Job ID = 2007231 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,133,400 reads read : 1,133,400 reads written : 1,133,400 spots read : 1,094,617 reads read : 1,094,617 reads written : 1,094,617 spots read : 1,118,787 reads read : 1,118,787 reads written : 1,118,787 spots read : 1,147,175 reads read : 1,147,175 reads written : 1,147,175 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529646.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529647.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529648.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: 00:03:40 4493979 reads; of these: 4493979 (100.00%) were unpaired; of these: 220920 (4.92%) aligned 0 times 3620984 (80.57%) aligned exactly 1 time 652075 (14.51%) aligned >1 times 95.08% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 4222773 / 4273059 = 0.9882 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 16:02:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.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 16:02:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:02:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:02:27: #1 tag size is determined as 139 bps INFO @ Fri, 05 Jul 2019 16:02:27: #1 tag size = 139 INFO @ Fri, 05 Jul 2019 16:02:27: #1 total tags in treatment: 50286 INFO @ Fri, 05 Jul 2019 16:02:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:02:27: #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 16:02:27: #1 tags after filtering in treatment: 50286 INFO @ Fri, 05 Jul 2019 16:02:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:02:27: #1 finished! INFO @ Fri, 05 Jul 2019 16:02:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:02:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:02:27: #2 number of paired peaks: 256 WARNING @ Fri, 05 Jul 2019 16:02:27: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 05 Jul 2019 16:02:27: start model_add_line... INFO @ Fri, 05 Jul 2019 16:02:27: start X-correlation... INFO @ Fri, 05 Jul 2019 16:02:27: end of X-cor INFO @ Fri, 05 Jul 2019 16:02:27: #2 finished! INFO @ Fri, 05 Jul 2019 16:02:27: #2 predicted fragment length is 229 bps INFO @ Fri, 05 Jul 2019 16:02:27: #2 alternative fragment length(s) may be 12,29,46,73,105,140,163,197,229,260,296,323,355,387,429,452,471,496,518,546,583 bps INFO @ Fri, 05 Jul 2019 16:02:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.05_model.r WARNING @ Fri, 05 Jul 2019 16:02:27: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:02:27: #2 You may need to consider one of the other alternative d(s): 12,29,46,73,105,140,163,197,229,260,296,323,355,387,429,452,471,496,518,546,583 WARNING @ Fri, 05 Jul 2019 16:02:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:02:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:02:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:02:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.05_summits.bed INFO @ Fri, 05 Jul 2019 16:02:28: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:02:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.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 16:02:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:02:28: #1 read treatment tags... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:02:28: #1 tag size is determined as 139 bps INFO @ Fri, 05 Jul 2019 16:02:28: #1 tag size = 139 INFO @ Fri, 05 Jul 2019 16:02:28: #1 total tags in treatment: 50286 INFO @ Fri, 05 Jul 2019 16:02:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:02:28: #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 16:02:28: #1 tags after filtering in treatment: 50286 INFO @ Fri, 05 Jul 2019 16:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:02:28: #1 finished! INFO @ Fri, 05 Jul 2019 16:02:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:02:28: #2 number of paired peaks: 256 WARNING @ Fri, 05 Jul 2019 16:02:28: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 05 Jul 2019 16:02:28: start model_add_line... INFO @ Fri, 05 Jul 2019 16:02:28: start X-correlation... INFO @ Fri, 05 Jul 2019 16:02:28: end of X-cor INFO @ Fri, 05 Jul 2019 16:02:28: #2 finished! INFO @ Fri, 05 Jul 2019 16:02:28: #2 predicted fragment length is 229 bps INFO @ Fri, 05 Jul 2019 16:02:28: #2 alternative fragment length(s) may be 12,29,46,73,105,140,163,197,229,260,296,323,355,387,429,452,471,496,518,546,583 bps INFO @ Fri, 05 Jul 2019 16:02:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.10_model.r WARNING @ Fri, 05 Jul 2019 16:02:28: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:02:28: #2 You may need to consider one of the other alternative d(s): 12,29,46,73,105,140,163,197,229,260,296,323,355,387,429,452,471,496,518,546,583 WARNING @ Fri, 05 Jul 2019 16:02:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:02:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:02:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:02:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.10_summits.bed INFO @ Fri, 05 Jul 2019 16:02:29: Done! INFO @ Fri, 05 Jul 2019 16:02:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.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 16:02:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:02:29: #1 read treatment tags... pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:02:29: #1 tag size is determined as 139 bps INFO @ Fri, 05 Jul 2019 16:02:29: #1 tag size = 139 INFO @ Fri, 05 Jul 2019 16:02:29: #1 total tags in treatment: 50286 INFO @ Fri, 05 Jul 2019 16:02:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:02:29: #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 16:02:29: #1 tags after filtering in treatment: 50286 INFO @ Fri, 05 Jul 2019 16:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:02:29: #1 finished! INFO @ Fri, 05 Jul 2019 16:02:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:02:29: #2 number of paired peaks: 256 WARNING @ Fri, 05 Jul 2019 16:02:29: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 05 Jul 2019 16:02:29: start model_add_line... INFO @ Fri, 05 Jul 2019 16:02:29: start X-correlation... INFO @ Fri, 05 Jul 2019 16:02:29: end of X-cor INFO @ Fri, 05 Jul 2019 16:02:29: #2 finished! INFO @ Fri, 05 Jul 2019 16:02:29: #2 predicted fragment length is 229 bps INFO @ Fri, 05 Jul 2019 16:02:29: #2 alternative fragment length(s) may be 12,29,46,73,105,140,163,197,229,260,296,323,355,387,429,452,471,496,518,546,583 bps INFO @ Fri, 05 Jul 2019 16:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.20_model.r WARNING @ Fri, 05 Jul 2019 16:02:29: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:02:29: #2 You may need to consider one of the other alternative d(s): 12,29,46,73,105,140,163,197,229,260,296,323,355,387,429,452,471,496,518,546,583 WARNING @ Fri, 05 Jul 2019 16:02:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:02:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:02:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:02:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:02:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:02:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:02:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548201/ERX2548201.20_summits.bed INFO @ Fri, 05 Jul 2019 16:02:30: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling