Job ID = 4178598 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,258,272 reads read : 4,516,544 reads written : 2,258,272 reads 0-length : 2,258,272 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: 00:00:50 2258272 reads; of these: 2258272 (100.00%) were unpaired; of these: 760 (0.03%) aligned 0 times 1586049 (70.23%) aligned exactly 1 time 671463 (29.73%) aligned >1 times 99.97% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 104891 / 2257512 = 0.0465 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:13:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.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 @ Thu, 05 Dec 2019 13:13:17: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:13:17: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:13:24: 1000000 INFO @ Thu, 05 Dec 2019 13:13:31: 2000000 INFO @ Thu, 05 Dec 2019 13:13:32: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:13:32: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:13:32: #1 total tags in treatment: 2152621 INFO @ Thu, 05 Dec 2019 13:13:32: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:13:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:13:32: #1 tags after filtering in treatment: 2152621 INFO @ Thu, 05 Dec 2019 13:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:13:32: #1 finished! INFO @ Thu, 05 Dec 2019 13:13:32: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:13:32: #2 number of paired peaks: 759 WARNING @ Thu, 05 Dec 2019 13:13:32: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Thu, 05 Dec 2019 13:13:32: start model_add_line... INFO @ Thu, 05 Dec 2019 13:13:32: start X-correlation... INFO @ Thu, 05 Dec 2019 13:13:32: end of X-cor INFO @ Thu, 05 Dec 2019 13:13:32: #2 finished! INFO @ Thu, 05 Dec 2019 13:13:32: #2 predicted fragment length is 64 bps INFO @ Thu, 05 Dec 2019 13:13:32: #2 alternative fragment length(s) may be 64 bps INFO @ Thu, 05 Dec 2019 13:13:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.05_model.r WARNING @ Thu, 05 Dec 2019 13:13:32: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:13:32: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Thu, 05 Dec 2019 13:13:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:13:32: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:13:36: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:13:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:13:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:13:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.05_summits.bed INFO @ Thu, 05 Dec 2019 13:13:39: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (715 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:13:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.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 @ Thu, 05 Dec 2019 13:13:47: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:13:47: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:13:53: 1000000 INFO @ Thu, 05 Dec 2019 13:14:00: 2000000 INFO @ Thu, 05 Dec 2019 13:14:01: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:14:01: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:14:01: #1 total tags in treatment: 2152621 INFO @ Thu, 05 Dec 2019 13:14:01: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:14:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:14:01: #1 tags after filtering in treatment: 2152621 INFO @ Thu, 05 Dec 2019 13:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:14:01: #1 finished! INFO @ Thu, 05 Dec 2019 13:14:01: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:14:01: #2 number of paired peaks: 759 WARNING @ Thu, 05 Dec 2019 13:14:01: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Thu, 05 Dec 2019 13:14:01: start model_add_line... INFO @ Thu, 05 Dec 2019 13:14:01: start X-correlation... INFO @ Thu, 05 Dec 2019 13:14:01: end of X-cor INFO @ Thu, 05 Dec 2019 13:14:01: #2 finished! INFO @ Thu, 05 Dec 2019 13:14:01: #2 predicted fragment length is 64 bps INFO @ Thu, 05 Dec 2019 13:14:01: #2 alternative fragment length(s) may be 64 bps INFO @ Thu, 05 Dec 2019 13:14:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.10_model.r WARNING @ Thu, 05 Dec 2019 13:14:01: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:14:01: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Thu, 05 Dec 2019 13:14:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:14:01: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:14:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:14:05: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:14:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:14:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:14:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.10_summits.bed INFO @ Thu, 05 Dec 2019 13:14:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (301 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.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 @ Thu, 05 Dec 2019 13:14:17: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:14:17: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:14:24: 1000000 INFO @ Thu, 05 Dec 2019 13:14:30: 2000000 INFO @ Thu, 05 Dec 2019 13:14:31: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:14:31: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:14:31: #1 total tags in treatment: 2152621 INFO @ Thu, 05 Dec 2019 13:14:31: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:14:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:14:31: #1 tags after filtering in treatment: 2152621 INFO @ Thu, 05 Dec 2019 13:14:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:14:31: #1 finished! INFO @ Thu, 05 Dec 2019 13:14:31: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:14:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:14:31: #2 number of paired peaks: 759 WARNING @ Thu, 05 Dec 2019 13:14:31: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Thu, 05 Dec 2019 13:14:31: start model_add_line... INFO @ Thu, 05 Dec 2019 13:14:32: start X-correlation... INFO @ Thu, 05 Dec 2019 13:14:32: end of X-cor INFO @ Thu, 05 Dec 2019 13:14:32: #2 finished! INFO @ Thu, 05 Dec 2019 13:14:32: #2 predicted fragment length is 64 bps INFO @ Thu, 05 Dec 2019 13:14:32: #2 alternative fragment length(s) may be 64 bps INFO @ Thu, 05 Dec 2019 13:14:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.20_model.r WARNING @ Thu, 05 Dec 2019 13:14:32: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:14:32: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Thu, 05 Dec 2019 13:14:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:14:32: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:14:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:14:36: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:14:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:14:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:14:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6420692/SRX6420692.20_summits.bed INFO @ Thu, 05 Dec 2019 13:14:38: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (102 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。