Job ID = 9158660 sra ファイルのダウンロード中... Completed: 294893K bytes transferred in 5 seconds (420359K 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: PAIRED fastq に変換中... Written 4364807 spots for /home/okishinya/chipatlas/results/dm3/SRX2065445/SRR4095604.sra Written 4364807 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: 00:04:38 4364807 reads; of these: 4364807 (100.00%) were paired; of these: 2441505 (55.94%) aligned concordantly 0 times 1487824 (34.09%) aligned concordantly exactly 1 time 435478 (9.98%) aligned concordantly >1 times ---- 2441505 pairs aligned concordantly 0 times; of these: 31161 (1.28%) aligned discordantly 1 time ---- 2410344 pairs aligned 0 times concordantly or discordantly; of these: 4820688 mates make up the pairs; of these: 4577213 (94.95%) aligned 0 times 168224 (3.49%) aligned exactly 1 time 75251 (1.56%) aligned >1 times 47.57% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 1579060 / 1953730 = 0.8082 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 19:06:36: # Command line: callpeak -t SRX2065445.bam -f BAM -g dm -n SRX2065445.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2065445.10 # format = BAM # ChIP-seq file = ['SRX2065445.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 19:06:36: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:06:36: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:06:36: # Command line: callpeak -t SRX2065445.bam -f BAM -g dm -n SRX2065445.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2065445.20 # format = BAM # ChIP-seq file = ['SRX2065445.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 19:06:36: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:06:36: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:06:36: # Command line: callpeak -t SRX2065445.bam -f BAM -g dm -n SRX2065445.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2065445.05 # format = BAM # ChIP-seq file = ['SRX2065445.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 19:06:36: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:06:36: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:06:42: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 19:06:42: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 19:06:42: #1 total tags in treatment: 362974 INFO @ Tue, 27 Jun 2017 19:06:42: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:06:42: #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 19:06:42: #1 tags after filtering in treatment: 292561 INFO @ Tue, 27 Jun 2017 19:06:42: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 27 Jun 2017 19:06:42: #1 finished! INFO @ Tue, 27 Jun 2017 19:06:42: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:06:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:06:42: #2 number of paired peaks: 3152 INFO @ Tue, 27 Jun 2017 19:06:42: start model_add_line... INFO @ Tue, 27 Jun 2017 19:06:42: start X-correlation... INFO @ Tue, 27 Jun 2017 19:06:42: end of X-cor INFO @ Tue, 27 Jun 2017 19:06:42: #2 finished! INFO @ Tue, 27 Jun 2017 19:06:42: #2 predicted fragment length is 219 bps INFO @ Tue, 27 Jun 2017 19:06:42: #2 alternative fragment length(s) may be 5,219 bps INFO @ Tue, 27 Jun 2017 19:06:42: #2.2 Generate R script for model : SRX2065445.05_model.r INFO @ Tue, 27 Jun 2017 19:06:42: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:06:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:06:43: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 19:06:43: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 19:06:43: #1 total tags in treatment: 362974 INFO @ Tue, 27 Jun 2017 19:06:43: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:06:43: #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 19:06:43: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 19:06:43: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 19:06:43: #1 total tags in treatment: 362974 INFO @ Tue, 27 Jun 2017 19:06:43: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:06:43: #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 19:06:43: #1 tags after filtering in treatment: 292561 INFO @ Tue, 27 Jun 2017 19:06:43: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 27 Jun 2017 19:06:43: #1 finished! INFO @ Tue, 27 Jun 2017 19:06:43: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:06:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:06:43: #1 tags after filtering in treatment: 292561 INFO @ Tue, 27 Jun 2017 19:06:43: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 27 Jun 2017 19:06:43: #1 finished! INFO @ Tue, 27 Jun 2017 19:06:43: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:06:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:06:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:06:43: #2 number of paired peaks: 3152 INFO @ Tue, 27 Jun 2017 19:06:43: start model_add_line... INFO @ Tue, 27 Jun 2017 19:06:43: #2 number of paired peaks: 3152 INFO @ Tue, 27 Jun 2017 19:06:43: start model_add_line... INFO @ Tue, 27 Jun 2017 19:06:43: start X-correlation... INFO @ Tue, 27 Jun 2017 19:06:43: start X-correlation... INFO @ Tue, 27 Jun 2017 19:06:43: end of X-cor INFO @ Tue, 27 Jun 2017 19:06:43: #2 finished! INFO @ Tue, 27 Jun 2017 19:06:43: #2 predicted fragment length is 219 bps INFO @ Tue, 27 Jun 2017 19:06:43: #2 alternative fragment length(s) may be 5,219 bps INFO @ Tue, 27 Jun 2017 19:06:43: #2.2 Generate R script for model : SRX2065445.20_model.r INFO @ Tue, 27 Jun 2017 19:06:43: end of X-cor INFO @ Tue, 27 Jun 2017 19:06:43: #2 finished! INFO @ Tue, 27 Jun 2017 19:06:43: #2 predicted fragment length is 219 bps INFO @ Tue, 27 Jun 2017 19:06:43: #2 alternative fragment length(s) may be 5,219 bps INFO @ Tue, 27 Jun 2017 19:06:43: #2.2 Generate R script for model : SRX2065445.10_model.r INFO @ Tue, 27 Jun 2017 19:06:43: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:06:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:06:43: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:06:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:06:43: #4 Write output xls file... SRX2065445.05_peaks.xls INFO @ Tue, 27 Jun 2017 19:06:44: #4 Write peak in narrowPeak format file... SRX2065445.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:06:44: #4 Write summits bed file... SRX2065445.05_summits.bed INFO @ Tue, 27 Jun 2017 19:06:44: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:06:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:06:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:06:44: #4 Write output xls file... SRX2065445.20_peaks.xls INFO @ Tue, 27 Jun 2017 19:06:44: #4 Write peak in narrowPeak format file... SRX2065445.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:06:44: #4 Write summits bed file... SRX2065445.20_summits.bed INFO @ Tue, 27 Jun 2017 19:06:44: Done! INFO @ Tue, 27 Jun 2017 19:06:44: #4 Write output xls file... SRX2065445.10_peaks.xls INFO @ Tue, 27 Jun 2017 19:06:44: #4 Write peak in narrowPeak format file... SRX2065445.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:06:44: #4 Write summits bed file... SRX2065445.10_summits.bed INFO @ Tue, 27 Jun 2017 19:06:44: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (16 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。