Job ID = 11388951 sra ファイルのダウンロード中... Completed: 279784K bytes transferred in 7 seconds (292956K 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 5149772 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5041896/SRR8223348.sra Written 5149772 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5041896/SRR8223348.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: 00:01:14 5149772 reads; of these: 5149772 (100.00%) were paired; of these: 5116643 (99.36%) aligned concordantly 0 times 27020 (0.52%) aligned concordantly exactly 1 time 6109 (0.12%) aligned concordantly >1 times ---- 5116643 pairs aligned concordantly 0 times; of these: 22 (0.00%) aligned discordantly 1 time ---- 5116621 pairs aligned 0 times concordantly or discordantly; of these: 10233242 mates make up the pairs; of these: 10230824 (99.98%) aligned 0 times 1653 (0.02%) aligned exactly 1 time 765 (0.01%) aligned >1 times 0.67% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 27177 / 33140 = 0.8201 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 @ Thu, 13 Dec 2018 00:22:24: # Command line: callpeak -t SRX5041896.bam -f BAM -g 12100000 -n SRX5041896.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5041896.20 # format = BAM # ChIP-seq file = ['SRX5041896.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Thu, 13 Dec 2018 00:22:24: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:22:24: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:22:24: # Command line: callpeak -t SRX5041896.bam -f BAM -g 12100000 -n SRX5041896.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5041896.05 # format = BAM # ChIP-seq file = ['SRX5041896.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Thu, 13 Dec 2018 00:22:24: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:22:24: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:22:24: # Command line: callpeak -t SRX5041896.bam -f BAM -g 12100000 -n SRX5041896.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5041896.10 # format = BAM # ChIP-seq file = ['SRX5041896.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Thu, 13 Dec 2018 00:22:24: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:22:24: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:22:24: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:22:24: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:22:24: #1 total tags in treatment: 5965 INFO @ Thu, 13 Dec 2018 00:22:24: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:22:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:22:24: #1 tags after filtering in treatment: 5870 INFO @ Thu, 13 Dec 2018 00:22:24: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 13 Dec 2018 00:22:24: #1 finished! INFO @ Thu, 13 Dec 2018 00:22:24: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:22:24: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:22:24: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:22:24: #1 total tags in treatment: 5965 INFO @ Thu, 13 Dec 2018 00:22:24: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:22:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:22:24: #1 tags after filtering in treatment: 5870 INFO @ Thu, 13 Dec 2018 00:22:24: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 13 Dec 2018 00:22:24: #1 finished! INFO @ Thu, 13 Dec 2018 00:22:24: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:22:24: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:22:24: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:22:24: #1 total tags in treatment: 5965 INFO @ Thu, 13 Dec 2018 00:22:24: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:22:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:22:24: #2 number of paired peaks: 174 WARNING @ Thu, 13 Dec 2018 00:22:24: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Thu, 13 Dec 2018 00:22:24: start model_add_line... INFO @ Thu, 13 Dec 2018 00:22:24: start X-correlation... INFO @ Thu, 13 Dec 2018 00:22:24: #1 tags after filtering in treatment: 5870 INFO @ Thu, 13 Dec 2018 00:22:24: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 13 Dec 2018 00:22:24: #1 finished! INFO @ Thu, 13 Dec 2018 00:22:24: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:22:24: end of X-cor INFO @ Thu, 13 Dec 2018 00:22:24: #2 finished! INFO @ Thu, 13 Dec 2018 00:22:24: #2 predicted fragment length is 281 bps INFO @ Thu, 13 Dec 2018 00:22:24: #2 number of paired peaks: 174 INFO @ Thu, 13 Dec 2018 00:22:24: #2 alternative fragment length(s) may be 116,221,236,266,281,300,514,590 bps WARNING @ Thu, 13 Dec 2018 00:22:24: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Thu, 13 Dec 2018 00:22:24: #2.2 Generate R script for model : SRX5041896.20_model.r INFO @ Thu, 13 Dec 2018 00:22:24: start model_add_line... INFO @ Thu, 13 Dec 2018 00:22:24: start X-correlation... INFO @ Thu, 13 Dec 2018 00:22:24: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:22:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:22:24: end of X-cor INFO @ Thu, 13 Dec 2018 00:22:24: #2 finished! INFO @ Thu, 13 Dec 2018 00:22:24: #2 predicted fragment length is 281 bps INFO @ Thu, 13 Dec 2018 00:22:24: #2 alternative fragment length(s) may be 116,221,236,266,281,300,514,590 bps INFO @ Thu, 13 Dec 2018 00:22:24: #2.2 Generate R script for model : SRX5041896.05_model.r INFO @ Thu, 13 Dec 2018 00:22:24: #2 number of paired peaks: 174 WARNING @ Thu, 13 Dec 2018 00:22:24: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Thu, 13 Dec 2018 00:22:24: start model_add_line... INFO @ Thu, 13 Dec 2018 00:22:24: start X-correlation... INFO @ Thu, 13 Dec 2018 00:22:24: end of X-cor INFO @ Thu, 13 Dec 2018 00:22:24: #2 finished! INFO @ Thu, 13 Dec 2018 00:22:24: #2 predicted fragment length is 281 bps INFO @ Thu, 13 Dec 2018 00:22:24: #2 alternative fragment length(s) may be 116,221,236,266,281,300,514,590 bps INFO @ Thu, 13 Dec 2018 00:22:24: #2.2 Generate R script for model : SRX5041896.10_model.r INFO @ Thu, 13 Dec 2018 00:22:24: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:22:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:22:24: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:22:24: #4 Write output xls file... SRX5041896.20_peaks.xls INFO @ Thu, 13 Dec 2018 00:22:24: #4 Write peak in narrowPeak format file... SRX5041896.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:22:24: #4 Write summits bed file... SRX5041896.20_summits.bed INFO @ Thu, 13 Dec 2018 00:22:24: Done! INFO @ Thu, 13 Dec 2018 00:22:24: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:22:24: #4 Write output xls file... SRX5041896.10_peaks.xls INFO @ Thu, 13 Dec 2018 00:22:24: #4 Write peak in narrowPeak format file... SRX5041896.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:22:24: #4 Write summits bed file... SRX5041896.10_summits.bed INFO @ Thu, 13 Dec 2018 00:22:24: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BedGraph に変換しました。 CompletedMACS2peakCalling BigWig に変換中... BigWig に変換しました。 INFO @ Thu, 13 Dec 2018 00:22:24: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:22:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:22:24: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:22:24: #4 Write output xls file... SRX5041896.05_peaks.xls INFO @ Thu, 13 Dec 2018 00:22:24: #4 Write peak in narrowPeak format file... SRX5041896.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:22:24: #4 Write summits bed file... SRX5041896.05_summits.bed INFO @ Thu, 13 Dec 2018 00:22:24: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling