Job ID = 2010569 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,969,418 reads read : 11,938,836 reads written : 11,938,836 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:25 5969418 reads; of these: 5969418 (100.00%) were paired; of these: 5289712 (88.61%) aligned concordantly 0 times 516929 (8.66%) aligned concordantly exactly 1 time 162777 (2.73%) aligned concordantly >1 times ---- 5289712 pairs aligned concordantly 0 times; of these: 5404 (0.10%) aligned discordantly 1 time ---- 5284308 pairs aligned 0 times concordantly or discordantly; of these: 10568616 mates make up the pairs; of these: 10496547 (99.32%) aligned 0 times 45031 (0.43%) aligned exactly 1 time 27038 (0.26%) aligned >1 times 12.08% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 33449 / 684199 = 0.0489 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 23:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.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 23:20:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.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 23:20:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.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 23:20:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:28: 1000000 INFO @ Fri, 05 Jul 2019 23:20:29: 1000000 INFO @ Fri, 05 Jul 2019 23:20:29: 1000000 INFO @ Fri, 05 Jul 2019 23:20:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:20:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:20:31: #1 total tags in treatment: 646314 INFO @ Fri, 05 Jul 2019 23:20:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:20:31: #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 23:20:31: #1 tags after filtering in treatment: 457751 INFO @ Fri, 05 Jul 2019 23:20:31: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 23:20:31: #1 finished! INFO @ Fri, 05 Jul 2019 23:20:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:20:31: #2 number of paired peaks: 995 WARNING @ Fri, 05 Jul 2019 23:20:31: Fewer paired peaks (995) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 995 pairs to build model! INFO @ Fri, 05 Jul 2019 23:20:31: start model_add_line... INFO @ Fri, 05 Jul 2019 23:20:31: start X-correlation... INFO @ Fri, 05 Jul 2019 23:20:32: end of X-cor INFO @ Fri, 05 Jul 2019 23:20:32: #2 finished! INFO @ Fri, 05 Jul 2019 23:20:32: #2 predicted fragment length is 230 bps INFO @ Fri, 05 Jul 2019 23:20:32: #2 alternative fragment length(s) may be 2,230,251,261,591 bps INFO @ Fri, 05 Jul 2019 23:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.20_model.r BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 23:20:32: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:20:32: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:20:32: #1 total tags in treatment: 646314 INFO @ Fri, 05 Jul 2019 23:20:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:20:32: #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 23:20:32: #1 tags after filtering in treatment: 457751 INFO @ Fri, 05 Jul 2019 23:20:32: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 23:20:32: #1 finished! INFO @ Fri, 05 Jul 2019 23:20:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:20:32: #2 number of paired peaks: 995 WARNING @ Fri, 05 Jul 2019 23:20:32: Fewer paired peaks (995) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 995 pairs to build model! INFO @ Fri, 05 Jul 2019 23:20:32: start model_add_line... INFO @ Fri, 05 Jul 2019 23:20:32: start X-correlation... INFO @ Fri, 05 Jul 2019 23:20:32: end of X-cor INFO @ Fri, 05 Jul 2019 23:20:32: #2 finished! INFO @ Fri, 05 Jul 2019 23:20:32: #2 predicted fragment length is 230 bps INFO @ Fri, 05 Jul 2019 23:20:32: #2 alternative fragment length(s) may be 2,230,251,261,591 bps INFO @ Fri, 05 Jul 2019 23:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.05_model.r INFO @ Fri, 05 Jul 2019 23:20:33: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:20:33: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:20:33: #1 total tags in treatment: 646314 INFO @ Fri, 05 Jul 2019 23:20:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:20:33: #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 23:20:33: #1 tags after filtering in treatment: 457751 INFO @ Fri, 05 Jul 2019 23:20:33: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 23:20:33: #1 finished! INFO @ Fri, 05 Jul 2019 23:20:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:20:33: #2 number of paired peaks: 995 WARNING @ Fri, 05 Jul 2019 23:20:33: Fewer paired peaks (995) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 995 pairs to build model! INFO @ Fri, 05 Jul 2019 23:20:33: start model_add_line... INFO @ Fri, 05 Jul 2019 23:20:33: start X-correlation... INFO @ Fri, 05 Jul 2019 23:20:33: end of X-cor INFO @ Fri, 05 Jul 2019 23:20:33: #2 finished! INFO @ Fri, 05 Jul 2019 23:20:33: #2 predicted fragment length is 230 bps INFO @ Fri, 05 Jul 2019 23:20:33: #2 alternative fragment length(s) may be 2,230,251,261,591 bps INFO @ Fri, 05 Jul 2019 23:20:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.10_model.r BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:20:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:20:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:20:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:20:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:20:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:20:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:20:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.10_summits.bed INFO @ Fri, 05 Jul 2019 23:20:49: Done! INFO @ Fri, 05 Jul 2019 23:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.20_summits.bed INFO @ Fri, 05 Jul 2019 23:20:49: Done! INFO @ Fri, 05 Jul 2019 23:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381270/SRX381270.05_summits.bed INFO @ Fri, 05 Jul 2019 23:20:49: Done! pass1 - making usageList (16 chroms): 2 millis pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (91 records, 4 fields): 3 millis pass2 - checking and writing primary data (248 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling