Job ID = 2005873 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,174,227 reads read : 2,174,227 reads written : 2,174,227 spots read : 2,148,406 reads read : 2,148,406 reads written : 2,148,406 spots read : 2,129,010 reads read : 2,129,010 reads written : 2,129,010 spots read : 2,071,200 reads read : 2,071,200 reads written : 2,071,200 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: 00:06:19 8522843 reads; of these: 8522843 (100.00%) were unpaired; of these: 252541 (2.96%) aligned 0 times 6736560 (79.04%) aligned exactly 1 time 1533742 (18.00%) aligned >1 times 97.04% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 8048588 / 8270302 = 0.9732 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 15:04:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.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 15:04:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:04:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:04:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.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 15:04:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:04:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.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 15:04:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:04:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:04:23: #1 tag size is determined as 138 bps INFO @ Fri, 05 Jul 2019 15:04:23: #1 tag size = 138 INFO @ Fri, 05 Jul 2019 15:04:23: #1 total tags in treatment: 221714 INFO @ Fri, 05 Jul 2019 15:04:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:04:23: #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 15:04:23: #1 tags after filtering in treatment: 221714 INFO @ Fri, 05 Jul 2019 15:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:04:23: #1 finished! INFO @ Fri, 05 Jul 2019 15:04:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:04:23: #2 number of paired peaks: 340 WARNING @ Fri, 05 Jul 2019 15:04:23: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Fri, 05 Jul 2019 15:04:23: start model_add_line... INFO @ Fri, 05 Jul 2019 15:04:23: start X-correlation... INFO @ Fri, 05 Jul 2019 15:04:23: end of X-cor INFO @ Fri, 05 Jul 2019 15:04:23: #2 finished! INFO @ Fri, 05 Jul 2019 15:04:23: #2 predicted fragment length is 169 bps INFO @ Fri, 05 Jul 2019 15:04:23: #2 alternative fragment length(s) may be 143,169,236,329,523,546,576,593 bps INFO @ Fri, 05 Jul 2019 15:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.05_model.r WARNING @ Fri, 05 Jul 2019 15:04:23: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:04:23: #2 You may need to consider one of the other alternative d(s): 143,169,236,329,523,546,576,593 WARNING @ Fri, 05 Jul 2019 15:04:23: #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 15:04:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:04:24: #1 tag size is determined as 138 bps INFO @ Fri, 05 Jul 2019 15:04:24: #1 tag size = 138 INFO @ Fri, 05 Jul 2019 15:04:24: #1 total tags in treatment: 221714 INFO @ Fri, 05 Jul 2019 15:04:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:04:24: #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 15:04:24: #1 tags after filtering in treatment: 221714 INFO @ Fri, 05 Jul 2019 15:04:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:04:24: #1 finished! INFO @ Fri, 05 Jul 2019 15:04:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:04:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:04:24: #2 number of paired peaks: 340 WARNING @ Fri, 05 Jul 2019 15:04:24: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Fri, 05 Jul 2019 15:04:24: start model_add_line... INFO @ Fri, 05 Jul 2019 15:04:24: start X-correlation... INFO @ Fri, 05 Jul 2019 15:04:24: end of X-cor INFO @ Fri, 05 Jul 2019 15:04:24: #2 finished! INFO @ Fri, 05 Jul 2019 15:04:24: #2 predicted fragment length is 169 bps INFO @ Fri, 05 Jul 2019 15:04:24: #2 alternative fragment length(s) may be 143,169,236,329,523,546,576,593 bps INFO @ Fri, 05 Jul 2019 15:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.10_model.r WARNING @ Fri, 05 Jul 2019 15:04:24: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:04:24: #2 You may need to consider one of the other alternative d(s): 143,169,236,329,523,546,576,593 WARNING @ Fri, 05 Jul 2019 15:04:24: #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 15:04:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:04:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:04:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:04:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:04:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.05_summits.bed INFO @ Fri, 05 Jul 2019 15:04:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 15:04:25: #1 tag size is determined as 138 bps INFO @ Fri, 05 Jul 2019 15:04:25: #1 tag size = 138 INFO @ Fri, 05 Jul 2019 15:04:25: #1 total tags in treatment: 221714 INFO @ Fri, 05 Jul 2019 15:04:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:04:25: #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 15:04:25: #1 tags after filtering in treatment: 221714 INFO @ Fri, 05 Jul 2019 15:04:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:04:25: #1 finished! INFO @ Fri, 05 Jul 2019 15:04:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:04:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:04:25: #2 number of paired peaks: 340 WARNING @ Fri, 05 Jul 2019 15:04:25: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Fri, 05 Jul 2019 15:04:25: start model_add_line... INFO @ Fri, 05 Jul 2019 15:04:25: start X-correlation... INFO @ Fri, 05 Jul 2019 15:04:25: end of X-cor INFO @ Fri, 05 Jul 2019 15:04:25: #2 finished! INFO @ Fri, 05 Jul 2019 15:04:25: #2 predicted fragment length is 169 bps INFO @ Fri, 05 Jul 2019 15:04:25: #2 alternative fragment length(s) may be 143,169,236,329,523,546,576,593 bps INFO @ Fri, 05 Jul 2019 15:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.20_model.r WARNING @ Fri, 05 Jul 2019 15:04:25: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:04:25: #2 You may need to consider one of the other alternative d(s): 143,169,236,329,523,546,576,593 WARNING @ Fri, 05 Jul 2019 15:04:25: #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 15:04:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:04:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:04:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:04:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:04:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.10_summits.bed INFO @ Fri, 05 Jul 2019 15:04:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:04:26: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:04:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548083/ERX2548083.20_summits.bed INFO @ Fri, 05 Jul 2019 15:04:26: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。