Job ID = 2006152 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,606,964 reads read : 1,606,964 reads written : 1,606,964 spots read : 1,546,376 reads read : 1,546,376 reads written : 1,546,376 spots read : 1,589,628 reads read : 1,589,628 reads written : 1,589,628 spots read : 1,597,977 reads read : 1,597,977 reads written : 1,597,977 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529363.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529364.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529365.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: 00:05:57 6340945 reads; of these: 6340945 (100.00%) were unpaired; of these: 302920 (4.78%) aligned 0 times 5027445 (79.29%) aligned exactly 1 time 1010580 (15.94%) aligned >1 times 95.22% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 5978976 / 6038025 = 0.9902 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 15:19:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.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 15:19:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:19:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:19:27: #1 tag size is determined as 145 bps INFO @ Fri, 05 Jul 2019 15:19:27: #1 tag size = 145 INFO @ Fri, 05 Jul 2019 15:19:27: #1 total tags in treatment: 59049 INFO @ Fri, 05 Jul 2019 15:19:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:19:27: #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 15:19:27: #1 tags after filtering in treatment: 59049 INFO @ Fri, 05 Jul 2019 15:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:19:27: #1 finished! INFO @ Fri, 05 Jul 2019 15:19:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:19:27: #2 number of paired peaks: 314 WARNING @ Fri, 05 Jul 2019 15:19:27: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 05 Jul 2019 15:19:27: start model_add_line... INFO @ Fri, 05 Jul 2019 15:19:27: start X-correlation... INFO @ Fri, 05 Jul 2019 15:19:27: end of X-cor INFO @ Fri, 05 Jul 2019 15:19:27: #2 finished! INFO @ Fri, 05 Jul 2019 15:19:27: #2 predicted fragment length is 153 bps INFO @ Fri, 05 Jul 2019 15:19:27: #2 alternative fragment length(s) may be 61,103,130,153,179,197,227,271,292,339,367,388,407,444,459,480,511,531,576 bps INFO @ Fri, 05 Jul 2019 15:19:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.05_model.r INFO @ Fri, 05 Jul 2019 15:19:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.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 15:19:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:19:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:19:28: #1 tag size is determined as 145 bps INFO @ Fri, 05 Jul 2019 15:19:28: #1 tag size = 145 INFO @ Fri, 05 Jul 2019 15:19:28: #1 total tags in treatment: 59049 INFO @ Fri, 05 Jul 2019 15:19:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:19:28: #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 15:19:28: #1 tags after filtering in treatment: 59049 INFO @ Fri, 05 Jul 2019 15:19:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:19:28: #1 finished! INFO @ Fri, 05 Jul 2019 15:19:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:19:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:19:28: #2 number of paired peaks: 314 WARNING @ Fri, 05 Jul 2019 15:19:28: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 05 Jul 2019 15:19:28: start model_add_line... INFO @ Fri, 05 Jul 2019 15:19:28: start X-correlation... INFO @ Fri, 05 Jul 2019 15:19:28: end of X-cor INFO @ Fri, 05 Jul 2019 15:19:28: #2 finished! INFO @ Fri, 05 Jul 2019 15:19:28: #2 predicted fragment length is 153 bps INFO @ Fri, 05 Jul 2019 15:19:28: #2 alternative fragment length(s) may be 61,103,130,153,179,197,227,271,292,339,367,388,407,444,459,480,511,531,576 bps INFO @ Fri, 05 Jul 2019 15:19:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.10_model.r WARNING @ Fri, 05 Jul 2019 15:19:30: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:19:30: #2 You may need to consider one of the other alternative d(s): 61,103,130,153,179,197,227,271,292,339,367,388,407,444,459,480,511,531,576 WARNING @ Fri, 05 Jul 2019 15:19:30: #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 15:19:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:19:30: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 05 Jul 2019 15:19:30: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:19:30: #2 You may need to consider one of the other alternative d(s): 61,103,130,153,179,197,227,271,292,339,367,388,407,444,459,480,511,531,576 WARNING @ Fri, 05 Jul 2019 15:19:30: #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 15:19:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:19:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:19:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:19:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:19:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:19:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.05_summits.bed INFO @ Fri, 05 Jul 2019 15:19:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:19:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:19:31: Done! INFO @ Fri, 05 Jul 2019 15:19:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.10_summits.bed INFO @ Fri, 05 Jul 2019 15:19:31: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.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 15:19:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:19:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:19:33: #1 tag size is determined as 145 bps INFO @ Fri, 05 Jul 2019 15:19:33: #1 tag size = 145 INFO @ Fri, 05 Jul 2019 15:19:33: #1 total tags in treatment: 59049 INFO @ Fri, 05 Jul 2019 15:19:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:19:33: #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 15:19:33: #1 tags after filtering in treatment: 59049 INFO @ Fri, 05 Jul 2019 15:19:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:19:33: #1 finished! INFO @ Fri, 05 Jul 2019 15:19:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:19:33: #2 number of paired peaks: 314 WARNING @ Fri, 05 Jul 2019 15:19:33: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 05 Jul 2019 15:19:33: start model_add_line... INFO @ Fri, 05 Jul 2019 15:19:33: start X-correlation... INFO @ Fri, 05 Jul 2019 15:19:34: end of X-cor INFO @ Fri, 05 Jul 2019 15:19:34: #2 finished! INFO @ Fri, 05 Jul 2019 15:19:34: #2 predicted fragment length is 153 bps INFO @ Fri, 05 Jul 2019 15:19:34: #2 alternative fragment length(s) may be 61,103,130,153,179,197,227,271,292,339,367,388,407,444,459,480,511,531,576 bps INFO @ Fri, 05 Jul 2019 15:19:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.20_model.r WARNING @ Fri, 05 Jul 2019 15:19:34: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:19:34: #2 You may need to consider one of the other alternative d(s): 61,103,130,153,179,197,227,271,292,339,367,388,407,444,459,480,511,531,576 WARNING @ Fri, 05 Jul 2019 15:19:34: #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 15:19:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:19:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:19:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:19:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:19:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:19:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548118/ERX2548118.20_summits.bed INFO @ Fri, 05 Jul 2019 15:19:34: Done! CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling