Job ID = 2006102 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,607,168 reads read : 1,607,168 reads written : 1,607,168 spots read : 1,585,671 reads read : 1,585,671 reads written : 1,585,671 spots read : 1,571,210 reads read : 1,571,210 reads written : 1,571,210 spots read : 1,514,993 reads read : 1,514,993 reads written : 1,514,993 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: 00:02:44 6279042 reads; of these: 6279042 (100.00%) were unpaired; of these: 282635 (4.50%) aligned 0 times 4890858 (77.89%) aligned exactly 1 time 1105549 (17.61%) aligned >1 times 95.50% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:45 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] 5871971 / 5996407 = 0.9792 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 15:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.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 15:17:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:17:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:17:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.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 15:17:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:17:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:17:02: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:17:02: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:17:02: #1 total tags in treatment: 124436 INFO @ Fri, 05 Jul 2019 15:17:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:17:02: #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 15:17:02: #1 tags after filtering in treatment: 124436 INFO @ Fri, 05 Jul 2019 15:17:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:17:02: #1 finished! INFO @ Fri, 05 Jul 2019 15:17:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:17:02: #2 number of paired peaks: 275 WARNING @ Fri, 05 Jul 2019 15:17:02: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Fri, 05 Jul 2019 15:17:02: start model_add_line... INFO @ Fri, 05 Jul 2019 15:17:02: start X-correlation... INFO @ Fri, 05 Jul 2019 15:17:02: end of X-cor INFO @ Fri, 05 Jul 2019 15:17:02: #2 finished! INFO @ Fri, 05 Jul 2019 15:17:02: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 15:17:02: #2 alternative fragment length(s) may be 14,38,59,142,163,219,262,289,314,425,449,488,522,571 bps INFO @ Fri, 05 Jul 2019 15:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.05_model.r WARNING @ Fri, 05 Jul 2019 15:17:02: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:17:02: #2 You may need to consider one of the other alternative d(s): 14,38,59,142,163,219,262,289,314,425,449,488,522,571 WARNING @ Fri, 05 Jul 2019 15:17:02: #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 15:17:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.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 15:17:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:17:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:17:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.05_summits.bed INFO @ Fri, 05 Jul 2019 15:17:03: Done! INFO @ Fri, 05 Jul 2019 15:17:03: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:17:03: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:17:03: #1 total tags in treatment: 124436 INFO @ Fri, 05 Jul 2019 15:17:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:17:03: #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 15:17:03: #1 tags after filtering in treatment: 124436 INFO @ Fri, 05 Jul 2019 15:17:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:17:03: #1 finished! INFO @ Fri, 05 Jul 2019 15:17:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:17:03: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:17:03: #2 number of paired peaks: 275 WARNING @ Fri, 05 Jul 2019 15:17:03: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Fri, 05 Jul 2019 15:17:03: start model_add_line... INFO @ Fri, 05 Jul 2019 15:17:03: start X-correlation... INFO @ Fri, 05 Jul 2019 15:17:03: end of X-cor INFO @ Fri, 05 Jul 2019 15:17:03: #2 finished! INFO @ Fri, 05 Jul 2019 15:17:03: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 15:17:03: #2 alternative fragment length(s) may be 14,38,59,142,163,219,262,289,314,425,449,488,522,571 bps INFO @ Fri, 05 Jul 2019 15:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.10_model.r WARNING @ Fri, 05 Jul 2019 15:17:03: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:17:03: #2 You may need to consider one of the other alternative d(s): 14,38,59,142,163,219,262,289,314,425,449,488,522,571 WARNING @ Fri, 05 Jul 2019 15:17:03: #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 15:17:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:17:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:17:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:17:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:17:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.10_summits.bed INFO @ Fri, 05 Jul 2019 15:17:04: Done! pass1 - making usageList (5 chroms): 1 millis INFO @ Fri, 05 Jul 2019 15:17:04: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:17:04: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:17:04: #1 total tags in treatment: 124436 INFO @ Fri, 05 Jul 2019 15:17:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:17:04: #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 15:17:04: #1 tags after filtering in treatment: 124436 INFO @ Fri, 05 Jul 2019 15:17:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:17:04: #1 finished! INFO @ Fri, 05 Jul 2019 15:17:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:17:04: #2 number of paired peaks: 275 WARNING @ Fri, 05 Jul 2019 15:17:04: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Fri, 05 Jul 2019 15:17:04: start model_add_line... INFO @ Fri, 05 Jul 2019 15:17:04: start X-correlation... INFO @ Fri, 05 Jul 2019 15:17:04: end of X-cor INFO @ Fri, 05 Jul 2019 15:17:04: #2 finished! INFO @ Fri, 05 Jul 2019 15:17:04: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 15:17:04: #2 alternative fragment length(s) may be 14,38,59,142,163,219,262,289,314,425,449,488,522,571 bps INFO @ Fri, 05 Jul 2019 15:17:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.20_model.r WARNING @ Fri, 05 Jul 2019 15:17:04: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:17:04: #2 You may need to consider one of the other alternative d(s): 14,38,59,142,163,219,262,289,314,425,449,488,522,571 WARNING @ Fri, 05 Jul 2019 15:17:04: #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 15:17:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:17:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:17:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:17:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:17:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:17:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548109/ERX2548109.20_summits.bed INFO @ Fri, 05 Jul 2019 15:17:05: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1316 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。