Job ID = 1295624 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,469,024 reads read : 9,469,024 reads written : 9,469,024 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: 00:00:45 9469024 reads; of these: 9469024 (100.00%) were unpaired; of these: 9171356 (96.86%) aligned 0 times 242065 (2.56%) aligned exactly 1 time 55603 (0.59%) aligned >1 times 3.14% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 34420 / 297668 = 0.1156 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 14:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.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 14:43:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:43:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.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 14:43:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:43:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.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 14:43:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:43:14: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 14:43:16: #1 tag size is determined as 35 bps INFO @ Mon, 03 Jun 2019 14:43:16: #1 tag size = 35 INFO @ Mon, 03 Jun 2019 14:43:16: #1 total tags in treatment: 263248 INFO @ Mon, 03 Jun 2019 14:43:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:43:16: #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 14:43:16: #1 tags after filtering in treatment: 263248 INFO @ Mon, 03 Jun 2019 14:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:43:16: #1 finished! INFO @ Mon, 03 Jun 2019 14:43:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:43:16: #1 tag size is determined as 35 bps INFO @ Mon, 03 Jun 2019 14:43:16: #1 tag size = 35 INFO @ Mon, 03 Jun 2019 14:43:16: #1 total tags in treatment: 263248 INFO @ Mon, 03 Jun 2019 14:43:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:43:16: #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 14:43:16: #1 tags after filtering in treatment: 263248 INFO @ Mon, 03 Jun 2019 14:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:43:16: #1 finished! INFO @ Mon, 03 Jun 2019 14:43:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:43:16: #1 tag size is determined as 35 bps INFO @ Mon, 03 Jun 2019 14:43:16: #1 tag size = 35 INFO @ Mon, 03 Jun 2019 14:43:16: #1 total tags in treatment: 263248 INFO @ Mon, 03 Jun 2019 14:43:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:43:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 14:43:16: #1 tags after filtering in treatment: 263248 INFO @ Mon, 03 Jun 2019 14:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:43:16: #1 finished! INFO @ Mon, 03 Jun 2019 14:43:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:43:16: #2 number of paired peaks: 3837 INFO @ Mon, 03 Jun 2019 14:43:16: start model_add_line... INFO @ Mon, 03 Jun 2019 14:43:16: start X-correlation... INFO @ Mon, 03 Jun 2019 14:43:16: end of X-cor INFO @ Mon, 03 Jun 2019 14:43:16: #2 finished! INFO @ Mon, 03 Jun 2019 14:43:16: #2 predicted fragment length is 91 bps INFO @ Mon, 03 Jun 2019 14:43:16: #2 alternative fragment length(s) may be 91 bps INFO @ Mon, 03 Jun 2019 14:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.20_model.r INFO @ Mon, 03 Jun 2019 14:43:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:43:16: #2 number of paired peaks: 3837 INFO @ Mon, 03 Jun 2019 14:43:16: start model_add_line... INFO @ Mon, 03 Jun 2019 14:43:16: start X-correlation... INFO @ Mon, 03 Jun 2019 14:43:16: end of X-cor INFO @ Mon, 03 Jun 2019 14:43:16: #2 finished! INFO @ Mon, 03 Jun 2019 14:43:16: #2 predicted fragment length is 91 bps INFO @ Mon, 03 Jun 2019 14:43:16: #2 alternative fragment length(s) may be 91 bps INFO @ Mon, 03 Jun 2019 14:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.05_model.r INFO @ Mon, 03 Jun 2019 14:43:16: #2 number of paired peaks: 3837 INFO @ Mon, 03 Jun 2019 14:43:16: start model_add_line... INFO @ Mon, 03 Jun 2019 14:43:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:43:16: start X-correlation... INFO @ Mon, 03 Jun 2019 14:43:16: end of X-cor INFO @ Mon, 03 Jun 2019 14:43:16: #2 finished! INFO @ Mon, 03 Jun 2019 14:43:16: #2 predicted fragment length is 91 bps INFO @ Mon, 03 Jun 2019 14:43:16: #2 alternative fragment length(s) may be 91 bps INFO @ Mon, 03 Jun 2019 14:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.10_model.r INFO @ Mon, 03 Jun 2019 14:43:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:43:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:43:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:43:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.20_summits.bed INFO @ Mon, 03 Jun 2019 14:43:18: Done! INFO @ Mon, 03 Jun 2019 14:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.05_summits.bed INFO @ Mon, 03 Jun 2019 14:43:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX386287/SRX386287.10_summits.bed INFO @ Mon, 03 Jun 2019 14:43:18: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 18 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 3 millis CompletedMACS2peakCalling