Job ID = 10924615 sra ファイルのダウンロード中... Completed: 386533K bytes transferred in 11 seconds (285465K 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: PAIRED fastq に変換中... Read 6586201 spots for /home/okishinya/chipatlas/results/dm3/SRX2396702/SRR5078072.sra Written 6586201 spots for /home/okishinya/chipatlas/results/dm3/SRX2396702/SRR5078072.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: 00:03:39 6586201 reads; of these: 6586201 (100.00%) were paired; of these: 4508231 (68.45%) aligned concordantly 0 times 1887231 (28.65%) aligned concordantly exactly 1 time 190739 (2.90%) aligned concordantly >1 times ---- 4508231 pairs aligned concordantly 0 times; of these: 74153 (1.64%) aligned discordantly 1 time ---- 4434078 pairs aligned 0 times concordantly or discordantly; of these: 8868156 mates make up the pairs; of these: 8713994 (98.26%) aligned 0 times 114575 (1.29%) aligned exactly 1 time 39587 (0.45%) aligned >1 times 33.85% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 280918 / 2150985 = 0.1306 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 @ Mon, 06 Aug 2018 10:31:15: # Command line: callpeak -t SRX2396702.bam -f BAM -g dm -n SRX2396702.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2396702.20 # format = BAM # ChIP-seq file = ['SRX2396702.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 @ Mon, 06 Aug 2018 10:31:15: # Command line: callpeak -t SRX2396702.bam -f BAM -g dm -n SRX2396702.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2396702.05 # format = BAM # ChIP-seq file = ['SRX2396702.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 @ Mon, 06 Aug 2018 10:31:15: # Command line: callpeak -t SRX2396702.bam -f BAM -g dm -n SRX2396702.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2396702.10 # format = BAM # ChIP-seq file = ['SRX2396702.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 @ Mon, 06 Aug 2018 10:31:15: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:31:15: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:31:15: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:31:15: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:31:15: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:31:15: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:31:22: 1000000 INFO @ Mon, 06 Aug 2018 10:31:22: 1000000 INFO @ Mon, 06 Aug 2018 10:31:22: 1000000 INFO @ Mon, 06 Aug 2018 10:31:28: 2000000 INFO @ Mon, 06 Aug 2018 10:31:28: 2000000 INFO @ Mon, 06 Aug 2018 10:31:28: 2000000 INFO @ Mon, 06 Aug 2018 10:31:34: 3000000 INFO @ Mon, 06 Aug 2018 10:31:35: 3000000 INFO @ Mon, 06 Aug 2018 10:31:35: 3000000 INFO @ Mon, 06 Aug 2018 10:31:40: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:31:40: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:31:40: #1 total tags in treatment: 1799301 INFO @ Mon, 06 Aug 2018 10:31:40: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:31:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:31:40: #1 tags after filtering in treatment: 1781204 INFO @ Mon, 06 Aug 2018 10:31:40: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 06 Aug 2018 10:31:40: #1 finished! INFO @ Mon, 06 Aug 2018 10:31:40: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:31:40: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:31:40: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:31:40: #1 total tags in treatment: 1799301 INFO @ Mon, 06 Aug 2018 10:31:40: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:31:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:31:40: #2 number of paired peaks: 1547 INFO @ Mon, 06 Aug 2018 10:31:40: start model_add_line... INFO @ Mon, 06 Aug 2018 10:31:40: #1 tags after filtering in treatment: 1781204 INFO @ Mon, 06 Aug 2018 10:31:40: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 06 Aug 2018 10:31:40: #1 finished! INFO @ Mon, 06 Aug 2018 10:31:40: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:31:40: start X-correlation... INFO @ Mon, 06 Aug 2018 10:31:41: #1 tag size is determined as 50 bps INFO @ Mon, 06 Aug 2018 10:31:41: #1 tag size = 50 INFO @ Mon, 06 Aug 2018 10:31:41: #1 total tags in treatment: 1799301 INFO @ Mon, 06 Aug 2018 10:31:41: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:31:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:31:41: end of X-cor INFO @ Mon, 06 Aug 2018 10:31:41: #2 finished! INFO @ Mon, 06 Aug 2018 10:31:41: #2 predicted fragment length is 296 bps INFO @ Mon, 06 Aug 2018 10:31:41: #2 alternative fragment length(s) may be 296 bps INFO @ Mon, 06 Aug 2018 10:31:41: #2.2 Generate R script for model : SRX2396702.05_model.r INFO @ Mon, 06 Aug 2018 10:31:41: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:31:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:31:41: #1 tags after filtering in treatment: 1781204 INFO @ Mon, 06 Aug 2018 10:31:41: #1 Redundant rate of treatment: 0.01 INFO @ Mon, 06 Aug 2018 10:31:41: #1 finished! INFO @ Mon, 06 Aug 2018 10:31:41: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:31:41: #2 number of paired peaks: 1547 INFO @ Mon, 06 Aug 2018 10:31:41: start model_add_line... INFO @ Mon, 06 Aug 2018 10:31:41: start X-correlation... INFO @ Mon, 06 Aug 2018 10:31:41: end of X-cor INFO @ Mon, 06 Aug 2018 10:31:41: #2 finished! INFO @ Mon, 06 Aug 2018 10:31:41: #2 predicted fragment length is 296 bps INFO @ Mon, 06 Aug 2018 10:31:41: #2 alternative fragment length(s) may be 296 bps INFO @ Mon, 06 Aug 2018 10:31:41: #2.2 Generate R script for model : SRX2396702.20_model.r INFO @ Mon, 06 Aug 2018 10:31:41: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:31:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:31:41: #2 number of paired peaks: 1547 INFO @ Mon, 06 Aug 2018 10:31:41: start model_add_line... INFO @ Mon, 06 Aug 2018 10:31:41: start X-correlation... INFO @ Mon, 06 Aug 2018 10:31:41: end of X-cor INFO @ Mon, 06 Aug 2018 10:31:41: #2 finished! INFO @ Mon, 06 Aug 2018 10:31:41: #2 predicted fragment length is 296 bps INFO @ Mon, 06 Aug 2018 10:31:41: #2 alternative fragment length(s) may be 296 bps INFO @ Mon, 06 Aug 2018 10:31:41: #2.2 Generate R script for model : SRX2396702.10_model.r INFO @ Mon, 06 Aug 2018 10:31:41: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:31:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:31:45: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:31:45: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:31:45: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:31:48: #4 Write output xls file... SRX2396702.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:31:48: #4 Write peak in narrowPeak format file... SRX2396702.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:31:48: #4 Write summits bed file... SRX2396702.05_summits.bed INFO @ Mon, 06 Aug 2018 10:31:48: Done! pass1 - making usageList (11 chroms): 1 millis INFO @ Mon, 06 Aug 2018 10:31:48: #4 Write output xls file... SRX2396702.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:31:48: #4 Write peak in narrowPeak format file... SRX2396702.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:31:48: #4 Write summits bed file... SRX2396702.20_summits.bed INFO @ Mon, 06 Aug 2018 10:31:48: Done! INFO @ Mon, 06 Aug 2018 10:31:48: #4 Write output xls file... SRX2396702.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:31:48: #4 Write peak in narrowPeak format file... SRX2396702.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:31:48: #4 Write summits bed file... SRX2396702.10_summits.bed INFO @ Mon, 06 Aug 2018 10:31:48: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (115 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 2 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (612 records, 4 fields): 3088 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。