Job ID = 2006618 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,754,871 reads read : 1,754,871 reads written : 1,754,871 spots read : 1,652,397 reads read : 1,652,397 reads written : 1,652,397 spots read : 1,829,522 reads read : 1,829,522 reads written : 1,829,522 spots read : 1,644,946 reads read : 1,644,946 reads written : 1,644,946 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: 00:01:38 6881736 reads; of these: 6881736 (100.00%) were unpaired; of these: 256770 (3.73%) aligned 0 times 5457634 (79.31%) aligned exactly 1 time 1167332 (16.96%) aligned >1 times 96.27% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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_rmdupse_core] 6473694 / 6624966 = 0.9772 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 15:40:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.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 15:40:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:40:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:40:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.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 15:40:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:40:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:40:22: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:40:22: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:40:22: #1 total tags in treatment: 151272 INFO @ Fri, 05 Jul 2019 15:40:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:40:22: #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 15:40:22: #1 tags after filtering in treatment: 151272 INFO @ Fri, 05 Jul 2019 15:40:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:40:22: #1 finished! INFO @ Fri, 05 Jul 2019 15:40:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:40:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:40:22: #2 number of paired peaks: 414 WARNING @ Fri, 05 Jul 2019 15:40:22: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Fri, 05 Jul 2019 15:40:22: start model_add_line... INFO @ Fri, 05 Jul 2019 15:40:22: start X-correlation... INFO @ Fri, 05 Jul 2019 15:40:22: end of X-cor INFO @ Fri, 05 Jul 2019 15:40:22: #2 finished! INFO @ Fri, 05 Jul 2019 15:40:22: #2 predicted fragment length is 76 bps INFO @ Fri, 05 Jul 2019 15:40:22: #2 alternative fragment length(s) may be 76,170,196,215,245,270,386,419,543,577,589 bps INFO @ Fri, 05 Jul 2019 15:40:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.05_model.r WARNING @ Fri, 05 Jul 2019 15:40:22: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:40:22: #2 You may need to consider one of the other alternative d(s): 76,170,196,215,245,270,386,419,543,577,589 WARNING @ Fri, 05 Jul 2019 15:40:22: #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 15:40:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:40:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:40:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.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 15:40:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:40:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:40:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:40:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:40:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:40:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.05_summits.bed INFO @ Fri, 05 Jul 2019 15:40:23: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:40:23: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:40:23: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:40:23: #1 total tags in treatment: 151272 INFO @ Fri, 05 Jul 2019 15:40:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:40:23: #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 15:40:23: #1 tags after filtering in treatment: 151272 INFO @ Fri, 05 Jul 2019 15:40:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:40:23: #1 finished! INFO @ Fri, 05 Jul 2019 15:40:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:40:23: #2 number of paired peaks: 414 WARNING @ Fri, 05 Jul 2019 15:40:23: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Fri, 05 Jul 2019 15:40:23: start model_add_line... INFO @ Fri, 05 Jul 2019 15:40:23: start X-correlation... INFO @ Fri, 05 Jul 2019 15:40:23: end of X-cor INFO @ Fri, 05 Jul 2019 15:40:23: #2 finished! INFO @ Fri, 05 Jul 2019 15:40:23: #2 predicted fragment length is 76 bps INFO @ Fri, 05 Jul 2019 15:40:23: #2 alternative fragment length(s) may be 76,170,196,215,245,270,386,419,543,577,589 bps INFO @ Fri, 05 Jul 2019 15:40:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.10_model.r WARNING @ Fri, 05 Jul 2019 15:40:23: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:40:23: #2 You may need to consider one of the other alternative d(s): 76,170,196,215,245,270,386,419,543,577,589 WARNING @ Fri, 05 Jul 2019 15:40:23: #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 15:40:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:40:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:40:24: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:40:24: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:40:24: #1 total tags in treatment: 151272 INFO @ Fri, 05 Jul 2019 15:40:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:40:24: #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 15:40:24: #1 tags after filtering in treatment: 151272 INFO @ Fri, 05 Jul 2019 15:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:40:24: #1 finished! INFO @ Fri, 05 Jul 2019 15:40:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:40:24: #2 number of paired peaks: 414 WARNING @ Fri, 05 Jul 2019 15:40:24: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Fri, 05 Jul 2019 15:40:24: start model_add_line... INFO @ Fri, 05 Jul 2019 15:40:24: start X-correlation... INFO @ Fri, 05 Jul 2019 15:40:24: end of X-cor INFO @ Fri, 05 Jul 2019 15:40:24: #2 finished! INFO @ Fri, 05 Jul 2019 15:40:24: #2 predicted fragment length is 76 bps INFO @ Fri, 05 Jul 2019 15:40:24: #2 alternative fragment length(s) may be 76,170,196,215,245,270,386,419,543,577,589 bps INFO @ Fri, 05 Jul 2019 15:40:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.20_model.r WARNING @ Fri, 05 Jul 2019 15:40:24: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:40:24: #2 You may need to consider one of the other alternative d(s): 76,170,196,215,245,270,386,419,543,577,589 WARNING @ Fri, 05 Jul 2019 15:40:24: #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 15:40:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:40:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:40:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:40:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:40:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.10_summits.bed INFO @ Fri, 05 Jul 2019 15:40:24: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:40:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:40:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:40:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:40:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548164/ERX2548164.20_summits.bed INFO @ Fri, 05 Jul 2019 15:40:25: Done! 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... CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。