Job ID = 2006277 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,659,369 reads read : 2,659,369 reads written : 2,659,369 spots read : 2,627,981 reads read : 2,627,981 reads written : 2,627,981 spots read : 2,613,801 reads read : 2,613,801 reads written : 2,613,801 spots read : 2,553,598 reads read : 2,553,598 reads written : 2,553,598 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: 00:02:36 10454749 reads; of these: 10454749 (100.00%) were unpaired; of these: 500174 (4.78%) aligned 0 times 9087581 (86.92%) aligned exactly 1 time 866994 (8.29%) aligned >1 times 95.22% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 9447852 / 9954575 = 0.9491 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 15:29:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.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 15:29:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:29:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:29:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.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 15:29:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:29:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.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 15:29:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:29:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:29:16: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:29:16: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:29:16: #1 total tags in treatment: 506723 INFO @ Fri, 05 Jul 2019 15:29:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:29:16: #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 15:29:16: #1 tags after filtering in treatment: 506723 INFO @ Fri, 05 Jul 2019 15:29:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:29:16: #1 finished! INFO @ Fri, 05 Jul 2019 15:29:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:29:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:29:16: #2 number of paired peaks: 697 WARNING @ Fri, 05 Jul 2019 15:29:16: Fewer paired peaks (697) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 697 pairs to build model! INFO @ Fri, 05 Jul 2019 15:29:16: start model_add_line... INFO @ Fri, 05 Jul 2019 15:29:16: start X-correlation... INFO @ Fri, 05 Jul 2019 15:29:16: end of X-cor INFO @ Fri, 05 Jul 2019 15:29:16: #2 finished! INFO @ Fri, 05 Jul 2019 15:29:16: #2 predicted fragment length is 197 bps INFO @ Fri, 05 Jul 2019 15:29:16: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 05 Jul 2019 15:29:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.05_model.r INFO @ Fri, 05 Jul 2019 15:29:17: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:29:17: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:29:17: #1 total tags in treatment: 506723 INFO @ Fri, 05 Jul 2019 15:29:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:29:17: #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 15:29:17: #1 tags after filtering in treatment: 506723 INFO @ Fri, 05 Jul 2019 15:29:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:29:17: #1 finished! INFO @ Fri, 05 Jul 2019 15:29:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:29:17: #2 number of paired peaks: 697 WARNING @ Fri, 05 Jul 2019 15:29:17: Fewer paired peaks (697) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 697 pairs to build model! INFO @ Fri, 05 Jul 2019 15:29:17: start model_add_line... INFO @ Fri, 05 Jul 2019 15:29:17: start X-correlation... INFO @ Fri, 05 Jul 2019 15:29:17: end of X-cor INFO @ Fri, 05 Jul 2019 15:29:17: #2 finished! INFO @ Fri, 05 Jul 2019 15:29:17: #2 predicted fragment length is 197 bps INFO @ Fri, 05 Jul 2019 15:29:17: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 05 Jul 2019 15:29:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.10_model.r INFO @ Fri, 05 Jul 2019 15:29:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:29:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:29:18: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:29:18: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:29:18: #1 total tags in treatment: 506723 INFO @ Fri, 05 Jul 2019 15:29:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:29:18: #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 15:29:18: #1 tags after filtering in treatment: 506723 INFO @ Fri, 05 Jul 2019 15:29:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:29:18: #1 finished! INFO @ Fri, 05 Jul 2019 15:29:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:29:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:29:18: #2 number of paired peaks: 697 WARNING @ Fri, 05 Jul 2019 15:29:18: Fewer paired peaks (697) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 697 pairs to build model! INFO @ Fri, 05 Jul 2019 15:29:18: start model_add_line... INFO @ Fri, 05 Jul 2019 15:29:18: start X-correlation... INFO @ Fri, 05 Jul 2019 15:29:18: end of X-cor INFO @ Fri, 05 Jul 2019 15:29:18: #2 finished! INFO @ Fri, 05 Jul 2019 15:29:18: #2 predicted fragment length is 197 bps INFO @ Fri, 05 Jul 2019 15:29:18: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 05 Jul 2019 15:29:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.20_model.r INFO @ Fri, 05 Jul 2019 15:29:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:29:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:29:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:29:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:29:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:29:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.10_summits.bed INFO @ Fri, 05 Jul 2019 15:29:20: Done! INFO @ Fri, 05 Jul 2019 15:29:20: #3 Call peaks for each chromosome... pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (670 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 15:29:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:29:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:29:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.05_summits.bed INFO @ Fri, 05 Jul 2019 15:29:21: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (881 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 15:29:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:29:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:29:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548128/ERX2548128.20_summits.bed INFO @ Fri, 05 Jul 2019 15:29:21: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (513 records, 4 fields): 89 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。