Job ID = 2007634 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,597,633 reads read : 2,597,633 reads written : 2,597,633 spots read : 2,557,442 reads read : 2,557,442 reads written : 2,557,442 spots read : 2,534,660 reads read : 2,534,660 reads written : 2,534,660 spots read : 2,442,260 reads read : 2,442,260 reads written : 2,442,260 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529759.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529760.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529761.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: 00:07:15 10131995 reads; of these: 10131995 (100.00%) were unpaired; of these: 466053 (4.60%) aligned 0 times 7852371 (77.50%) aligned exactly 1 time 1813571 (17.90%) aligned >1 times 95.40% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 9469227 / 9665942 = 0.9796 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 16:22:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.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 16:22:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.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 16:22:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.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 16:22:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:52: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 16:22:52: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 16:22:52: #1 total tags in treatment: 196715 INFO @ Fri, 05 Jul 2019 16:22:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:52: #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 16:22:52: #1 tags after filtering in treatment: 196715 INFO @ Fri, 05 Jul 2019 16:22:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:52: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:52: #2 number of paired peaks: 265 WARNING @ Fri, 05 Jul 2019 16:22:52: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:52: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:52: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:52: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:52: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:52: #2 predicted fragment length is 153 bps INFO @ Fri, 05 Jul 2019 16:22:52: #2 alternative fragment length(s) may be 91,122,153,168,197,225,543,568 bps INFO @ Fri, 05 Jul 2019 16:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.05_model.r WARNING @ Fri, 05 Jul 2019 16:22:52: #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 16:22:52: #2 You may need to consider one of the other alternative d(s): 91,122,153,168,197,225,543,568 WARNING @ Fri, 05 Jul 2019 16:22:52: #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 16:22:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.05_summits.bed INFO @ Fri, 05 Jul 2019 16:22:54: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 16:22:54: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 16:22:54: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 16:22:54: #1 total tags in treatment: 196715 INFO @ Fri, 05 Jul 2019 16:22:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:54: #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 16:22:54: #1 tags after filtering in treatment: 196715 INFO @ Fri, 05 Jul 2019 16:22:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:54: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:54: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:22:54: #2 number of paired peaks: 265 WARNING @ Fri, 05 Jul 2019 16:22:54: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:54: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:54: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:54: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:54: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:54: #2 predicted fragment length is 153 bps INFO @ Fri, 05 Jul 2019 16:22:54: #2 alternative fragment length(s) may be 91,122,153,168,197,225,543,568 bps INFO @ Fri, 05 Jul 2019 16:22:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.10_model.r WARNING @ Fri, 05 Jul 2019 16:22:54: #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 16:22:54: #2 You may need to consider one of the other alternative d(s): 91,122,153,168,197,225,543,568 WARNING @ Fri, 05 Jul 2019 16:22:54: #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 16:22:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:54: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 16:22:54: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 16:22:54: #1 total tags in treatment: 196715 INFO @ Fri, 05 Jul 2019 16:22:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:54: #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 16:22:54: #1 tags after filtering in treatment: 196715 INFO @ Fri, 05 Jul 2019 16:22:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:54: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:55: #2 number of paired peaks: 265 WARNING @ Fri, 05 Jul 2019 16:22:55: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:55: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:55: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:55: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:55: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:55: #2 predicted fragment length is 153 bps INFO @ Fri, 05 Jul 2019 16:22:55: #2 alternative fragment length(s) may be 91,122,153,168,197,225,543,568 bps INFO @ Fri, 05 Jul 2019 16:22:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.20_model.r WARNING @ Fri, 05 Jul 2019 16:22:55: #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 16:22:55: #2 You may need to consider one of the other alternative d(s): 91,122,153,168,197,225,543,568 WARNING @ Fri, 05 Jul 2019 16:22:55: #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 16:22:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:22:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.10_summits.bed INFO @ Fri, 05 Jul 2019 16:22:55: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:22:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548235/ERX2548235.20_summits.bed INFO @ Fri, 05 Jul 2019 16:22:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling