Job ID = 11388956 sra ファイルのダウンロード中... Completed: 432756K bytes transferred in 13 seconds (256380K 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 8064147 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5041899/SRR8223351.sra Written 8064147 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5041899/SRR8223351.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: 00:01:56 8064147 reads; of these: 8064147 (100.00%) were paired; of these: 8025670 (99.52%) aligned concordantly 0 times 29208 (0.36%) aligned concordantly exactly 1 time 9269 (0.11%) aligned concordantly >1 times ---- 8025670 pairs aligned concordantly 0 times; of these: 35 (0.00%) aligned discordantly 1 time ---- 8025635 pairs aligned 0 times concordantly or discordantly; of these: 16051270 mates make up the pairs; of these: 16048124 (99.98%) aligned 0 times 2242 (0.01%) aligned exactly 1 time 904 (0.01%) aligned >1 times 0.50% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 31640 / 38495 = 0.8219 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 00:24:42: # Command line: callpeak -t SRX5041899.bam -f BAM -g 12100000 -n SRX5041899.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5041899.05 # format = BAM # ChIP-seq file = ['SRX5041899.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 00:24:42: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:24:42: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:24:42: # Command line: callpeak -t SRX5041899.bam -f BAM -g 12100000 -n SRX5041899.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5041899.10 # format = BAM # ChIP-seq file = ['SRX5041899.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 00:24:42: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:24:42: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:24:42: # Command line: callpeak -t SRX5041899.bam -f BAM -g 12100000 -n SRX5041899.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5041899.20 # format = BAM # ChIP-seq file = ['SRX5041899.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 00:24:42: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:24:42: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:24:42: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:24:42: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:24:42: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:24:42: #1 total tags in treatment: 6863 INFO @ Thu, 13 Dec 2018 00:24:42: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:24:42: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:24:42: #1 total tags in treatment: 6863 INFO @ Thu, 13 Dec 2018 00:24:42: #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 00:24:42: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:24:42: #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 00:24:42: #1 tags after filtering in treatment: 6750 INFO @ Thu, 13 Dec 2018 00:24:42: #1 tags after filtering in treatment: 6750 INFO @ Thu, 13 Dec 2018 00:24:42: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 13 Dec 2018 00:24:42: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 13 Dec 2018 00:24:42: #1 finished! INFO @ Thu, 13 Dec 2018 00:24:42: #1 finished! INFO @ Thu, 13 Dec 2018 00:24:42: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:24:42: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:24:42: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:24:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:24:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:24:42: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:24:42: #1 total tags in treatment: 6863 INFO @ Thu, 13 Dec 2018 00:24:42: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:24:42: #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 00:24:42: #1 tags after filtering in treatment: 6750 INFO @ Thu, 13 Dec 2018 00:24:42: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 13 Dec 2018 00:24:42: #1 finished! INFO @ Thu, 13 Dec 2018 00:24:42: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:24:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:24:42: #2 number of paired peaks: 203 WARNING @ Thu, 13 Dec 2018 00:24:42: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Thu, 13 Dec 2018 00:24:42: start model_add_line... INFO @ Thu, 13 Dec 2018 00:24:42: start X-correlation... INFO @ Thu, 13 Dec 2018 00:24:42: #2 number of paired peaks: 203 WARNING @ Thu, 13 Dec 2018 00:24:42: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Thu, 13 Dec 2018 00:24:42: start model_add_line... INFO @ Thu, 13 Dec 2018 00:24:42: start X-correlation... INFO @ Thu, 13 Dec 2018 00:24:42: #2 number of paired peaks: 203 WARNING @ Thu, 13 Dec 2018 00:24:42: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Thu, 13 Dec 2018 00:24:42: start model_add_line... INFO @ Thu, 13 Dec 2018 00:24:42: start X-correlation... INFO @ Thu, 13 Dec 2018 00:24:42: end of X-cor INFO @ Thu, 13 Dec 2018 00:24:42: end of X-cor INFO @ Thu, 13 Dec 2018 00:24:42: #2 finished! INFO @ Thu, 13 Dec 2018 00:24:42: #2 finished! INFO @ Thu, 13 Dec 2018 00:24:42: #2 predicted fragment length is 278 bps INFO @ Thu, 13 Dec 2018 00:24:42: #2 predicted fragment length is 278 bps INFO @ Thu, 13 Dec 2018 00:24:42: #2 alternative fragment length(s) may be 115,146,177,202,235,278,299,358,387,457,574 bps INFO @ Thu, 13 Dec 2018 00:24:42: #2 alternative fragment length(s) may be 115,146,177,202,235,278,299,358,387,457,574 bps INFO @ Thu, 13 Dec 2018 00:24:42: #2.2 Generate R script for model : SRX5041899.10_model.r INFO @ Thu, 13 Dec 2018 00:24:42: #2.2 Generate R script for model : SRX5041899.05_model.r INFO @ Thu, 13 Dec 2018 00:24:42: end of X-cor INFO @ Thu, 13 Dec 2018 00:24:42: #2 finished! INFO @ Thu, 13 Dec 2018 00:24:42: #2 predicted fragment length is 278 bps INFO @ Thu, 13 Dec 2018 00:24:42: #2 alternative fragment length(s) may be 115,146,177,202,235,278,299,358,387,457,574 bps INFO @ Thu, 13 Dec 2018 00:24:42: #2.2 Generate R script for model : SRX5041899.20_model.r INFO @ Thu, 13 Dec 2018 00:24:42: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:24:42: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:24:42: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:24:42: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:24:42: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:24:42: #4 Write output xls file... SRX5041899.10_peaks.xls INFO @ Thu, 13 Dec 2018 00:24:42: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:24:42: #4 Write peak in narrowPeak format file... SRX5041899.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:24:42: #4 Write summits bed file... SRX5041899.10_summits.bed INFO @ Thu, 13 Dec 2018 00:24:42: Done! INFO @ Thu, 13 Dec 2018 00:24:42: #4 Write output xls file... SRX5041899.05_peaks.xls INFO @ Thu, 13 Dec 2018 00:24:42: #4 Write output xls file... SRX5041899.20_peaks.xls INFO @ Thu, 13 Dec 2018 00:24:42: #4 Write peak in narrowPeak format file... SRX5041899.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:24:42: #4 Write peak in narrowPeak format file... SRX5041899.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:24:42: #4 Write summits bed file... SRX5041899.05_summits.bed INFO @ Thu, 13 Dec 2018 00:24:42: #4 Write summits bed file... SRX5041899.20_summits.bed INFO @ Thu, 13 Dec 2018 00:24:42: Done! INFO @ Thu, 13 Dec 2018 00:24:42: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (0 chroms): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 2 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (3 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。