Job ID = 9157971 sra ファイルのダウンロード中... Completed: 64724K bytes transferred in 3 seconds (132833K 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 5817621 spots for /home/okishinya/chipatlas/results/dm3/SRX2748310/SRR5460297.sra Written 5817621 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: 00:01:08 5817621 reads; of these: 5817621 (100.00%) were unpaired; of these: 1340675 (23.05%) aligned 0 times 3767451 (64.76%) aligned exactly 1 time 709495 (12.20%) aligned >1 times 76.95% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1853888 / 4476946 = 0.4141 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 14:17:46: # Command line: callpeak -t SRX2748310.bam -f BAM -g dm -n SRX2748310.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2748310.05 # format = BAM # ChIP-seq file = ['SRX2748310.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:17:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:17:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:17:46: # Command line: callpeak -t SRX2748310.bam -f BAM -g dm -n SRX2748310.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2748310.10 # format = BAM # ChIP-seq file = ['SRX2748310.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:17:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:17:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:17:46: # Command line: callpeak -t SRX2748310.bam -f BAM -g dm -n SRX2748310.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2748310.20 # format = BAM # ChIP-seq file = ['SRX2748310.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:17:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:17:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:17:52: 1000000 INFO @ Tue, 27 Jun 2017 14:17:52: 1000000 INFO @ Tue, 27 Jun 2017 14:17:52: 1000000 INFO @ Tue, 27 Jun 2017 14:17:58: 2000000 INFO @ Tue, 27 Jun 2017 14:17:59: 2000000 INFO @ Tue, 27 Jun 2017 14:17:59: 2000000 INFO @ Tue, 27 Jun 2017 14:18:02: #1 tag size is determined as 25 bps INFO @ Tue, 27 Jun 2017 14:18:02: #1 tag size = 25 INFO @ Tue, 27 Jun 2017 14:18:02: #1 total tags in treatment: 2623058 INFO @ Tue, 27 Jun 2017 14:18:02: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:18:02: #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 14:18:02: #1 tags after filtering in treatment: 2623058 INFO @ Tue, 27 Jun 2017 14:18:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:18:02: #1 finished! INFO @ Tue, 27 Jun 2017 14:18:02: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:18:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:18:03: #2 number of paired peaks: 7927 INFO @ Tue, 27 Jun 2017 14:18:03: start model_add_line... INFO @ Tue, 27 Jun 2017 14:18:03: start X-correlation... INFO @ Tue, 27 Jun 2017 14:18:03: end of X-cor INFO @ Tue, 27 Jun 2017 14:18:03: #2 finished! INFO @ Tue, 27 Jun 2017 14:18:03: #2 predicted fragment length is 155 bps INFO @ Tue, 27 Jun 2017 14:18:03: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 27 Jun 2017 14:18:03: #2.2 Generate R script for model : SRX2748310.10_model.r INFO @ Tue, 27 Jun 2017 14:18:03: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:18:03: #1 tag size is determined as 25 bps INFO @ Tue, 27 Jun 2017 14:18:03: #1 tag size = 25 INFO @ Tue, 27 Jun 2017 14:18:03: #1 total tags in treatment: 2623058 INFO @ Tue, 27 Jun 2017 14:18:03: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:18:03: #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 14:18:03: #1 tag size is determined as 25 bps INFO @ Tue, 27 Jun 2017 14:18:03: #1 tag size = 25 INFO @ Tue, 27 Jun 2017 14:18:03: #1 total tags in treatment: 2623058 INFO @ Tue, 27 Jun 2017 14:18:03: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:18:03: #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 14:18:03: #1 tags after filtering in treatment: 2623058 INFO @ Tue, 27 Jun 2017 14:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:18:03: #1 finished! INFO @ Tue, 27 Jun 2017 14:18:03: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:18:04: #1 tags after filtering in treatment: 2623058 INFO @ Tue, 27 Jun 2017 14:18:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:18:04: #1 finished! INFO @ Tue, 27 Jun 2017 14:18:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:18:04: #2 number of paired peaks: 7927 INFO @ Tue, 27 Jun 2017 14:18:04: start model_add_line... INFO @ Tue, 27 Jun 2017 14:18:04: #2 number of paired peaks: 7927 INFO @ Tue, 27 Jun 2017 14:18:04: start model_add_line... INFO @ Tue, 27 Jun 2017 14:18:04: start X-correlation... INFO @ Tue, 27 Jun 2017 14:18:04: end of X-cor INFO @ Tue, 27 Jun 2017 14:18:04: #2 finished! INFO @ Tue, 27 Jun 2017 14:18:04: #2 predicted fragment length is 155 bps INFO @ Tue, 27 Jun 2017 14:18:04: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 27 Jun 2017 14:18:04: #2.2 Generate R script for model : SRX2748310.05_model.r INFO @ Tue, 27 Jun 2017 14:18:04: start X-correlation... INFO @ Tue, 27 Jun 2017 14:18:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:18:04: end of X-cor INFO @ Tue, 27 Jun 2017 14:18:04: #2 finished! INFO @ Tue, 27 Jun 2017 14:18:04: #2 predicted fragment length is 155 bps INFO @ Tue, 27 Jun 2017 14:18:04: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 27 Jun 2017 14:18:04: #2.2 Generate R script for model : SRX2748310.20_model.r INFO @ Tue, 27 Jun 2017 14:18:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:18:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:18:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:18:12: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:18:15: #4 Write output xls file... SRX2748310.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:18:15: #4 Write peak in narrowPeak format file... SRX2748310.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:18:15: #4 Write summits bed file... SRX2748310.10_summits.bed INFO @ Tue, 27 Jun 2017 14:18:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5496 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:18:15: #4 Write output xls file... SRX2748310.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:18:15: #4 Write peak in narrowPeak format file... SRX2748310.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:18:15: #4 Write summits bed file... SRX2748310.20_summits.bed INFO @ Tue, 27 Jun 2017 14:18:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3170 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:18:16: #4 Write output xls file... SRX2748310.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:18:16: #4 Write peak in narrowPeak format file... SRX2748310.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:18:16: #4 Write summits bed file... SRX2748310.05_summits.bed INFO @ Tue, 27 Jun 2017 14:18:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7280 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。