Job ID = 2590886 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,543,465 reads read : 2,543,465 reads written : 2,543,465 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:31 2543465 reads; of these: 2543465 (100.00%) were unpaired; of these: 751420 (29.54%) aligned 0 times 1722406 (67.72%) aligned exactly 1 time 69639 (2.74%) aligned >1 times 70.46% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 1666674 / 1792045 = 0.9300 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, 12 Aug 2019 23:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.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, 12 Aug 2019 23:51:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:51:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.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, 12 Aug 2019 23:51:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:51:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:51:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:49: #1 total tags in treatment: 125371 INFO @ Mon, 12 Aug 2019 23:51:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:51:49: #1 tags after filtering in treatment: 125371 INFO @ Mon, 12 Aug 2019 23:51:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:49: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:49: #2 number of paired peaks: 129 WARNING @ Mon, 12 Aug 2019 23:51:49: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Mon, 12 Aug 2019 23:51:49: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:49: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:49: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:49: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:49: #2 predicted fragment length is 62 bps INFO @ Mon, 12 Aug 2019 23:51:49: #2 alternative fragment length(s) may be 62,162,361,465,536,568 bps INFO @ Mon, 12 Aug 2019 23:51:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.05_model.r WARNING @ Mon, 12 Aug 2019 23:51:49: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:51:49: #2 You may need to consider one of the other alternative d(s): 62,162,361,465,536,568 WARNING @ Mon, 12 Aug 2019 23:51:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:51:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 23:51:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 23:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.05_summits.bed INFO @ Mon, 12 Aug 2019 23:51:50: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:50: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:50: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:50: #1 total tags in treatment: 125371 INFO @ Mon, 12 Aug 2019 23:51:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:51:50: #1 tags after filtering in treatment: 125371 INFO @ Mon, 12 Aug 2019 23:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:50: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:50: #2 number of paired peaks: 129 WARNING @ Mon, 12 Aug 2019 23:51:50: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Mon, 12 Aug 2019 23:51:50: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:50: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:50: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:50: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:50: #2 predicted fragment length is 62 bps INFO @ Mon, 12 Aug 2019 23:51:50: #2 alternative fragment length(s) may be 62,162,361,465,536,568 bps INFO @ Mon, 12 Aug 2019 23:51:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.10_model.r WARNING @ Mon, 12 Aug 2019 23:51:50: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:51:50: #2 You may need to consider one of the other alternative d(s): 62,162,361,465,536,568 WARNING @ Mon, 12 Aug 2019 23:51:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:51:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.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, 12 Aug 2019 23:51:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:51:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:51:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.10_summits.bed INFO @ Mon, 12 Aug 2019 23:51:51: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (121 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:51: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:51: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:51: #1 total tags in treatment: 125371 INFO @ Mon, 12 Aug 2019 23:51:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:51:51: #1 tags after filtering in treatment: 125371 INFO @ Mon, 12 Aug 2019 23:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:51: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:51: #2 number of paired peaks: 129 WARNING @ Mon, 12 Aug 2019 23:51:51: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Mon, 12 Aug 2019 23:51:51: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:51: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:51: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:51: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:51: #2 predicted fragment length is 62 bps INFO @ Mon, 12 Aug 2019 23:51:51: #2 alternative fragment length(s) may be 62,162,361,465,536,568 bps INFO @ Mon, 12 Aug 2019 23:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.20_model.r WARNING @ Mon, 12 Aug 2019 23:51:51: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:51:51: #2 You may need to consider one of the other alternative d(s): 62,162,361,465,536,568 WARNING @ Mon, 12 Aug 2019 23:51:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:51:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360569/SRX5360569.20_summits.bed INFO @ Mon, 12 Aug 2019 23:51:52: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 1 millis CompletedMACS2peakCalling