Job ID = 11240800 sra ファイルのダウンロード中... Completed: 188165K bytes transferred in 5 seconds (275709K bits/sec), in 1 file. 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... Read 5952131 spots for /home/okishinya/chipatlas/results/dm3/SRX4798847/SRR7965222.sra Written 5952131 spots for /home/okishinya/chipatlas/results/dm3/SRX4798847/SRR7965222.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:39 5952131 reads; of these: 5952131 (100.00%) were unpaired; of these: 4943245 (83.05%) aligned 0 times 908046 (15.26%) aligned exactly 1 time 100840 (1.69%) aligned >1 times 16.95% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 218809 / 1008886 = 0.2169 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 @ Sun, 07 Oct 2018 20:41:49: # Command line: callpeak -t SRX4798847.bam -f BAM -g dm -n SRX4798847.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798847.20 # format = BAM # ChIP-seq file = ['SRX4798847.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 @ Sun, 07 Oct 2018 20:41:49: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:41:49: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:41:49: # Command line: callpeak -t SRX4798847.bam -f BAM -g dm -n SRX4798847.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798847.10 # format = BAM # ChIP-seq file = ['SRX4798847.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 @ Sun, 07 Oct 2018 20:41:49: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:41:49: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:41:49: # Command line: callpeak -t SRX4798847.bam -f BAM -g dm -n SRX4798847.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798847.05 # format = BAM # ChIP-seq file = ['SRX4798847.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 @ Sun, 07 Oct 2018 20:41:49: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:41:49: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:41:54: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:41:54: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:41:54: #1 total tags in treatment: 790077 INFO @ Sun, 07 Oct 2018 20:41:54: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:41:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:41:54: #1 tags after filtering in treatment: 790077 INFO @ Sun, 07 Oct 2018 20:41:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:41:54: #1 finished! INFO @ Sun, 07 Oct 2018 20:41:54: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:41:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:41:55: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:41:55: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:41:55: #1 total tags in treatment: 790077 INFO @ Sun, 07 Oct 2018 20:41:55: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:41:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:41:55: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:41:55: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:41:55: #1 total tags in treatment: 790077 INFO @ Sun, 07 Oct 2018 20:41:55: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:41:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:41:55: #1 tags after filtering in treatment: 790077 INFO @ Sun, 07 Oct 2018 20:41:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:41:55: #1 finished! INFO @ Sun, 07 Oct 2018 20:41:55: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:41:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:41:55: #1 tags after filtering in treatment: 790077 INFO @ Sun, 07 Oct 2018 20:41:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:41:55: #1 finished! INFO @ Sun, 07 Oct 2018 20:41:55: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:41:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:41:55: #2 number of paired peaks: 4486 INFO @ Sun, 07 Oct 2018 20:41:55: start model_add_line... INFO @ Sun, 07 Oct 2018 20:41:55: start X-correlation... INFO @ Sun, 07 Oct 2018 20:41:55: end of X-cor INFO @ Sun, 07 Oct 2018 20:41:55: #2 finished! INFO @ Sun, 07 Oct 2018 20:41:55: #2 predicted fragment length is 239 bps INFO @ Sun, 07 Oct 2018 20:41:55: #2 alternative fragment length(s) may be 212,239 bps INFO @ Sun, 07 Oct 2018 20:41:55: #2.2 Generate R script for model : SRX4798847.05_model.r INFO @ Sun, 07 Oct 2018 20:41:55: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:41:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:41:55: #2 number of paired peaks: 4486 INFO @ Sun, 07 Oct 2018 20:41:55: start model_add_line... INFO @ Sun, 07 Oct 2018 20:41:55: #2 number of paired peaks: 4486 INFO @ Sun, 07 Oct 2018 20:41:55: start model_add_line... INFO @ Sun, 07 Oct 2018 20:41:55: start X-correlation... INFO @ Sun, 07 Oct 2018 20:41:55: end of X-cor INFO @ Sun, 07 Oct 2018 20:41:55: start X-correlation... INFO @ Sun, 07 Oct 2018 20:41:55: #2 finished! INFO @ Sun, 07 Oct 2018 20:41:55: #2 predicted fragment length is 239 bps INFO @ Sun, 07 Oct 2018 20:41:55: #2 alternative fragment length(s) may be 212,239 bps INFO @ Sun, 07 Oct 2018 20:41:55: #2.2 Generate R script for model : SRX4798847.10_model.r INFO @ Sun, 07 Oct 2018 20:41:55: end of X-cor INFO @ Sun, 07 Oct 2018 20:41:55: #2 finished! INFO @ Sun, 07 Oct 2018 20:41:55: #2 predicted fragment length is 239 bps INFO @ Sun, 07 Oct 2018 20:41:55: #2 alternative fragment length(s) may be 212,239 bps INFO @ Sun, 07 Oct 2018 20:41:55: #2.2 Generate R script for model : SRX4798847.20_model.r INFO @ Sun, 07 Oct 2018 20:41:55: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:41:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:41:55: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:41:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:41:57: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:41:57: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:41:57: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:41:58: #4 Write output xls file... SRX4798847.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:41:58: #4 Write peak in narrowPeak format file... SRX4798847.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:41:58: #4 Write summits bed file... SRX4798847.05_summits.bed INFO @ Sun, 07 Oct 2018 20:41:58: #4 Write output xls file... SRX4798847.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:41:58: #4 Write peak in narrowPeak format file... SRX4798847.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:41:58: Done! INFO @ Sun, 07 Oct 2018 20:41:58: #4 Write summits bed file... SRX4798847.10_summits.bed INFO @ Sun, 07 Oct 2018 20:41:58: Done! pass1 - making usageList (8 chroms): 0 millis pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (119 records, 4 fields): 5 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:41:58: #4 Write output xls file... SRX4798847.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:41:58: #4 Write peak in narrowPeak format file... SRX4798847.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:41:58: #4 Write summits bed file... SRX4798847.20_summits.bed INFO @ Sun, 07 Oct 2018 20:41:58: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (8 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。