Job ID = 2007590 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,158,043 reads read : 3,158,043 reads written : 3,158,043 spots read : 2,996,372 reads read : 2,996,372 reads written : 2,996,372 spots read : 3,074,212 reads read : 3,074,212 reads written : 3,074,212 spots read : 3,029,242 reads read : 3,029,242 reads written : 3,029,242 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: 00:02:54 12257869 reads; of these: 12257869 (100.00%) were unpaired; of these: 343178 (2.80%) aligned 0 times 10331191 (84.28%) aligned exactly 1 time 1583500 (12.92%) aligned >1 times 97.20% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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_sort_core] merging from 8 files... [bam_rmdupse_core] 11175900 / 11914691 = 0.9380 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 16:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.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 16:13:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.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 16:13:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.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 16:13:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:11: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:11: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:11: #1 total tags in treatment: 738791 INFO @ Fri, 05 Jul 2019 16:13:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:11: #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 16:13:11: #1 tags after filtering in treatment: 738791 INFO @ Fri, 05 Jul 2019 16:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:11: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:11: #2 number of paired peaks: 430 WARNING @ Fri, 05 Jul 2019 16:13:11: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:11: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:11: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:11: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:11: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:11: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 16:13:11: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 05 Jul 2019 16:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.05_model.r INFO @ Fri, 05 Jul 2019 16:13:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:11: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:11: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:11: #1 total tags in treatment: 738791 INFO @ Fri, 05 Jul 2019 16:13:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:11: #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 16:13:11: #1 tags after filtering in treatment: 738791 INFO @ Fri, 05 Jul 2019 16:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:11: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:11: #2 number of paired peaks: 430 WARNING @ Fri, 05 Jul 2019 16:13:11: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:11: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:11: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:11: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:11: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:11: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 16:13:11: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 05 Jul 2019 16:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.10_model.r INFO @ Fri, 05 Jul 2019 16:13:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:13: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:13: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:13: #1 total tags in treatment: 738791 INFO @ Fri, 05 Jul 2019 16:13:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:13: #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 16:13:13: #1 tags after filtering in treatment: 738791 INFO @ Fri, 05 Jul 2019 16:13:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:13: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:13: #2 number of paired peaks: 430 WARNING @ Fri, 05 Jul 2019 16:13:13: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:13: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:13: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:13: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:13: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:13: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 16:13:13: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 05 Jul 2019 16:13:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.20_model.r INFO @ Fri, 05 Jul 2019 16:13:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.05_summits.bed INFO @ Fri, 05 Jul 2019 16:13:15: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1089 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 16:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.10_summits.bed INFO @ Fri, 05 Jul 2019 16:13:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (812 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 16:13:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548216/ERX2548216.20_summits.bed INFO @ Fri, 05 Jul 2019 16:13:17: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 3 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling