Job ID = 2006136 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,389,064 reads read : 2,389,064 reads written : 2,389,064 spots read : 2,286,676 reads read : 2,286,676 reads written : 2,286,676 spots read : 2,331,203 reads read : 2,331,203 reads written : 2,331,203 spots read : 2,278,410 reads read : 2,278,410 reads written : 2,278,410 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: 00:04:59 9285353 reads; of these: 9285353 (100.00%) were unpaired; of these: 300252 (3.23%) aligned 0 times 7518359 (80.97%) aligned exactly 1 time 1466742 (15.80%) aligned >1 times 96.77% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 8600039 / 8985101 = 0.9571 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 @ Fri, 05 Jul 2019 15:16:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Fri, 05 Jul 2019 15:16:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:16:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:16:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Fri, 05 Jul 2019 15:16:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:16:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:16:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Fri, 05 Jul 2019 15:16:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:16:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:16:57: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:16:57: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:16:57: #1 total tags in treatment: 385062 INFO @ Fri, 05 Jul 2019 15:16:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:16:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:16:57: #1 tags after filtering in treatment: 385062 INFO @ Fri, 05 Jul 2019 15:16:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:16:57: #1 finished! INFO @ Fri, 05 Jul 2019 15:16:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:16:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:16:57: #2 number of paired peaks: 439 WARNING @ Fri, 05 Jul 2019 15:16:57: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Fri, 05 Jul 2019 15:16:57: start model_add_line... INFO @ Fri, 05 Jul 2019 15:16:57: start X-correlation... INFO @ Fri, 05 Jul 2019 15:16:57: end of X-cor INFO @ Fri, 05 Jul 2019 15:16:57: #2 finished! INFO @ Fri, 05 Jul 2019 15:16:57: #2 predicted fragment length is 149 bps INFO @ Fri, 05 Jul 2019 15:16:57: #2 alternative fragment length(s) may be 4,122,149,170,598 bps INFO @ Fri, 05 Jul 2019 15:16:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.05_model.r WARNING @ Fri, 05 Jul 2019 15:16:57: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:16:57: #2 You may need to consider one of the other alternative d(s): 4,122,149,170,598 WARNING @ Fri, 05 Jul 2019 15:16:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:16:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:16:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:16:59: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:16:59: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:16:59: #1 total tags in treatment: 385062 INFO @ Fri, 05 Jul 2019 15:16:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:16:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:16:59: #1 tags after filtering in treatment: 385062 INFO @ Fri, 05 Jul 2019 15:16:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:16:59: #1 finished! INFO @ Fri, 05 Jul 2019 15:16:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:16:59: #2 number of paired peaks: 439 WARNING @ Fri, 05 Jul 2019 15:16:59: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Fri, 05 Jul 2019 15:16:59: start model_add_line... INFO @ Fri, 05 Jul 2019 15:16:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:16:59: start X-correlation... INFO @ Fri, 05 Jul 2019 15:16:59: end of X-cor INFO @ Fri, 05 Jul 2019 15:16:59: #2 finished! INFO @ Fri, 05 Jul 2019 15:16:59: #2 predicted fragment length is 149 bps INFO @ Fri, 05 Jul 2019 15:16:59: #2 alternative fragment length(s) may be 4,122,149,170,598 bps INFO @ Fri, 05 Jul 2019 15:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.10_model.r WARNING @ Fri, 05 Jul 2019 15:16:59: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:16:59: #2 You may need to consider one of the other alternative d(s): 4,122,149,170,598 WARNING @ Fri, 05 Jul 2019 15:16:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:16:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:16:59: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:16:59: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:16:59: #1 total tags in treatment: 385062 INFO @ Fri, 05 Jul 2019 15:16:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:16:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:16:59: #1 tags after filtering in treatment: 385062 INFO @ Fri, 05 Jul 2019 15:16:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:16:59: #1 finished! INFO @ Fri, 05 Jul 2019 15:16:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:16:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:16:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:16:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.05_summits.bed INFO @ Fri, 05 Jul 2019 15:16:59: Done! INFO @ Fri, 05 Jul 2019 15:16:59: #2 number of paired peaks: 439 WARNING @ Fri, 05 Jul 2019 15:16:59: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Fri, 05 Jul 2019 15:16:59: start model_add_line... INFO @ Fri, 05 Jul 2019 15:16:59: start X-correlation... INFO @ Fri, 05 Jul 2019 15:16:59: end of X-cor INFO @ Fri, 05 Jul 2019 15:16:59: #2 finished! INFO @ Fri, 05 Jul 2019 15:16:59: #2 predicted fragment length is 149 bps INFO @ Fri, 05 Jul 2019 15:16:59: #2 alternative fragment length(s) may be 4,122,149,170,598 bps INFO @ Fri, 05 Jul 2019 15:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.20_model.r WARNING @ Fri, 05 Jul 2019 15:16:59: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:16:59: #2 You may need to consider one of the other alternative d(s): 4,122,149,170,598 WARNING @ Fri, 05 Jul 2019 15:16:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:16:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:16:59: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (170 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:17:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:17:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.10_summits.bed INFO @ Fri, 05 Jul 2019 15:17:01: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 3 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:17:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548112/ERX2548112.20_summits.bed INFO @ Fri, 05 Jul 2019 15:17:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 2 millis BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling