Job ID = 1295817 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,110,787 reads read : 7,110,787 reads written : 7,110,787 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: 00:02:22 7110787 reads; of these: 7110787 (100.00%) were unpaired; of these: 1646576 (23.16%) aligned 0 times 4092062 (57.55%) aligned exactly 1 time 1372149 (19.30%) aligned >1 times 76.84% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 1482917 / 5464211 = 0.2714 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 15:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.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 15:48:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:48:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.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 15:48:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:48:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.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 15:48:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:48:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:48:14: 1000000 INFO @ Mon, 03 Jun 2019 15:48:14: 1000000 INFO @ Mon, 03 Jun 2019 15:48:14: 1000000 INFO @ Mon, 03 Jun 2019 15:48:22: 2000000 INFO @ Mon, 03 Jun 2019 15:48:22: 2000000 INFO @ Mon, 03 Jun 2019 15:48:22: 2000000 INFO @ Mon, 03 Jun 2019 15:48:30: 3000000 INFO @ Mon, 03 Jun 2019 15:48:30: 3000000 INFO @ Mon, 03 Jun 2019 15:48:30: 3000000 INFO @ Mon, 03 Jun 2019 15:48:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:48:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:48:38: #1 total tags in treatment: 3981294 INFO @ Mon, 03 Jun 2019 15:48:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:48:38: #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 15:48:38: #1 tags after filtering in treatment: 3981294 INFO @ Mon, 03 Jun 2019 15:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:48:38: #1 finished! INFO @ Mon, 03 Jun 2019 15:48:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:48:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:48:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:48:38: #1 total tags in treatment: 3981294 INFO @ Mon, 03 Jun 2019 15:48:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:48:38: #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 15:48:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:48:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:48:38: #1 total tags in treatment: 3981294 INFO @ Mon, 03 Jun 2019 15:48:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:48:38: #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 15:48:38: #1 tags after filtering in treatment: 3981294 INFO @ Mon, 03 Jun 2019 15:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:48:38: #1 finished! INFO @ Mon, 03 Jun 2019 15:48:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:48:38: #1 tags after filtering in treatment: 3981294 INFO @ Mon, 03 Jun 2019 15:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:48:38: #1 finished! INFO @ Mon, 03 Jun 2019 15:48:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:48:38: #2 number of paired peaks: 950 WARNING @ Mon, 03 Jun 2019 15:48:38: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Mon, 03 Jun 2019 15:48:38: start model_add_line... INFO @ Mon, 03 Jun 2019 15:48:38: start X-correlation... INFO @ Mon, 03 Jun 2019 15:48:39: end of X-cor INFO @ Mon, 03 Jun 2019 15:48:39: #2 finished! INFO @ Mon, 03 Jun 2019 15:48:39: #2 predicted fragment length is 159 bps INFO @ Mon, 03 Jun 2019 15:48:39: #2 alternative fragment length(s) may be 159 bps INFO @ Mon, 03 Jun 2019 15:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.20_model.r INFO @ Mon, 03 Jun 2019 15:48:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:48:39: #2 number of paired peaks: 950 WARNING @ Mon, 03 Jun 2019 15:48:39: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Mon, 03 Jun 2019 15:48:39: start model_add_line... INFO @ Mon, 03 Jun 2019 15:48:39: #2 number of paired peaks: 950 WARNING @ Mon, 03 Jun 2019 15:48:39: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Mon, 03 Jun 2019 15:48:39: start model_add_line... INFO @ Mon, 03 Jun 2019 15:48:39: start X-correlation... INFO @ Mon, 03 Jun 2019 15:48:39: start X-correlation... INFO @ Mon, 03 Jun 2019 15:48:39: end of X-cor INFO @ Mon, 03 Jun 2019 15:48:39: #2 finished! INFO @ Mon, 03 Jun 2019 15:48:39: #2 predicted fragment length is 159 bps INFO @ Mon, 03 Jun 2019 15:48:39: #2 alternative fragment length(s) may be 159 bps INFO @ Mon, 03 Jun 2019 15:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.05_model.r INFO @ Mon, 03 Jun 2019 15:48:39: end of X-cor INFO @ Mon, 03 Jun 2019 15:48:39: #2 finished! INFO @ Mon, 03 Jun 2019 15:48:39: #2 predicted fragment length is 159 bps INFO @ Mon, 03 Jun 2019 15:48:39: #2 alternative fragment length(s) may be 159 bps INFO @ Mon, 03 Jun 2019 15:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.10_model.r INFO @ Mon, 03 Jun 2019 15:48:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:48:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:48:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:48:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:48:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.20_summits.bed INFO @ Mon, 03 Jun 2019 15:48:57: Done! INFO @ Mon, 03 Jun 2019 15:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.10_summits.bed INFO @ Mon, 03 Jun 2019 15:48:57: Done! pass1 - making usageList (12 chroms): 1 millis INFO @ Mon, 03 Jun 2019 15:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.05_peaks.xls pass2 - checking and writing primary data (700 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563533/SRX4563533.05_summits.bed INFO @ Mon, 03 Jun 2019 15:48:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1264 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2085 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。