Job ID = 11293668 sra ファイルのダウンロード中... Completed: 725765K bytes transferred in 29 seconds (203895K 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 22010851 spots for /home/okishinya/chipatlas/results/dm3/SRX4375830/SRR7506484.sra Written 22010851 spots for /home/okishinya/chipatlas/results/dm3/SRX4375830/SRR7506484.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: 00:03:45 22010851 reads; of these: 22010851 (100.00%) were unpaired; of these: 16367874 (74.36%) aligned 0 times 4644193 (21.10%) aligned exactly 1 time 998784 (4.54%) aligned >1 times 25.64% overall alignment rate Time searching: 00:03:45 Overall time: 00:03:45 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] 2828326 / 5642977 = 0.5012 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, 04 Nov 2018 17:53:28: # Command line: callpeak -t SRX4375830.bam -f BAM -g dm -n SRX4375830.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375830.05 # format = BAM # ChIP-seq file = ['SRX4375830.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, 04 Nov 2018 17:53:28: # Command line: callpeak -t SRX4375830.bam -f BAM -g dm -n SRX4375830.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375830.10 # format = BAM # ChIP-seq file = ['SRX4375830.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, 04 Nov 2018 17:53:28: # Command line: callpeak -t SRX4375830.bam -f BAM -g dm -n SRX4375830.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375830.20 # format = BAM # ChIP-seq file = ['SRX4375830.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, 04 Nov 2018 17:53:28: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:28: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:28: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:28: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:28: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:28: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:35: 1000000 INFO @ Sun, 04 Nov 2018 17:53:35: 1000000 INFO @ Sun, 04 Nov 2018 17:53:35: 1000000 INFO @ Sun, 04 Nov 2018 17:53:42: 2000000 INFO @ Sun, 04 Nov 2018 17:53:42: 2000000 INFO @ Sun, 04 Nov 2018 17:53:42: 2000000 INFO @ Sun, 04 Nov 2018 17:53:48: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:53:48: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:53:48: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:53:48: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:53:48: #1 total tags in treatment: 2814651 INFO @ Sun, 04 Nov 2018 17:53:48: #1 total tags in treatment: 2814651 INFO @ Sun, 04 Nov 2018 17:53:48: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:53:48: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:53:48: #1 tags after filtering in treatment: 2814651 INFO @ Sun, 04 Nov 2018 17:53:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:53:48: #1 tags after filtering in treatment: 2814651 INFO @ Sun, 04 Nov 2018 17:53:48: #1 finished! INFO @ Sun, 04 Nov 2018 17:53:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:53:48: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:53:48: #1 finished! INFO @ Sun, 04 Nov 2018 17:53:48: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:53:48: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:53:48: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:53:48: #1 total tags in treatment: 2814651 INFO @ Sun, 04 Nov 2018 17:53:48: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:53:48: #1 tags after filtering in treatment: 2814651 INFO @ Sun, 04 Nov 2018 17:53:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:53:48: #1 finished! INFO @ Sun, 04 Nov 2018 17:53:48: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:53:48: #2 number of paired peaks: 5990 INFO @ Sun, 04 Nov 2018 17:53:48: start model_add_line... INFO @ Sun, 04 Nov 2018 17:53:48: #2 number of paired peaks: 5990 INFO @ Sun, 04 Nov 2018 17:53:48: start model_add_line... INFO @ Sun, 04 Nov 2018 17:53:49: start X-correlation... INFO @ Sun, 04 Nov 2018 17:53:49: start X-correlation... INFO @ Sun, 04 Nov 2018 17:53:49: end of X-cor INFO @ Sun, 04 Nov 2018 17:53:49: end of X-cor INFO @ Sun, 04 Nov 2018 17:53:49: #2 finished! INFO @ Sun, 04 Nov 2018 17:53:49: #2 finished! INFO @ Sun, 04 Nov 2018 17:53:49: #2 predicted fragment length is 179 bps INFO @ Sun, 04 Nov 2018 17:53:49: #2 predicted fragment length is 179 bps INFO @ Sun, 04 Nov 2018 17:53:49: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 04 Nov 2018 17:53:49: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 04 Nov 2018 17:53:49: #2.2 Generate R script for model : SRX4375830.10_model.r INFO @ Sun, 04 Nov 2018 17:53:49: #2.2 Generate R script for model : SRX4375830.05_model.r INFO @ Sun, 04 Nov 2018 17:53:49: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:53:49: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:53:49: #2 number of paired peaks: 5990 INFO @ Sun, 04 Nov 2018 17:53:49: start model_add_line... INFO @ Sun, 04 Nov 2018 17:53:49: start X-correlation... INFO @ Sun, 04 Nov 2018 17:53:49: end of X-cor INFO @ Sun, 04 Nov 2018 17:53:49: #2 finished! INFO @ Sun, 04 Nov 2018 17:53:49: #2 predicted fragment length is 179 bps INFO @ Sun, 04 Nov 2018 17:53:49: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 04 Nov 2018 17:53:49: #2.2 Generate R script for model : SRX4375830.20_model.r INFO @ Sun, 04 Nov 2018 17:53:49: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:53:58: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:58: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:59: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:54:02: #4 Write output xls file... SRX4375830.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:54:02: #4 Write peak in narrowPeak format file... SRX4375830.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:54:02: #4 Write summits bed file... SRX4375830.05_summits.bed INFO @ Sun, 04 Nov 2018 17:54:02: Done! INFO @ Sun, 04 Nov 2018 17:54:02: #4 Write output xls file... SRX4375830.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:54:02: #4 Write peak in narrowPeak format file... SRX4375830.10_peaks.narrowPeak pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7278 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:54:03: #4 Write summits bed file... SRX4375830.10_summits.bed INFO @ Sun, 04 Nov 2018 17:54:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5903 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:54:03: #4 Write output xls file... SRX4375830.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:54:03: #4 Write peak in narrowPeak format file... SRX4375830.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:54:03: #4 Write summits bed file... SRX4375830.20_summits.bed INFO @ Sun, 04 Nov 2018 17:54:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4198 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。