Job ID = 9156960 sra ファイルのダウンロード中... Completed: 208786K bytes transferred in 4 seconds (350387K 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 12255316 spots for /home/okishinya/chipatlas/results/ce10/SRX2228859/SRR4380315.sra Written 12255316 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: 00:00:01 Multiseed full-index search: 00:01:58 12255316 reads; of these: 12255316 (100.00%) were unpaired; of these: 8643828 (70.53%) aligned 0 times 3002528 (24.50%) aligned exactly 1 time 608960 (4.97%) aligned >1 times 29.47% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 1882367 / 3611488 = 0.5212 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 10:35:15: # Command line: callpeak -t SRX2228859.bam -f BAM -g ce -n SRX2228859.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228859.10 # format = BAM # ChIP-seq file = ['SRX2228859.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 10:35:15: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:35:15: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:35:15: # Command line: callpeak -t SRX2228859.bam -f BAM -g ce -n SRX2228859.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228859.05 # format = BAM # ChIP-seq file = ['SRX2228859.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 10:35:15: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:35:15: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:35:15: # Command line: callpeak -t SRX2228859.bam -f BAM -g ce -n SRX2228859.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228859.20 # format = BAM # ChIP-seq file = ['SRX2228859.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 10:35:15: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:35:15: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:35:23: 1000000 INFO @ Tue, 27 Jun 2017 10:35:24: 1000000 INFO @ Tue, 27 Jun 2017 10:35:24: 1000000 INFO @ Tue, 27 Jun 2017 10:35:29: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:35:29: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:35:29: #1 total tags in treatment: 1729121 INFO @ Tue, 27 Jun 2017 10:35:29: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:35:29: #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 10:35:29: #1 tags after filtering in treatment: 1729121 INFO @ Tue, 27 Jun 2017 10:35:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:35:29: #1 finished! INFO @ Tue, 27 Jun 2017 10:35:29: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:35:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:35:29: #2 number of paired peaks: 620 WARNING @ Tue, 27 Jun 2017 10:35:29: Fewer paired peaks (620) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 620 pairs to build model! INFO @ Tue, 27 Jun 2017 10:35:29: start model_add_line... INFO @ Tue, 27 Jun 2017 10:35:29: start X-correlation... INFO @ Tue, 27 Jun 2017 10:35:29: end of X-cor INFO @ Tue, 27 Jun 2017 10:35:29: #2 finished! INFO @ Tue, 27 Jun 2017 10:35:29: #2 predicted fragment length is 91 bps INFO @ Tue, 27 Jun 2017 10:35:29: #2 alternative fragment length(s) may be 91,567 bps INFO @ Tue, 27 Jun 2017 10:35:29: #2.2 Generate R script for model : SRX2228859.10_model.r INFO @ Tue, 27 Jun 2017 10:35:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:35:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:35:30: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:35:30: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:35:30: #1 total tags in treatment: 1729121 INFO @ Tue, 27 Jun 2017 10:35:30: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:35:30: #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 10:35:30: #1 tags after filtering in treatment: 1729121 INFO @ Tue, 27 Jun 2017 10:35:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:35:30: #1 finished! INFO @ Tue, 27 Jun 2017 10:35:30: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:35:30: #1 tag size is determined as 35 bps INFO @ Tue, 27 Jun 2017 10:35:30: #1 tag size = 35 INFO @ Tue, 27 Jun 2017 10:35:30: #1 total tags in treatment: 1729121 INFO @ Tue, 27 Jun 2017 10:35:30: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:35:30: #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 10:35:30: #1 tags after filtering in treatment: 1729121 INFO @ Tue, 27 Jun 2017 10:35:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:35:30: #1 finished! INFO @ Tue, 27 Jun 2017 10:35:30: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:35:31: #2 number of paired peaks: 620 WARNING @ Tue, 27 Jun 2017 10:35:31: Fewer paired peaks (620) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 620 pairs to build model! INFO @ Tue, 27 Jun 2017 10:35:31: start model_add_line... INFO @ Tue, 27 Jun 2017 10:35:31: start X-correlation... INFO @ Tue, 27 Jun 2017 10:35:31: end of X-cor INFO @ Tue, 27 Jun 2017 10:35:31: #2 finished! INFO @ Tue, 27 Jun 2017 10:35:31: #2 predicted fragment length is 91 bps INFO @ Tue, 27 Jun 2017 10:35:31: #2 alternative fragment length(s) may be 91,567 bps INFO @ Tue, 27 Jun 2017 10:35:31: #2.2 Generate R script for model : SRX2228859.05_model.r INFO @ Tue, 27 Jun 2017 10:35:31: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:35:31: #2 number of paired peaks: 620 WARNING @ Tue, 27 Jun 2017 10:35:31: Fewer paired peaks (620) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 620 pairs to build model! INFO @ Tue, 27 Jun 2017 10:35:31: start model_add_line... INFO @ Tue, 27 Jun 2017 10:35:31: start X-correlation... INFO @ Tue, 27 Jun 2017 10:35:31: end of X-cor INFO @ Tue, 27 Jun 2017 10:35:31: #2 finished! INFO @ Tue, 27 Jun 2017 10:35:31: #2 predicted fragment length is 91 bps INFO @ Tue, 27 Jun 2017 10:35:31: #2 alternative fragment length(s) may be 91,567 bps INFO @ Tue, 27 Jun 2017 10:35:31: #2.2 Generate R script for model : SRX2228859.20_model.r INFO @ Tue, 27 Jun 2017 10:35:31: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:35:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:35:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:35:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:35:37: #4 Write output xls file... SRX2228859.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:35:37: #4 Write peak in narrowPeak format file... SRX2228859.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:35:37: #4 Write summits bed file... SRX2228859.10_summits.bed INFO @ Tue, 27 Jun 2017 10:35:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:35:37: #4 Write output xls file... SRX2228859.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:35:37: #4 Write peak in narrowPeak format file... SRX2228859.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:35:37: #4 Write summits bed file... SRX2228859.05_summits.bed INFO @ Tue, 27 Jun 2017 10:35:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (439 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:35:38: #4 Write output xls file... SRX2228859.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:35:38: #4 Write peak in narrowPeak format file... SRX2228859.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:35:38: #4 Write summits bed file... SRX2228859.20_summits.bed INFO @ Tue, 27 Jun 2017 10:35:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (112 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。