun 2019 05:09:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:09:33: #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 05:09:33: #1 tags after filtering in treatment: 5801860 INFO @ Mon, 03 Jun 2019 05:09:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:09:33: #1 finished! INFO @ Mon, 03 Jun 2019 05:09:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:09:34: #2 number of paired peaks: 4169 INFO @ Mon, 03 Jun 2019 05:09:34: start model_add_line... INFO @ Mon, 03 Jun 2019 05:09:34: start X-correlation... INFO @ Mon, 03 Jun 2019 05:09:34: end of X-cor INFO @ Mon, 03 Jun 2019 05:09:34: #2 finished! INFO @ Mon, 03 Jun 2019 05:09:34: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 05:09:34: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 03 Jun 2019 05:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.20_model.r INFO @ Mon, 03 Jun 2019 05:09:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:09:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.05_summits.bed INFO @ Mon, 03 Jun 2019 05:09:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8414 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:09:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:09:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:10:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.10_summits.bed INFO @ Mon, 03 Jun 2019 05:10:00: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6427 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 05:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX191911/SRX191911.20_summits.bed INFO @ Mon, 03 Jun 2019 05:10:03: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4562 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。