Job ID = 10937652 sra ファイルのダウンロード中... Completed: 119774K bytes transferred in 18 seconds (53785K 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 3580553 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3463301/SRR6367840.sra Written 3580553 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3463301/SRR6367840.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: 00:00:33 3580553 reads; of these: 3580553 (100.00%) were unpaired; of these: 460751 (12.87%) aligned 0 times 2814623 (78.61%) aligned exactly 1 time 305179 (8.52%) aligned >1 times 87.13% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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_rmdupse_core] 733671 / 3119802 = 0.2352 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 @ Fri, 10 Aug 2018 02:46:25: # Command line: callpeak -t SRX3463301.bam -f BAM -g 12100000 -n SRX3463301.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3463301.10 # format = BAM # ChIP-seq file = ['SRX3463301.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 @ Fri, 10 Aug 2018 02:46:25: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:46:25: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:46:25: # Command line: callpeak -t SRX3463301.bam -f BAM -g 12100000 -n SRX3463301.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3463301.05 # format = BAM # ChIP-seq file = ['SRX3463301.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 @ Fri, 10 Aug 2018 02:46:25: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:46:25: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:46:25: # Command line: callpeak -t SRX3463301.bam -f BAM -g 12100000 -n SRX3463301.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3463301.20 # format = BAM # ChIP-seq file = ['SRX3463301.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 @ Fri, 10 Aug 2018 02:46:25: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:46:25: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:46:33: 1000000 INFO @ Fri, 10 Aug 2018 02:46:33: 1000000 INFO @ Fri, 10 Aug 2018 02:46:33: 1000000 INFO @ Fri, 10 Aug 2018 02:46:42: 2000000 INFO @ Fri, 10 Aug 2018 02:46:42: 2000000 INFO @ Fri, 10 Aug 2018 02:46:42: 2000000 INFO @ Fri, 10 Aug 2018 02:46:45: #1 tag size is determined as 45 bps INFO @ Fri, 10 Aug 2018 02:46:45: #1 tag size = 45 INFO @ Fri, 10 Aug 2018 02:46:45: #1 total tags in treatment: 2386131 INFO @ Fri, 10 Aug 2018 02:46:45: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:46:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:46:45: #1 tag size is determined as 45 bps INFO @ Fri, 10 Aug 2018 02:46:45: #1 tag size = 45 INFO @ Fri, 10 Aug 2018 02:46:45: #1 total tags in treatment: 2386131 INFO @ Fri, 10 Aug 2018 02:46:45: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:46:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:46:45: #1 tag size is determined as 45 bps INFO @ Fri, 10 Aug 2018 02:46:45: #1 tag size = 45 INFO @ Fri, 10 Aug 2018 02:46:45: #1 total tags in treatment: 2386131 INFO @ Fri, 10 Aug 2018 02:46:45: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:46:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:46:45: #1 tags after filtering in treatment: 2386131 INFO @ Fri, 10 Aug 2018 02:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 02:46:45: #1 finished! INFO @ Fri, 10 Aug 2018 02:46:45: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:46:45: #1 tags after filtering in treatment: 2386131 INFO @ Fri, 10 Aug 2018 02:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 02:46:45: #1 finished! INFO @ Fri, 10 Aug 2018 02:46:45: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:46:45: #1 tags after filtering in treatment: 2386131 INFO @ Fri, 10 Aug 2018 02:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 02:46:45: #1 finished! INFO @ Fri, 10 Aug 2018 02:46:45: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:46:45: #2 number of paired peaks: 151 WARNING @ Fri, 10 Aug 2018 02:46:45: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Fri, 10 Aug 2018 02:46:45: start model_add_line... INFO @ Fri, 10 Aug 2018 02:46:45: #2 number of paired peaks: 151 WARNING @ Fri, 10 Aug 2018 02:46:45: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Fri, 10 Aug 2018 02:46:45: start model_add_line... INFO @ Fri, 10 Aug 2018 02:46:45: start X-correlation... INFO @ Fri, 10 Aug 2018 02:46:45: start X-correlation... INFO @ Fri, 10 Aug 2018 02:46:45: end of X-cor INFO @ Fri, 10 Aug 2018 02:46:45: #2 finished! INFO @ Fri, 10 Aug 2018 02:46:45: #2 predicted fragment length is 121 bps INFO @ Fri, 10 Aug 2018 02:46:45: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 10 Aug 2018 02:46:45: #2.2 Generate R script for model : SRX3463301.10_model.r INFO @ Fri, 10 Aug 2018 02:46:45: end of X-cor INFO @ Fri, 10 Aug 2018 02:46:45: #2 finished! INFO @ Fri, 10 Aug 2018 02:46:45: #2 predicted fragment length is 121 bps INFO @ Fri, 10 Aug 2018 02:46:45: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 10 Aug 2018 02:46:45: #2.2 Generate R script for model : SRX3463301.05_model.r INFO @ Fri, 10 Aug 2018 02:46:45: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:46:45: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:46:45: #2 number of paired peaks: 151 WARNING @ Fri, 10 Aug 2018 02:46:45: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Fri, 10 Aug 2018 02:46:45: start model_add_line... INFO @ Fri, 10 Aug 2018 02:46:45: start X-correlation... INFO @ Fri, 10 Aug 2018 02:46:45: end of X-cor INFO @ Fri, 10 Aug 2018 02:46:45: #2 finished! INFO @ Fri, 10 Aug 2018 02:46:45: #2 predicted fragment length is 121 bps INFO @ Fri, 10 Aug 2018 02:46:45: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 10 Aug 2018 02:46:45: #2.2 Generate R script for model : SRX3463301.20_model.r INFO @ Fri, 10 Aug 2018 02:46:45: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:46:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:46:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:46:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:46:54: #4 Write output xls file... SRX3463301.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:46:54: #4 Write peak in narrowPeak format file... SRX3463301.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:46:54: #4 Write summits bed file... SRX3463301.05_summits.bed INFO @ Fri, 10 Aug 2018 02:46:54: Done! INFO @ Fri, 10 Aug 2018 02:46:54: #4 Write output xls file... SRX3463301.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:46:54: #4 Write peak in narrowPeak format file... SRX3463301.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:46:54: #4 Write summits bed file... SRX3463301.10_summits.bed pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1794 records, 4 fields): 5 millis INFO @ Fri, 10 Aug 2018 02:46:54: Done! CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1088 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:46:54: #4 Write output xls file... SRX3463301.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:46:54: #4 Write peak in narrowPeak format file... SRX3463301.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:46:54: #4 Write summits bed file... SRX3463301.20_summits.bed INFO @ Fri, 10 Aug 2018 02:46:54: Done! pass1 - making usageList (17 chroms): 3 millis pass2 - checking and writing primary data (546 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。