Job ID = 9157285 sra ファイルのダウンロード中... Completed: 381230K bytes transferred in 17 seconds (178907K bits/sec), in 1 file, 2 directories. 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... Written 7781222 spots for /home/okishinya/chipatlas/results/ce10/SRX2761381/SRR5476955.sra Written 7781222 spots total 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: 00:02:20 7781222 reads; of these: 7781222 (100.00%) were unpaired; of these: 347411 (4.46%) aligned 0 times 5689974 (73.12%) aligned exactly 1 time 1743837 (22.41%) aligned >1 times 95.54% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1950588 / 7433811 = 0.2624 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 @ Tue, 27 Jun 2017 11:23:30: # Command line: callpeak -t SRX2761381.bam -f BAM -g ce -n SRX2761381.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2761381.05 # format = BAM # ChIP-seq file = ['SRX2761381.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 27 Jun 2017 11:23:30: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:23:30: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:23:30: # Command line: callpeak -t SRX2761381.bam -f BAM -g ce -n SRX2761381.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2761381.10 # format = BAM # ChIP-seq file = ['SRX2761381.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 27 Jun 2017 11:23:30: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:23:30: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:23:30: # Command line: callpeak -t SRX2761381.bam -f BAM -g ce -n SRX2761381.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2761381.20 # format = BAM # ChIP-seq file = ['SRX2761381.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 27 Jun 2017 11:23:30: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:23:30: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:23:38: 1000000 INFO @ Tue, 27 Jun 2017 11:23:40: 1000000 INFO @ Tue, 27 Jun 2017 11:23:40: 1000000 INFO @ Tue, 27 Jun 2017 11:23:47: 2000000 INFO @ Tue, 27 Jun 2017 11:23:51: 2000000 INFO @ Tue, 27 Jun 2017 11:23:51: 2000000 INFO @ Tue, 27 Jun 2017 11:23:56: 3000000 INFO @ Tue, 27 Jun 2017 11:24:01: 3000000 INFO @ Tue, 27 Jun 2017 11:24:01: 3000000 INFO @ Tue, 27 Jun 2017 11:24:05: 4000000 INFO @ Tue, 27 Jun 2017 11:24:11: 4000000 INFO @ Tue, 27 Jun 2017 11:24:11: 4000000 INFO @ Tue, 27 Jun 2017 11:24:14: 5000000 INFO @ Tue, 27 Jun 2017 11:24:19: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:24:19: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:24:19: #1 total tags in treatment: 5483223 INFO @ Tue, 27 Jun 2017 11:24:19: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:24:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:24:19: #1 tags after filtering in treatment: 5483223 INFO @ Tue, 27 Jun 2017 11:24:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:24:19: #1 finished! INFO @ Tue, 27 Jun 2017 11:24:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:24:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:24:19: #2 number of paired peaks: 633 WARNING @ Tue, 27 Jun 2017 11:24:19: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Tue, 27 Jun 2017 11:24:19: start model_add_line... INFO @ Tue, 27 Jun 2017 11:24:19: start X-correlation... INFO @ Tue, 27 Jun 2017 11:24:19: end of X-cor INFO @ Tue, 27 Jun 2017 11:24:19: #2 finished! INFO @ Tue, 27 Jun 2017 11:24:19: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:24:19: #2 alternative fragment length(s) may be 4,51,542,566 bps INFO @ Tue, 27 Jun 2017 11:24:19: #2.2 Generate R script for model : SRX2761381.05_model.r WARNING @ Tue, 27 Jun 2017 11:24:19: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:24:19: #2 You may need to consider one of the other alternative d(s): 4,51,542,566 WARNING @ Tue, 27 Jun 2017 11:24:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:24:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:24:22: 5000000 INFO @ Tue, 27 Jun 2017 11:24:22: 5000000 INFO @ Tue, 27 Jun 2017 11:24:27: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:24:27: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:24:27: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:24:27: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:24:27: #1 total tags in treatment: 5483223 INFO @ Tue, 27 Jun 2017 11:24:27: #1 total tags in treatment: 5483223 INFO @ Tue, 27 Jun 2017 11:24:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:24:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:24:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:24:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:24:27: #1 tags after filtering in treatment: 5483223 INFO @ Tue, 27 Jun 2017 11:24:27: #1 tags after filtering in treatment: 5483223 INFO @ Tue, 27 Jun 2017 11:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:24:27: #1 finished! INFO @ Tue, 27 Jun 2017 11:24:27: #1 finished! INFO @ Tue, 27 Jun 2017 11:24:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:24:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:24:27: #2 number of paired peaks: 633 WARNING @ Tue, 27 Jun 2017 11:24:27: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Tue, 27 Jun 2017 11:24:27: start model_add_line... INFO @ Tue, 27 Jun 2017 11:24:27: #2 number of paired peaks: 633 WARNING @ Tue, 27 Jun 2017 11:24:27: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Tue, 27 Jun 2017 11:24:27: start model_add_line... INFO @ Tue, 27 Jun 2017 11:24:27: start X-correlation... INFO @ Tue, 27 Jun 2017 11:24:27: end of X-cor INFO @ Tue, 27 Jun 2017 11:24:27: #2 finished! INFO @ Tue, 27 Jun 2017 11:24:27: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:24:27: #2 alternative fragment length(s) may be 4,51,542,566 bps INFO @ Tue, 27 Jun 2017 11:24:27: #2.2 Generate R script for model : SRX2761381.10_model.r INFO @ Tue, 27 Jun 2017 11:24:27: start X-correlation... WARNING @ Tue, 27 Jun 2017 11:24:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:24:27: #2 You may need to consider one of the other alternative d(s): 4,51,542,566 WARNING @ Tue, 27 Jun 2017 11:24:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:24:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:24:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:24:27: end of X-cor INFO @ Tue, 27 Jun 2017 11:24:27: #2 finished! INFO @ Tue, 27 Jun 2017 11:24:27: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 11:24:27: #2 alternative fragment length(s) may be 4,51,542,566 bps INFO @ Tue, 27 Jun 2017 11:24:27: #2.2 Generate R script for model : SRX2761381.20_model.r WARNING @ Tue, 27 Jun 2017 11:24:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:24:27: #2 You may need to consider one of the other alternative d(s): 4,51,542,566 WARNING @ Tue, 27 Jun 2017 11:24:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:24:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:24:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:24:33: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:24:40: #4 Write output xls file... SRX2761381.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:24:40: #4 Write peak in narrowPeak format file... SRX2761381.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:24:40: #4 Write summits bed file... SRX2761381.05_summits.bed INFO @ Tue, 27 Jun 2017 11:24:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (683 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:24:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:24:42: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:24:48: #4 Write output xls file... SRX2761381.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:24:48: #4 Write peak in narrowPeak format file... SRX2761381.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:24:48: #4 Write summits bed file... SRX2761381.10_summits.bed INFO @ Tue, 27 Jun 2017 11:24:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (404 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:24:49: #4 Write output xls file... SRX2761381.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:24:49: #4 Write peak in narrowPeak format file... SRX2761381.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:24:49: #4 Write summits bed file... SRX2761381.20_summits.bed INFO @ Tue, 27 Jun 2017 11:24:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (161 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。