Job ID = 1295714 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,584,800 reads read : 7,584,800 reads written : 7,584,800 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: 00:01:07 7584800 reads; of these: 7584800 (100.00%) were unpaired; of these: 6284693 (82.86%) aligned 0 times 1043547 (13.76%) aligned exactly 1 time 256560 (3.38%) aligned >1 times 17.14% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 423220 / 1300107 = 0.3255 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 15:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.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 15:09:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.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 15:09:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.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 15:09:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:10:05: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:10:05: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:10:05: #1 total tags in treatment: 876887 INFO @ Mon, 03 Jun 2019 15:10:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:10:05: #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 15:10:05: #1 tags after filtering in treatment: 876887 INFO @ Mon, 03 Jun 2019 15:10:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:10:05: #1 finished! INFO @ Mon, 03 Jun 2019 15:10:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:10:05: #2 number of paired peaks: 2697 INFO @ Mon, 03 Jun 2019 15:10:05: start model_add_line... INFO @ Mon, 03 Jun 2019 15:10:05: start X-correlation... INFO @ Mon, 03 Jun 2019 15:10:05: end of X-cor INFO @ Mon, 03 Jun 2019 15:10:05: #2 finished! INFO @ Mon, 03 Jun 2019 15:10:05: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 15:10:05: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 15:10:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.20_model.r INFO @ Mon, 03 Jun 2019 15:10:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:10:06: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:10:06: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:10:06: #1 total tags in treatment: 876887 INFO @ Mon, 03 Jun 2019 15:10:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:10:06: #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 15:10:06: #1 tags after filtering in treatment: 876887 INFO @ Mon, 03 Jun 2019 15:10:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:10:06: #1 finished! INFO @ Mon, 03 Jun 2019 15:10:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:10:06: #2 number of paired peaks: 2697 INFO @ Mon, 03 Jun 2019 15:10:06: start model_add_line... INFO @ Mon, 03 Jun 2019 15:10:06: start X-correlation... INFO @ Mon, 03 Jun 2019 15:10:06: end of X-cor INFO @ Mon, 03 Jun 2019 15:10:06: #2 finished! INFO @ Mon, 03 Jun 2019 15:10:06: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 15:10:06: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 15:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.05_model.r INFO @ Mon, 03 Jun 2019 15:10:06: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:10:06: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:10:06: #1 total tags in treatment: 876887 INFO @ Mon, 03 Jun 2019 15:10:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:10:06: #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 15:10:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:10:06: #1 tags after filtering in treatment: 876887 INFO @ Mon, 03 Jun 2019 15:10:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:10:06: #1 finished! INFO @ Mon, 03 Jun 2019 15:10:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:10:06: #2 number of paired peaks: 2697 INFO @ Mon, 03 Jun 2019 15:10:06: start model_add_line... INFO @ Mon, 03 Jun 2019 15:10:06: start X-correlation... INFO @ Mon, 03 Jun 2019 15:10:06: end of X-cor INFO @ Mon, 03 Jun 2019 15:10:06: #2 finished! INFO @ Mon, 03 Jun 2019 15:10:06: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 15:10:06: #2 alternative fragment length(s) may be 221 bps INFO @ Mon, 03 Jun 2019 15:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.10_model.r INFO @ Mon, 03 Jun 2019 15:10:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:10:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:10:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:10:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.20_summits.bed INFO @ Mon, 03 Jun 2019 15:10:10: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (255 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:10:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:10:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.05_summits.bed INFO @ Mon, 03 Jun 2019 15:10:11: Done! INFO @ Mon, 03 Jun 2019 15:10:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.10_peaks.narrowPeak pass1 - making usageList (13 chroms): 7 millis pass2 - checking and writing primary data (1385 records, 4 fields): 6 millis INFO @ Mon, 03 Jun 2019 15:10:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4375816/SRX4375816.10_summits.bed INFO @ Mon, 03 Jun 2019 15:10:11: Done! CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (648 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。