Job ID = 2006115 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,823,071 reads read : 2,823,071 reads written : 2,823,071 spots read : 2,783,698 reads read : 2,783,698 reads written : 2,783,698 spots read : 2,757,949 reads read : 2,757,949 reads written : 2,757,949 spots read : 2,668,929 reads read : 2,668,929 reads written : 2,668,929 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: 00:09:16 11033647 reads; of these: 11033647 (100.00%) were unpaired; of these: 440384 (3.99%) aligned 0 times 8711176 (78.95%) aligned exactly 1 time 1882087 (17.06%) aligned >1 times 96.01% overall alignment rate Time searching: 00:09:16 Overall time: 00:09:16 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] 10388303 / 10593263 = 0.9807 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 15:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.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 15:33:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:33:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.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 15:33:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:33:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.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 15:33:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:33:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:33:37: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:33:37: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:33:37: #1 total tags in treatment: 204960 INFO @ Fri, 05 Jul 2019 15:33:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:33:37: #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 15:33:37: #1 tags after filtering in treatment: 204960 INFO @ Fri, 05 Jul 2019 15:33:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:33:37: #1 finished! INFO @ Fri, 05 Jul 2019 15:33:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:33:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:33:38: #2 number of paired peaks: 307 WARNING @ Fri, 05 Jul 2019 15:33:38: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 05 Jul 2019 15:33:38: start model_add_line... INFO @ Fri, 05 Jul 2019 15:33:38: start X-correlation... INFO @ Fri, 05 Jul 2019 15:33:38: end of X-cor INFO @ Fri, 05 Jul 2019 15:33:38: #2 finished! INFO @ Fri, 05 Jul 2019 15:33:38: #2 predicted fragment length is 159 bps INFO @ Fri, 05 Jul 2019 15:33:38: #2 alternative fragment length(s) may be 109,132,159,182,207,471,489,523,553,571,588 bps INFO @ Fri, 05 Jul 2019 15:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.05_model.r WARNING @ Fri, 05 Jul 2019 15:33:38: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:33:38: #2 You may need to consider one of the other alternative d(s): 109,132,159,182,207,471,489,523,553,571,588 WARNING @ Fri, 05 Jul 2019 15:33:38: #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 15:33:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:33:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:33:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:33:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:33:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:33:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.05_summits.bed INFO @ Fri, 05 Jul 2019 15:33:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (73 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:33:39: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:33:39: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:33:39: #1 total tags in treatment: 204960 INFO @ Fri, 05 Jul 2019 15:33:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:33:39: #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 15:33:39: #1 tags after filtering in treatment: 204960 INFO @ Fri, 05 Jul 2019 15:33:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:33:39: #1 finished! INFO @ Fri, 05 Jul 2019 15:33:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:33:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:33:39: #2 number of paired peaks: 307 WARNING @ Fri, 05 Jul 2019 15:33:39: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 05 Jul 2019 15:33:39: start model_add_line... INFO @ Fri, 05 Jul 2019 15:33:39: start X-correlation... INFO @ Fri, 05 Jul 2019 15:33:39: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:33:39: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:33:39: #1 total tags in treatment: 204960 INFO @ Fri, 05 Jul 2019 15:33:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:33:39: #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 15:33:39: #1 tags after filtering in treatment: 204960 INFO @ Fri, 05 Jul 2019 15:33:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:33:39: #1 finished! INFO @ Fri, 05 Jul 2019 15:33:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:33:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:33:39: end of X-cor INFO @ Fri, 05 Jul 2019 15:33:39: #2 finished! INFO @ Fri, 05 Jul 2019 15:33:39: #2 predicted fragment length is 159 bps INFO @ Fri, 05 Jul 2019 15:33:39: #2 alternative fragment length(s) may be 109,132,159,182,207,471,489,523,553,571,588 bps INFO @ Fri, 05 Jul 2019 15:33:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.20_model.r WARNING @ Fri, 05 Jul 2019 15:33:39: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:33:39: #2 You may need to consider one of the other alternative d(s): 109,132,159,182,207,471,489,523,553,571,588 WARNING @ Fri, 05 Jul 2019 15:33:39: #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 15:33:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:33:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:33:39: #2 number of paired peaks: 307 WARNING @ Fri, 05 Jul 2019 15:33:39: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 05 Jul 2019 15:33:39: start model_add_line... INFO @ Fri, 05 Jul 2019 15:33:39: start X-correlation... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:33:39: end of X-cor INFO @ Fri, 05 Jul 2019 15:33:39: #2 finished! INFO @ Fri, 05 Jul 2019 15:33:39: #2 predicted fragment length is 159 bps INFO @ Fri, 05 Jul 2019 15:33:39: #2 alternative fragment length(s) may be 109,132,159,182,207,471,489,523,553,571,588 bps INFO @ Fri, 05 Jul 2019 15:33:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.10_model.r WARNING @ Fri, 05 Jul 2019 15:33:39: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:33:39: #2 You may need to consider one of the other alternative d(s): 109,132,159,182,207,471,489,523,553,571,588 WARNING @ Fri, 05 Jul 2019 15:33:39: #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 15:33:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:33:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:33:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:33:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:33:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:33:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:33:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.20_summits.bed INFO @ Fri, 05 Jul 2019 15:33:41: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 15:33:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:33:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:33:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548110/ERX2548110.10_summits.bed INFO @ Fri, 05 Jul 2019 15:33:41: Done! CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling