Job ID = 9157426 sra ファイルのダウンロード中... Completed: 158449K bytes transferred in 4 seconds (268852K 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 6820219 spots for /home/okishinya/chipatlas/results/ce10/SRX2144179/SRR4188783.sra Written 6820219 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: 00:02:00 6820219 reads; of these: 6820219 (100.00%) were unpaired; of these: 979484 (14.36%) aligned 0 times 4462219 (65.43%) aligned exactly 1 time 1378516 (20.21%) aligned >1 times 85.64% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 491953 / 5840735 = 0.0842 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 11:56:13: # Command line: callpeak -t SRX2144179.bam -f BAM -g ce -n SRX2144179.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144179.10 # format = BAM # ChIP-seq file = ['SRX2144179.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 11:56:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:56:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:56:13: # Command line: callpeak -t SRX2144179.bam -f BAM -g ce -n SRX2144179.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144179.20 # format = BAM # ChIP-seq file = ['SRX2144179.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 11:56:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:56:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:56:13: # Command line: callpeak -t SRX2144179.bam -f BAM -g ce -n SRX2144179.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144179.05 # format = BAM # ChIP-seq file = ['SRX2144179.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 11:56:13: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:56:13: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:56:20: 1000000 INFO @ Tue, 27 Jun 2017 11:56:22: 1000000 INFO @ Tue, 27 Jun 2017 11:56:22: 1000000 INFO @ Tue, 27 Jun 2017 11:56:28: 2000000 INFO @ Tue, 27 Jun 2017 11:56:32: 2000000 INFO @ Tue, 27 Jun 2017 11:56:32: 2000000 INFO @ Tue, 27 Jun 2017 11:56:35: 3000000 INFO @ Tue, 27 Jun 2017 11:56:41: 3000000 INFO @ Tue, 27 Jun 2017 11:56:41: 3000000 INFO @ Tue, 27 Jun 2017 11:56:43: 4000000 INFO @ Tue, 27 Jun 2017 11:56:50: 5000000 INFO @ Tue, 27 Jun 2017 11:56:51: 4000000 INFO @ Tue, 27 Jun 2017 11:56:51: 4000000 INFO @ Tue, 27 Jun 2017 11:56:53: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:56:53: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:56:53: #1 total tags in treatment: 5348782 INFO @ Tue, 27 Jun 2017 11:56:53: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:56:53: #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 11:56:53: #1 tags after filtering in treatment: 5348782 INFO @ Tue, 27 Jun 2017 11:56:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:56:53: #1 finished! INFO @ Tue, 27 Jun 2017 11:56:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:56:53: #2 number of paired peaks: 551 WARNING @ Tue, 27 Jun 2017 11:56:53: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Tue, 27 Jun 2017 11:56:53: start model_add_line... INFO @ Tue, 27 Jun 2017 11:56:53: start X-correlation... INFO @ Tue, 27 Jun 2017 11:56:53: end of X-cor INFO @ Tue, 27 Jun 2017 11:56:53: #2 finished! INFO @ Tue, 27 Jun 2017 11:56:53: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:56:53: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 27 Jun 2017 11:56:53: #2.2 Generate R script for model : SRX2144179.10_model.r WARNING @ Tue, 27 Jun 2017 11:56:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:56:53: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 27 Jun 2017 11:56:53: #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 11:56:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:57:00: 5000000 INFO @ Tue, 27 Jun 2017 11:57:00: 5000000 INFO @ Tue, 27 Jun 2017 11:57:04: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:57:04: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:57:04: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:57:04: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:57:04: #1 total tags in treatment: 5348782 INFO @ Tue, 27 Jun 2017 11:57:04: #1 total tags in treatment: 5348782 INFO @ Tue, 27 Jun 2017 11:57:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:57:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:57:04: #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 11:57:04: #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 11:57:04: #1 tags after filtering in treatment: 5348782 INFO @ Tue, 27 Jun 2017 11:57:04: #1 tags after filtering in treatment: 5348782 INFO @ Tue, 27 Jun 2017 11:57:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:57:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:57:04: #1 finished! INFO @ Tue, 27 Jun 2017 11:57:04: #1 finished! INFO @ Tue, 27 Jun 2017 11:57:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:57:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:57:04: #2 number of paired peaks: 551 WARNING @ Tue, 27 Jun 2017 11:57:04: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Tue, 27 Jun 2017 11:57:04: start model_add_line... INFO @ Tue, 27 Jun 2017 11:57:04: #2 number of paired peaks: 551 WARNING @ Tue, 27 Jun 2017 11:57:04: Fewer paired peaks (551) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 551 pairs to build model! INFO @ Tue, 27 Jun 2017 11:57:04: start model_add_line... INFO @ Tue, 27 Jun 2017 11:57:04: start X-correlation... INFO @ Tue, 27 Jun 2017 11:57:04: end of X-cor INFO @ Tue, 27 Jun 2017 11:57:04: #2 finished! INFO @ Tue, 27 Jun 2017 11:57:04: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:57:04: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 27 Jun 2017 11:57:04: #2.2 Generate R script for model : SRX2144179.05_model.r INFO @ Tue, 27 Jun 2017 11:57:04: start X-correlation... INFO @ Tue, 27 Jun 2017 11:57:04: end of X-cor INFO @ Tue, 27 Jun 2017 11:57:04: #2 finished! INFO @ Tue, 27 Jun 2017 11:57:04: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:57:04: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 27 Jun 2017 11:57:04: #2.2 Generate R script for model : SRX2144179.20_model.r WARNING @ Tue, 27 Jun 2017 11:57:04: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:57:04: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 27 Jun 2017 11:57:04: #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 11:57:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:57:04: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 11:57:04: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:57:04: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 27 Jun 2017 11:57:04: #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 11:57:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:57:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:57:05: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:57:13: #4 Write output xls file... SRX2144179.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:57:13: #4 Write peak in narrowPeak format file... SRX2144179.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:57:13: #4 Write summits bed file... SRX2144179.10_summits.bed INFO @ Tue, 27 Jun 2017 11:57:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:57:17: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:57:17: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:57:24: #4 Write output xls file... SRX2144179.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:57:24: #4 Write peak in narrowPeak format file... SRX2144179.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:57:24: #4 Write summits bed file... SRX2144179.05_summits.bed INFO @ Tue, 27 Jun 2017 11:57:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (586 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:57:25: #4 Write output xls file... SRX2144179.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:57:25: #4 Write peak in narrowPeak format file... SRX2144179.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:57:25: #4 Write summits bed file... SRX2144179.20_summits.bed INFO @ Tue, 27 Jun 2017 11:57:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。