Job ID = 9156953 sra ファイルのダウンロード中... Completed: 158177K bytes transferred in 4 seconds (281195K 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 5242953 spots for /home/okishinya/chipatlas/results/ce10/SRX2228853/SRR4380309.sra Written 5242953 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:24 5242953 reads; of these: 5242953 (100.00%) were unpaired; of these: 513028 (9.79%) aligned 0 times 3956145 (75.46%) aligned exactly 1 time 773780 (14.76%) aligned >1 times 90.21% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 935590 / 4729925 = 0.1978 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 10:30:05: # Command line: callpeak -t SRX2228853.bam -f BAM -g ce -n SRX2228853.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228853.10 # format = BAM # ChIP-seq file = ['SRX2228853.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 10:30:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:30:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:30:05: # Command line: callpeak -t SRX2228853.bam -f BAM -g ce -n SRX2228853.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228853.20 # format = BAM # ChIP-seq file = ['SRX2228853.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 10:30:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:30:05: # Command line: callpeak -t SRX2228853.bam -f BAM -g ce -n SRX2228853.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228853.05 # format = BAM # ChIP-seq file = ['SRX2228853.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 10:30:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:30:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:30:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:30:13: 1000000 INFO @ Tue, 27 Jun 2017 10:30:14: 1000000 INFO @ Tue, 27 Jun 2017 10:30:14: 1000000 INFO @ Tue, 27 Jun 2017 10:30:20: 2000000 INFO @ Tue, 27 Jun 2017 10:30:22: 2000000 INFO @ Tue, 27 Jun 2017 10:30:22: 2000000 INFO @ Tue, 27 Jun 2017 10:30:28: 3000000 INFO @ Tue, 27 Jun 2017 10:30:30: 3000000 INFO @ Tue, 27 Jun 2017 10:30:30: 3000000 INFO @ Tue, 27 Jun 2017 10:30:34: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:30:34: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:30:34: #1 total tags in treatment: 3794335 INFO @ Tue, 27 Jun 2017 10:30:34: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:30:34: #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 10:30:34: #1 tags after filtering in treatment: 3794335 INFO @ Tue, 27 Jun 2017 10:30:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:30:34: #1 finished! INFO @ Tue, 27 Jun 2017 10:30:34: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:30:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:30:34: #2 number of paired peaks: 558 WARNING @ Tue, 27 Jun 2017 10:30:34: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 27 Jun 2017 10:30:34: start model_add_line... INFO @ Tue, 27 Jun 2017 10:30:34: start X-correlation... INFO @ Tue, 27 Jun 2017 10:30:34: end of X-cor INFO @ Tue, 27 Jun 2017 10:30:34: #2 finished! INFO @ Tue, 27 Jun 2017 10:30:34: #2 predicted fragment length is 180 bps INFO @ Tue, 27 Jun 2017 10:30:34: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 27 Jun 2017 10:30:34: #2.2 Generate R script for model : SRX2228853.10_model.r INFO @ Tue, 27 Jun 2017 10:30:34: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:30:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:30:36: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:30:36: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:30:36: #1 total tags in treatment: 3794335 INFO @ Tue, 27 Jun 2017 10:30:36: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:30:36: #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 10:30:36: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:30:36: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:30:36: #1 total tags in treatment: 3794335 INFO @ Tue, 27 Jun 2017 10:30:36: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:30:36: #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 10:30:36: #1 tags after filtering in treatment: 3794335 INFO @ Tue, 27 Jun 2017 10:30:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:30:36: #1 finished! INFO @ Tue, 27 Jun 2017 10:30:36: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:30:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:30:36: #1 tags after filtering in treatment: 3794335 INFO @ Tue, 27 Jun 2017 10:30:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:30:36: #1 finished! INFO @ Tue, 27 Jun 2017 10:30:36: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:30:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:30:37: #2 number of paired peaks: 558 WARNING @ Tue, 27 Jun 2017 10:30:37: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 27 Jun 2017 10:30:37: start model_add_line... INFO @ Tue, 27 Jun 2017 10:30:37: #2 number of paired peaks: 558 WARNING @ Tue, 27 Jun 2017 10:30:37: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 27 Jun 2017 10:30:37: start model_add_line... INFO @ Tue, 27 Jun 2017 10:30:37: start X-correlation... INFO @ Tue, 27 Jun 2017 10:30:37: end of X-cor INFO @ Tue, 27 Jun 2017 10:30:37: #2 finished! INFO @ Tue, 27 Jun 2017 10:30:37: #2 predicted fragment length is 180 bps INFO @ Tue, 27 Jun 2017 10:30:37: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 27 Jun 2017 10:30:37: #2.2 Generate R script for model : SRX2228853.05_model.r INFO @ Tue, 27 Jun 2017 10:30:37: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:30:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:30:37: start X-correlation... INFO @ Tue, 27 Jun 2017 10:30:37: end of X-cor INFO @ Tue, 27 Jun 2017 10:30:37: #2 finished! INFO @ Tue, 27 Jun 2017 10:30:37: #2 predicted fragment length is 180 bps INFO @ Tue, 27 Jun 2017 10:30:37: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 27 Jun 2017 10:30:37: #2.2 Generate R script for model : SRX2228853.20_model.r INFO @ Tue, 27 Jun 2017 10:30:37: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:30:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:30:45: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:30:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:30:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:30:50: #4 Write output xls file... SRX2228853.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:30:50: #4 Write peak in narrowPeak format file... SRX2228853.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:30:50: #4 Write summits bed file... SRX2228853.10_summits.bed INFO @ Tue, 27 Jun 2017 10:30:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:30:52: #4 Write output xls file... SRX2228853.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:30:52: #4 Write peak in narrowPeak format file... SRX2228853.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:30:52: #4 Write summits bed file... SRX2228853.20_summits.bed INFO @ Tue, 27 Jun 2017 10:30:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (265 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:30:52: #4 Write output xls file... SRX2228853.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:30:52: #4 Write peak in narrowPeak format file... SRX2228853.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:30:52: #4 Write summits bed file... SRX2228853.05_summits.bed INFO @ Tue, 27 Jun 2017 10:30:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (707 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。