Job ID = 2008376 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,862,395 reads read : 9,862,395 reads written : 9,862,395 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637564.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: 00:01:18 9862395 reads; of these: 9862395 (100.00%) were unpaired; of these: 5610266 (56.89%) aligned 0 times 3483822 (35.32%) aligned exactly 1 time 768307 (7.79%) aligned >1 times 43.11% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 2112692 / 4252129 = 0.4969 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 18:54:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.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 18:54:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:54:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:54:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.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 18:54:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:54:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:54:10: 1000000 INFO @ Fri, 05 Jul 2019 18:54:11: 1000000 INFO @ Fri, 05 Jul 2019 18:54:18: 2000000 INFO @ Fri, 05 Jul 2019 18:54:19: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:54:19: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:54:19: #1 total tags in treatment: 2139437 INFO @ Fri, 05 Jul 2019 18:54:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:54:19: #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 18:54:19: #1 tags after filtering in treatment: 2139437 INFO @ Fri, 05 Jul 2019 18:54:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:54:19: #1 finished! INFO @ Fri, 05 Jul 2019 18:54:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:54:20: #2 number of paired peaks: 370 WARNING @ Fri, 05 Jul 2019 18:54:20: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Fri, 05 Jul 2019 18:54:20: start model_add_line... INFO @ Fri, 05 Jul 2019 18:54:20: start X-correlation... INFO @ Fri, 05 Jul 2019 18:54:20: end of X-cor INFO @ Fri, 05 Jul 2019 18:54:20: #2 finished! INFO @ Fri, 05 Jul 2019 18:54:20: #2 predicted fragment length is 157 bps INFO @ Fri, 05 Jul 2019 18:54:20: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 05 Jul 2019 18:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.10_model.r INFO @ Fri, 05 Jul 2019 18:54:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:54:23: 2000000 INFO @ Fri, 05 Jul 2019 18:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.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 18:54:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:54:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:54:24: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:54:24: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:54:24: #1 total tags in treatment: 2139437 INFO @ Fri, 05 Jul 2019 18:54:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:54:24: #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 18:54:24: #1 tags after filtering in treatment: 2139437 INFO @ Fri, 05 Jul 2019 18:54:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:54:24: #1 finished! INFO @ Fri, 05 Jul 2019 18:54:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:54:24: #2 number of paired peaks: 370 WARNING @ Fri, 05 Jul 2019 18:54:24: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Fri, 05 Jul 2019 18:54:24: start model_add_line... INFO @ Fri, 05 Jul 2019 18:54:24: start X-correlation... INFO @ Fri, 05 Jul 2019 18:54:25: end of X-cor INFO @ Fri, 05 Jul 2019 18:54:25: #2 finished! INFO @ Fri, 05 Jul 2019 18:54:25: #2 predicted fragment length is 157 bps INFO @ Fri, 05 Jul 2019 18:54:25: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 05 Jul 2019 18:54:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.05_model.r INFO @ Fri, 05 Jul 2019 18:54:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:54:33: 1000000 INFO @ Fri, 05 Jul 2019 18:54:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:54:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:54:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:54:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.10_summits.bed INFO @ Fri, 05 Jul 2019 18:54:36: Done! INFO @ Fri, 05 Jul 2019 18:54:40: 2000000 INFO @ Fri, 05 Jul 2019 18:54:42: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 18:54:42: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 18:54:42: #1 total tags in treatment: 2139437 INFO @ Fri, 05 Jul 2019 18:54:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:54:42: #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 18:54:42: #1 tags after filtering in treatment: 2139437 INFO @ Fri, 05 Jul 2019 18:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 18:54:42: #1 finished! INFO @ Fri, 05 Jul 2019 18:54:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:54:43: #2 number of paired peaks: 370 WARNING @ Fri, 05 Jul 2019 18:54:43: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Fri, 05 Jul 2019 18:54:43: start model_add_line... INFO @ Fri, 05 Jul 2019 18:54:43: start X-correlation... INFO @ Fri, 05 Jul 2019 18:54:43: end of X-cor INFO @ Fri, 05 Jul 2019 18:54:43: #2 finished! INFO @ Fri, 05 Jul 2019 18:54:43: #2 predicted fragment length is 157 bps INFO @ Fri, 05 Jul 2019 18:54:43: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 05 Jul 2019 18:54:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.20_model.r INFO @ Fri, 05 Jul 2019 18:54:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:54:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:54:46: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (16 chroms): 4 millis pass2 - checking and writing primary data (2579 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.05_summits.bed INFO @ Fri, 05 Jul 2019 18:54:47: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (3166 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:54:59: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:55:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:55:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:55:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX593992/ERX593992.20_summits.bed INFO @ Fri, 05 Jul 2019 18:55:08: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1855 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。