Job ID = 11192906 sra ファイルのダウンロード中... Completed: 673224K bytes transferred in 10 seconds (517610K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 13616360 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3236753/SRR6124100.sra Written 13616360 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3236753/SRR6124100.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:07:12 13616360 reads; of these: 13616360 (100.00%) were unpaired; of these: 13593890 (99.83%) aligned 0 times 15153 (0.11%) aligned exactly 1 time 7317 (0.05%) aligned >1 times 0.17% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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] 1418 / 22470 = 0.0631 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 INFO @ Sat, 15 Sep 2018 10:31:11: # Command line: callpeak -t SRX3236753.bam -f BAM -g 12100000 -n SRX3236753.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3236753.20 # format = BAM # ChIP-seq file = ['SRX3236753.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 @ Sat, 15 Sep 2018 10:31:11: # Command line: callpeak -t SRX3236753.bam -f BAM -g 12100000 -n SRX3236753.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3236753.10 # format = BAM # ChIP-seq file = ['SRX3236753.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 @ Sat, 15 Sep 2018 10:31:11: # Command line: callpeak -t SRX3236753.bam -f BAM -g 12100000 -n SRX3236753.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3236753.05 # format = BAM # ChIP-seq file = ['SRX3236753.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 @ Sat, 15 Sep 2018 10:31:11: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:31:11: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:31:11: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:31:11: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:31:11: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:31:11: #1 read treatment tags... BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Sep 2018 10:31:11: #1 tag size is determined as 97 bps INFO @ Sat, 15 Sep 2018 10:31:11: #1 tag size = 97 INFO @ Sat, 15 Sep 2018 10:31:11: #1 total tags in treatment: 21052 INFO @ Sat, 15 Sep 2018 10:31:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:31:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:31:11: #1 tag size is determined as 97 bps INFO @ Sat, 15 Sep 2018 10:31:11: #1 tag size = 97 INFO @ Sat, 15 Sep 2018 10:31:11: #1 total tags in treatment: 21052 INFO @ Sat, 15 Sep 2018 10:31:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:31:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:31:11: #1 tags after filtering in treatment: 21052 INFO @ Sat, 15 Sep 2018 10:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:31:11: #1 finished! INFO @ Sat, 15 Sep 2018 10:31:11: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:31:11: #1 tag size is determined as 97 bps INFO @ Sat, 15 Sep 2018 10:31:11: #1 tag size = 97 INFO @ Sat, 15 Sep 2018 10:31:11: #1 total tags in treatment: 21052 INFO @ Sat, 15 Sep 2018 10:31:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:31:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:31:11: #1 tags after filtering in treatment: 21052 INFO @ Sat, 15 Sep 2018 10:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:31:11: #1 finished! INFO @ Sat, 15 Sep 2018 10:31:11: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:31:11: #1 tags after filtering in treatment: 21052 INFO @ Sat, 15 Sep 2018 10:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:31:11: #1 finished! INFO @ Sat, 15 Sep 2018 10:31:11: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:31:11: #2 number of paired peaks: 112 WARNING @ Sat, 15 Sep 2018 10:31:11: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 15 Sep 2018 10:31:11: start model_add_line... INFO @ Sat, 15 Sep 2018 10:31:11: start X-correlation... INFO @ Sat, 15 Sep 2018 10:31:11: #2 number of paired peaks: 112 WARNING @ Sat, 15 Sep 2018 10:31:11: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 15 Sep 2018 10:31:11: start model_add_line... INFO @ Sat, 15 Sep 2018 10:31:11: start X-correlation... INFO @ Sat, 15 Sep 2018 10:31:11: #2 number of paired peaks: 112 WARNING @ Sat, 15 Sep 2018 10:31:11: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 15 Sep 2018 10:31:11: start model_add_line... INFO @ Sat, 15 Sep 2018 10:31:11: start X-correlation... INFO @ Sat, 15 Sep 2018 10:31:11: end of X-cor INFO @ Sat, 15 Sep 2018 10:31:11: end of X-cor INFO @ Sat, 15 Sep 2018 10:31:11: end of X-cor INFO @ Sat, 15 Sep 2018 10:31:11: #2 finished! INFO @ Sat, 15 Sep 2018 10:31:11: #2 finished! INFO @ Sat, 15 Sep 2018 10:31:11: #2 finished! INFO @ Sat, 15 Sep 2018 10:31:11: #2 predicted fragment length is 166 bps INFO @ Sat, 15 Sep 2018 10:31:11: #2 predicted fragment length is 166 bps INFO @ Sat, 15 Sep 2018 10:31:11: #2 predicted fragment length is 166 bps INFO @ Sat, 15 Sep 2018 10:31:11: #2 alternative fragment length(s) may be 12,35,79,107,128,145,166,190,219,240,280,307,372,425,482,517,546,557,581 bps INFO @ Sat, 15 Sep 2018 10:31:11: #2 alternative fragment length(s) may be 12,35,79,107,128,145,166,190,219,240,280,307,372,425,482,517,546,557,581 bps INFO @ Sat, 15 Sep 2018 10:31:11: #2 alternative fragment length(s) may be 12,35,79,107,128,145,166,190,219,240,280,307,372,425,482,517,546,557,581 bps INFO @ Sat, 15 Sep 2018 10:31:11: #2.2 Generate R script for model : SRX3236753.05_model.r INFO @ Sat, 15 Sep 2018 10:31:11: #2.2 Generate R script for model : SRX3236753.10_model.r INFO @ Sat, 15 Sep 2018 10:31:11: #2.2 Generate R script for model : SRX3236753.20_model.r WARNING @ Sat, 15 Sep 2018 10:31:11: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:31:11: #2 You may need to consider one of the other alternative d(s): 12,35,79,107,128,145,166,190,219,240,280,307,372,425,482,517,546,557,581 WARNING @ Sat, 15 Sep 2018 10:31:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 10:31:11: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:31:11: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 15 Sep 2018 10:31:11: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:31:11: #2 You may need to consider one of the other alternative d(s): 12,35,79,107,128,145,166,190,219,240,280,307,372,425,482,517,546,557,581 WARNING @ Sat, 15 Sep 2018 10:31:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 10:31:11: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:31:11: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 15 Sep 2018 10:31:11: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:31:11: #2 You may need to consider one of the other alternative d(s): 12,35,79,107,128,145,166,190,219,240,280,307,372,425,482,517,546,557,581 WARNING @ Sat, 15 Sep 2018 10:31:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 10:31:11: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:31:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:31:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:31:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:31:12: #4 Write output xls file... SRX3236753.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:31:12: #4 Write output xls file... SRX3236753.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:31:12: #4 Write output xls file... SRX3236753.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:31:12: #4 Write peak in narrowPeak format file... SRX3236753.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:31:12: #4 Write peak in narrowPeak format file... SRX3236753.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:31:12: #4 Write summits bed file... SRX3236753.05_summits.bed INFO @ Sat, 15 Sep 2018 10:31:12: #4 Write peak in narrowPeak format file... SRX3236753.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:31:12: Done! INFO @ Sat, 15 Sep 2018 10:31:12: #4 Write summits bed file... SRX3236753.10_summits.bed INFO @ Sat, 15 Sep 2018 10:31:12: #4 Write summits bed file... SRX3236753.20_summits.bed INFO @ Sat, 15 Sep 2018 10:31:12: Done! INFO @ Sat, 15 Sep 2018 10:31:12: Done! pass1 - making usageList (1 chroms): 0 millis pass1 - making usageList (1 chroms): 0 millis pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling