Job ID = 2007222 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,201,107 reads read : 2,201,107 reads written : 2,201,107 spots read : 2,094,814 reads read : 2,094,814 reads written : 2,094,814 spots read : 2,063,654 reads read : 2,063,654 reads written : 2,063,654 spots read : 2,189,635 reads read : 2,189,635 reads written : 2,189,635 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529610.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529611.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529613.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: 00:00:01 Multiseed full-index search: 00:04:14 8549210 reads; of these: 8549210 (100.00%) were unpaired; of these: 505192 (5.91%) aligned 0 times 6812807 (79.69%) aligned exactly 1 time 1231211 (14.40%) aligned >1 times 94.09% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 7964112 / 8044018 = 0.9901 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 16:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.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 16:03:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:03:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:03:52: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 16:03:52: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 16:03:52: #1 total tags in treatment: 79906 INFO @ Fri, 05 Jul 2019 16:03:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:52: #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 16:03:52: #1 tags after filtering in treatment: 79906 INFO @ Fri, 05 Jul 2019 16:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:52: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:52: #2 number of paired peaks: 304 WARNING @ Fri, 05 Jul 2019 16:03:52: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Fri, 05 Jul 2019 16:03:52: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:52: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:52: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:52: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:52: #2 predicted fragment length is 175 bps INFO @ Fri, 05 Jul 2019 16:03:52: #2 alternative fragment length(s) may be 28,45,78,87,122,152,175,204,221,265,298,317,366,400,420,441,470,505,532,548,561,586 bps INFO @ Fri, 05 Jul 2019 16:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.05_model.r WARNING @ Fri, 05 Jul 2019 16:03:52: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:03:52: #2 You may need to consider one of the other alternative d(s): 28,45,78,87,122,152,175,204,221,265,298,317,366,400,420,441,470,505,532,548,561,586 WARNING @ Fri, 05 Jul 2019 16:03:52: #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 16:03:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.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 16:03:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:03:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:03:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:03:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:03:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:03:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.05_summits.bed INFO @ Fri, 05 Jul 2019 16:03:52: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.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 16:03:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:03:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:03:53: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 16:03:53: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 16:03:53: #1 total tags in treatment: 79906 INFO @ Fri, 05 Jul 2019 16:03:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:53: #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 16:03:53: #1 tags after filtering in treatment: 79906 INFO @ Fri, 05 Jul 2019 16:03:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:53: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:53: #2 number of paired peaks: 304 WARNING @ Fri, 05 Jul 2019 16:03:53: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Fri, 05 Jul 2019 16:03:53: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:53: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:53: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:53: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:53: #2 predicted fragment length is 175 bps INFO @ Fri, 05 Jul 2019 16:03:53: #2 alternative fragment length(s) may be 28,45,78,87,122,152,175,204,221,265,298,317,366,400,420,441,470,505,532,548,561,586 bps INFO @ Fri, 05 Jul 2019 16:03:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.10_model.r WARNING @ Fri, 05 Jul 2019 16:03:53: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:03:53: #2 You may need to consider one of the other alternative d(s): 28,45,78,87,122,152,175,204,221,265,298,317,366,400,420,441,470,505,532,548,561,586 WARNING @ Fri, 05 Jul 2019 16:03:53: #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 16:03:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:03:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:03:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:03:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:03:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.10_summits.bed INFO @ Fri, 05 Jul 2019 16:03:53: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:03:54: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 16:03:54: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 16:03:54: #1 total tags in treatment: 79906 INFO @ Fri, 05 Jul 2019 16:03:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:03:54: #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 16:03:54: #1 tags after filtering in treatment: 79906 INFO @ Fri, 05 Jul 2019 16:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:03:54: #1 finished! INFO @ Fri, 05 Jul 2019 16:03:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:03:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:03:54: #2 number of paired peaks: 304 WARNING @ Fri, 05 Jul 2019 16:03:54: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Fri, 05 Jul 2019 16:03:54: start model_add_line... INFO @ Fri, 05 Jul 2019 16:03:54: start X-correlation... INFO @ Fri, 05 Jul 2019 16:03:54: end of X-cor INFO @ Fri, 05 Jul 2019 16:03:54: #2 finished! INFO @ Fri, 05 Jul 2019 16:03:54: #2 predicted fragment length is 175 bps INFO @ Fri, 05 Jul 2019 16:03:54: #2 alternative fragment length(s) may be 28,45,78,87,122,152,175,204,221,265,298,317,366,400,420,441,470,505,532,548,561,586 bps INFO @ Fri, 05 Jul 2019 16:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.20_model.r WARNING @ Fri, 05 Jul 2019 16:03:54: #2 Since the d (175) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:03:54: #2 You may need to consider one of the other alternative d(s): 28,45,78,87,122,152,175,204,221,265,298,317,366,400,420,441,470,505,532,548,561,586 WARNING @ Fri, 05 Jul 2019 16:03:54: #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 16:03:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:03:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:03:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:03:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:03:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548192/ERX2548192.20_summits.bed INFO @ Fri, 05 Jul 2019 16:03:55: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。