Job ID = 2007586 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,405,920 reads read : 3,405,920 reads written : 3,405,920 spots read : 3,367,065 reads read : 3,367,065 reads written : 3,367,065 spots read : 3,351,224 reads read : 3,351,224 reads written : 3,351,224 spots read : 3,265,731 reads read : 3,265,731 reads written : 3,265,731 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529695.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529696.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529697.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: 00:04:08 13389940 reads; of these: 13389940 (100.00%) were unpaired; of these: 751244 (5.61%) aligned 0 times 11544834 (86.22%) aligned exactly 1 time 1093862 (8.17%) aligned >1 times 94.39% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 12048039 / 12638696 = 0.9533 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 16:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.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 16:10:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:10:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.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 16:10:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:10:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:10:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.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 16:10:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:10:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:10:14: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:10:14: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:10:14: #1 total tags in treatment: 590657 INFO @ Fri, 05 Jul 2019 16:10:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:10:14: #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 16:10:14: #1 tags after filtering in treatment: 590657 INFO @ Fri, 05 Jul 2019 16:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:10:14: #1 finished! INFO @ Fri, 05 Jul 2019 16:10:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:10:14: #2 number of paired peaks: 669 WARNING @ Fri, 05 Jul 2019 16:10:14: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Fri, 05 Jul 2019 16:10:14: start model_add_line... INFO @ Fri, 05 Jul 2019 16:10:14: start X-correlation... INFO @ Fri, 05 Jul 2019 16:10:14: end of X-cor INFO @ Fri, 05 Jul 2019 16:10:14: #2 finished! INFO @ Fri, 05 Jul 2019 16:10:14: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 16:10:14: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 05 Jul 2019 16:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.05_model.r INFO @ Fri, 05 Jul 2019 16:10:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:10:15: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:10:15: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:10:15: #1 total tags in treatment: 590657 INFO @ Fri, 05 Jul 2019 16:10:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:10:15: #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 16:10:15: #1 tags after filtering in treatment: 590657 INFO @ Fri, 05 Jul 2019 16:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:10:15: #1 finished! INFO @ Fri, 05 Jul 2019 16:10:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:10:15: #2 number of paired peaks: 669 WARNING @ Fri, 05 Jul 2019 16:10:15: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Fri, 05 Jul 2019 16:10:15: start model_add_line... INFO @ Fri, 05 Jul 2019 16:10:15: start X-correlation... INFO @ Fri, 05 Jul 2019 16:10:15: end of X-cor INFO @ Fri, 05 Jul 2019 16:10:15: #2 finished! INFO @ Fri, 05 Jul 2019 16:10:15: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 16:10:15: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 05 Jul 2019 16:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.10_model.r INFO @ Fri, 05 Jul 2019 16:10:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:10:16: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:10:16: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:10:16: #1 total tags in treatment: 590657 INFO @ Fri, 05 Jul 2019 16:10:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:10:16: #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 16:10:16: #1 tags after filtering in treatment: 590657 INFO @ Fri, 05 Jul 2019 16:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:10:16: #1 finished! INFO @ Fri, 05 Jul 2019 16:10:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:10:17: #2 number of paired peaks: 669 WARNING @ Fri, 05 Jul 2019 16:10:17: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Fri, 05 Jul 2019 16:10:17: start model_add_line... INFO @ Fri, 05 Jul 2019 16:10:17: start X-correlation... INFO @ Fri, 05 Jul 2019 16:10:17: end of X-cor INFO @ Fri, 05 Jul 2019 16:10:17: #2 finished! INFO @ Fri, 05 Jul 2019 16:10:17: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 16:10:17: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 05 Jul 2019 16:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.20_model.r INFO @ Fri, 05 Jul 2019 16:10:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:10:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:10:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:10:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:10:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:10:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.05_summits.bed INFO @ Fri, 05 Jul 2019 16:10:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (956 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.10_summits.bed INFO @ Fri, 05 Jul 2019 16:10:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 16:10:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:10:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:10:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:10:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548213/ERX2548213.20_summits.bed INFO @ Fri, 05 Jul 2019 16:10:20: Done! CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。