Job ID = 2006306 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,780,562 reads read : 2,780,562 reads written : 2,780,562 spots read : 2,668,824 reads read : 2,668,824 reads written : 2,668,824 spots read : 2,715,787 reads read : 2,715,787 reads written : 2,715,787 spots read : 2,648,202 reads read : 2,648,202 reads written : 2,648,202 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529482.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529483.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529484.sra.cache’: 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: 00:04:53 10813375 reads; of these: 10813375 (100.00%) were unpaired; of these: 876677 (8.11%) aligned 0 times 8398766 (77.67%) aligned exactly 1 time 1537932 (14.22%) aligned >1 times 91.89% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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] 9557190 / 9936698 = 0.9618 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 15:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.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 15:46:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.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 15:46:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.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 15:46:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:46:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:46:23: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:23: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:23: #1 total tags in treatment: 379508 INFO @ Fri, 05 Jul 2019 15:46:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:23: #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 15:46:23: #1 tags after filtering in treatment: 379508 INFO @ Fri, 05 Jul 2019 15:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:23: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:23: #2 number of paired peaks: 516 WARNING @ Fri, 05 Jul 2019 15:46:23: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:23: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:23: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:23: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:23: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:23: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 15:46:23: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 05 Jul 2019 15:46:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.05_model.r INFO @ Fri, 05 Jul 2019 15:46:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:24: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:24: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:24: #1 total tags in treatment: 379508 INFO @ Fri, 05 Jul 2019 15:46:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:24: #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 15:46:24: #1 tags after filtering in treatment: 379508 INFO @ Fri, 05 Jul 2019 15:46:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:24: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:24: #2 number of paired peaks: 516 WARNING @ Fri, 05 Jul 2019 15:46:24: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:24: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:24: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:24: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:24: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:24: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 15:46:24: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 05 Jul 2019 15:46:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.10_model.r INFO @ Fri, 05 Jul 2019 15:46:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.05_summits.bed INFO @ Fri, 05 Jul 2019 15:46:25: Done! INFO @ Fri, 05 Jul 2019 15:46:25: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:46:25: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:46:25: #1 total tags in treatment: 379508 INFO @ Fri, 05 Jul 2019 15:46:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:46:25: #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 15:46:25: #1 tags after filtering in treatment: 379508 INFO @ Fri, 05 Jul 2019 15:46:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:46:25: #1 finished! INFO @ Fri, 05 Jul 2019 15:46:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:46:25: #2 number of paired peaks: 516 WARNING @ Fri, 05 Jul 2019 15:46:25: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Fri, 05 Jul 2019 15:46:25: start model_add_line... INFO @ Fri, 05 Jul 2019 15:46:25: start X-correlation... INFO @ Fri, 05 Jul 2019 15:46:25: end of X-cor INFO @ Fri, 05 Jul 2019 15:46:25: #2 finished! INFO @ Fri, 05 Jul 2019 15:46:25: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 15:46:25: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 05 Jul 2019 15:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.20_model.r INFO @ Fri, 05 Jul 2019 15:46:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:46:25: #3 Call peaks for each chromosome... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.10_summits.bed INFO @ Fri, 05 Jul 2019 15:46:26: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:46:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:46:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:46:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:46:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548154/ERX2548154.20_summits.bed INFO @ Fri, 05 Jul 2019 15:46:27: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (68 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。