Job ID = 2006284 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,418,721 reads read : 1,418,721 reads written : 1,418,721 spots read : 1,369,264 reads read : 1,369,264 reads written : 1,369,264 spots read : 1,385,857 reads read : 1,385,857 reads written : 1,385,857 spots read : 1,360,279 reads read : 1,360,279 reads written : 1,360,279 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529426.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529427.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529428.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: 00:01:30 5534121 reads; of these: 5534121 (100.00%) were unpaired; of these: 253938 (4.59%) aligned 0 times 4009790 (72.46%) aligned exactly 1 time 1270393 (22.96%) aligned >1 times 95.41% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 5010990 / 5280183 = 0.9490 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 15:21:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.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 15:21:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:21:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:21:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.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 15:21:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:21:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:21:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.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 15:21:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:21:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:21:57: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:21:57: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:21:57: #1 total tags in treatment: 269193 INFO @ Fri, 05 Jul 2019 15:21:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:21:57: #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 15:21:57: #1 tags after filtering in treatment: 269193 INFO @ Fri, 05 Jul 2019 15:21:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:21:57: #1 finished! INFO @ Fri, 05 Jul 2019 15:21:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:21:57: #2 number of paired peaks: 416 WARNING @ Fri, 05 Jul 2019 15:21:57: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Fri, 05 Jul 2019 15:21:57: start model_add_line... INFO @ Fri, 05 Jul 2019 15:21:57: start X-correlation... INFO @ Fri, 05 Jul 2019 15:21:57: end of X-cor INFO @ Fri, 05 Jul 2019 15:21:57: #2 finished! INFO @ Fri, 05 Jul 2019 15:21:57: #2 predicted fragment length is 88 bps INFO @ Fri, 05 Jul 2019 15:21:57: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 05 Jul 2019 15:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.05_model.r WARNING @ Fri, 05 Jul 2019 15:21:57: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:21:57: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 05 Jul 2019 15:21:57: #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 15:21:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:21:58: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:21:58: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:21:58: #1 total tags in treatment: 269193 INFO @ Fri, 05 Jul 2019 15:21:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:21:58: #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 15:21:58: #1 tags after filtering in treatment: 269193 INFO @ Fri, 05 Jul 2019 15:21:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:21:58: #1 finished! INFO @ Fri, 05 Jul 2019 15:21:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:21:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:21:58: #2 number of paired peaks: 416 WARNING @ Fri, 05 Jul 2019 15:21:58: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Fri, 05 Jul 2019 15:21:58: start model_add_line... INFO @ Fri, 05 Jul 2019 15:21:58: start X-correlation... INFO @ Fri, 05 Jul 2019 15:21:58: end of X-cor INFO @ Fri, 05 Jul 2019 15:21:58: #2 finished! INFO @ Fri, 05 Jul 2019 15:21:58: #2 predicted fragment length is 88 bps INFO @ Fri, 05 Jul 2019 15:21:58: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 05 Jul 2019 15:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.10_model.r WARNING @ Fri, 05 Jul 2019 15:21:58: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:21:58: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 05 Jul 2019 15:21:58: #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 15:21:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:21:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:21:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:21:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:21:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:21:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.05_summits.bed INFO @ Fri, 05 Jul 2019 15:21:59: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (211 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:21:59: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:21:59: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:21:59: #1 total tags in treatment: 269193 INFO @ Fri, 05 Jul 2019 15:21:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:21:59: #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 15:21:59: #1 tags after filtering in treatment: 269193 INFO @ Fri, 05 Jul 2019 15:21:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:21:59: #1 finished! INFO @ Fri, 05 Jul 2019 15:21:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:21:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:21:59: #2 number of paired peaks: 416 WARNING @ Fri, 05 Jul 2019 15:21:59: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Fri, 05 Jul 2019 15:21:59: start model_add_line... INFO @ Fri, 05 Jul 2019 15:21:59: start X-correlation... INFO @ Fri, 05 Jul 2019 15:21:59: end of X-cor INFO @ Fri, 05 Jul 2019 15:21:59: #2 finished! INFO @ Fri, 05 Jul 2019 15:21:59: #2 predicted fragment length is 88 bps INFO @ Fri, 05 Jul 2019 15:21:59: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 05 Jul 2019 15:21:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.20_model.r INFO @ Fri, 05 Jul 2019 15:21:59: #3 Call peaks for each chromosome... WARNING @ Fri, 05 Jul 2019 15:22:00: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:22:00: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 05 Jul 2019 15:22:00: #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 15:22:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:22:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:22:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:22:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:22:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.10_summits.bed INFO @ Fri, 05 Jul 2019 15:22:00: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:22:01: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548134/ERX2548134.20_summits.bed INFO @ Fri, 05 Jul 2019 15:22:01: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。