Job ID = 11240815 sra ファイルのダウンロード中... Completed: 427405K bytes transferred in 8 seconds (428047K 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 12799188 spots for /home/okishinya/chipatlas/results/dm3/SRX4798863/SRR7965206.sra Written 12799188 spots for /home/okishinya/chipatlas/results/dm3/SRX4798863/SRR7965206.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: 00:01:32 12799188 reads; of these: 12799188 (100.00%) were unpaired; of these: 9913584 (77.45%) aligned 0 times 2646734 (20.68%) aligned exactly 1 time 238870 (1.87%) aligned >1 times 22.55% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 688824 / 2885604 = 0.2387 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 20:49:29: # Command line: callpeak -t SRX4798863.bam -f BAM -g dm -n SRX4798863.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798863.20 # format = BAM # ChIP-seq file = ['SRX4798863.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 20:49:29: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:49:29: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:49:29: # Command line: callpeak -t SRX4798863.bam -f BAM -g dm -n SRX4798863.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798863.05 # format = BAM # ChIP-seq file = ['SRX4798863.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 20:49:29: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:49:29: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:49:29: # Command line: callpeak -t SRX4798863.bam -f BAM -g dm -n SRX4798863.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798863.10 # format = BAM # ChIP-seq file = ['SRX4798863.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 20:49:29: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:49:29: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:49:36: 1000000 INFO @ Sun, 07 Oct 2018 20:49:36: 1000000 INFO @ Sun, 07 Oct 2018 20:49:36: 1000000 INFO @ Sun, 07 Oct 2018 20:49:43: 2000000 INFO @ Sun, 07 Oct 2018 20:49:43: 2000000 INFO @ Sun, 07 Oct 2018 20:49:43: 2000000 INFO @ Sun, 07 Oct 2018 20:49:44: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:49:44: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:49:44: #1 total tags in treatment: 2196780 INFO @ Sun, 07 Oct 2018 20:49:44: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:49:44: #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 20:49:44: #1 tags after filtering in treatment: 2196780 INFO @ Sun, 07 Oct 2018 20:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:49:44: #1 finished! INFO @ Sun, 07 Oct 2018 20:49:44: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:49:44: #2 number of paired peaks: 4280 INFO @ Sun, 07 Oct 2018 20:49:44: start model_add_line... INFO @ Sun, 07 Oct 2018 20:49:44: start X-correlation... INFO @ Sun, 07 Oct 2018 20:49:44: end of X-cor INFO @ Sun, 07 Oct 2018 20:49:44: #2 finished! INFO @ Sun, 07 Oct 2018 20:49:44: #2 predicted fragment length is 159 bps INFO @ Sun, 07 Oct 2018 20:49:44: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 07 Oct 2018 20:49:44: #2.2 Generate R script for model : SRX4798863.10_model.r INFO @ Sun, 07 Oct 2018 20:49:44: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:49:44: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:49:44: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:49:44: #1 total tags in treatment: 2196780 INFO @ Sun, 07 Oct 2018 20:49:44: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:49:44: #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 20:49:44: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:49:44: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:49:44: #1 total tags in treatment: 2196780 INFO @ Sun, 07 Oct 2018 20:49:44: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:49:44: #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 20:49:45: #1 tags after filtering in treatment: 2196780 INFO @ Sun, 07 Oct 2018 20:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:49:45: #1 finished! INFO @ Sun, 07 Oct 2018 20:49:45: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:49:45: #1 tags after filtering in treatment: 2196780 INFO @ Sun, 07 Oct 2018 20:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:49:45: #1 finished! INFO @ Sun, 07 Oct 2018 20:49:45: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:49:45: #2 number of paired peaks: 4280 INFO @ Sun, 07 Oct 2018 20:49:45: start model_add_line... INFO @ Sun, 07 Oct 2018 20:49:45: #2 number of paired peaks: 4280 INFO @ Sun, 07 Oct 2018 20:49:45: start model_add_line... INFO @ Sun, 07 Oct 2018 20:49:45: start X-correlation... INFO @ Sun, 07 Oct 2018 20:49:45: start X-correlation... INFO @ Sun, 07 Oct 2018 20:49:45: end of X-cor INFO @ Sun, 07 Oct 2018 20:49:45: #2 finished! INFO @ Sun, 07 Oct 2018 20:49:45: #2 predicted fragment length is 159 bps INFO @ Sun, 07 Oct 2018 20:49:45: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 07 Oct 2018 20:49:45: #2.2 Generate R script for model : SRX4798863.05_model.r INFO @ Sun, 07 Oct 2018 20:49:45: end of X-cor INFO @ Sun, 07 Oct 2018 20:49:45: #2 finished! INFO @ Sun, 07 Oct 2018 20:49:45: #2 predicted fragment length is 159 bps INFO @ Sun, 07 Oct 2018 20:49:45: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 07 Oct 2018 20:49:45: #2.2 Generate R script for model : SRX4798863.20_model.r INFO @ Sun, 07 Oct 2018 20:49:45: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:49:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:49:45: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:49:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:49:50: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:51: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:51: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:53: #4 Write output xls file... SRX4798863.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:53: #4 Write peak in narrowPeak format file... SRX4798863.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:49:54: #4 Write summits bed file... SRX4798863.10_summits.bed INFO @ Sun, 07 Oct 2018 20:49:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2533 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:49:54: #4 Write output xls file... SRX4798863.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:54: #4 Write peak in narrowPeak format file... SRX4798863.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:49:54: #4 Write summits bed file... SRX4798863.05_summits.bed INFO @ Sun, 07 Oct 2018 20:49:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4767 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:49:54: #4 Write output xls file... SRX4798863.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:54: #4 Write peak in narrowPeak format file... SRX4798863.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:49:54: #4 Write summits bed file... SRX4798863.20_summits.bed INFO @ Sun, 07 Oct 2018 20:49:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1065 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。