Job ID = 1293558 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,551,057 reads read : 7,551,057 reads written : 7,551,057 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: 00:02:26 7551057 reads; of these: 7551057 (100.00%) were unpaired; of these: 4642307 (61.48%) aligned 0 times 2084867 (27.61%) aligned exactly 1 time 823883 (10.91%) aligned >1 times 38.52% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 672255 / 2908750 = 0.2311 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 00:51:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.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 00:51:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:51:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:51:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.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 00:51:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:51:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:51:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.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 00:51:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:51:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:51:58: 1000000 INFO @ Mon, 03 Jun 2019 00:51:59: 1000000 INFO @ Mon, 03 Jun 2019 00:51:59: 1000000 INFO @ Mon, 03 Jun 2019 00:52:11: 2000000 INFO @ Mon, 03 Jun 2019 00:52:11: 2000000 INFO @ Mon, 03 Jun 2019 00:52:12: 2000000 INFO @ Mon, 03 Jun 2019 00:52:14: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 00:52:14: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 00:52:14: #1 total tags in treatment: 2236495 INFO @ Mon, 03 Jun 2019 00:52:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:52:14: #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 00:52:14: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 00:52:14: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 00:52:14: #1 total tags in treatment: 2236495 INFO @ Mon, 03 Jun 2019 00:52:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:52:14: #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 00:52:14: #1 tags after filtering in treatment: 2236495 INFO @ Mon, 03 Jun 2019 00:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:52:14: #1 finished! INFO @ Mon, 03 Jun 2019 00:52:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:52:14: #1 tags after filtering in treatment: 2236495 INFO @ Mon, 03 Jun 2019 00:52:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:52:14: #1 finished! INFO @ Mon, 03 Jun 2019 00:52:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:52:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:52:14: #2 number of paired peaks: 2020 INFO @ Mon, 03 Jun 2019 00:52:14: start model_add_line... INFO @ Mon, 03 Jun 2019 00:52:14: #2 number of paired peaks: 2020 INFO @ Mon, 03 Jun 2019 00:52:14: start model_add_line... INFO @ Mon, 03 Jun 2019 00:52:15: start X-correlation... INFO @ Mon, 03 Jun 2019 00:52:15: end of X-cor INFO @ Mon, 03 Jun 2019 00:52:15: #2 finished! INFO @ Mon, 03 Jun 2019 00:52:15: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 00:52:15: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 00:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.05_model.r INFO @ Mon, 03 Jun 2019 00:52:15: start X-correlation... INFO @ Mon, 03 Jun 2019 00:52:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:52:15: end of X-cor INFO @ Mon, 03 Jun 2019 00:52:15: #2 finished! INFO @ Mon, 03 Jun 2019 00:52:15: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 00:52:15: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 00:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.20_model.r INFO @ Mon, 03 Jun 2019 00:52:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:52:15: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 00:52:15: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 00:52:15: #1 total tags in treatment: 2236495 INFO @ Mon, 03 Jun 2019 00:52:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:52:15: #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 00:52:15: #1 tags after filtering in treatment: 2236495 INFO @ Mon, 03 Jun 2019 00:52:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:52:15: #1 finished! INFO @ Mon, 03 Jun 2019 00:52:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:52:15: #2 number of paired peaks: 2020 INFO @ Mon, 03 Jun 2019 00:52:15: start model_add_line... INFO @ Mon, 03 Jun 2019 00:52:15: start X-correlation... INFO @ Mon, 03 Jun 2019 00:52:15: end of X-cor INFO @ Mon, 03 Jun 2019 00:52:15: #2 finished! INFO @ Mon, 03 Jun 2019 00:52:15: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 00:52:15: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 00:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.10_model.r INFO @ Mon, 03 Jun 2019 00:52:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:52:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:52:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:52:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:52:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:52:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:52:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.05_summits.bed INFO @ Mon, 03 Jun 2019 00:52:30: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3238 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.20_summits.bed INFO @ Mon, 03 Jun 2019 00:52:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1771 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX100253/SRX100253.10_summits.bed INFO @ Mon, 03 Jun 2019 00:52:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2520 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。