Job ID = 11633679 sra ファイルのダウンロード中... Completed: 11992K bytes transferred in 3 seconds (32705K 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 380208 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420298/ERR1348774.sra Written 380208 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420298/ERR1348774.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: 00:00:03 380208 reads; of these: 380208 (100.00%) were unpaired; of these: 292077 (76.82%) aligned 0 times 74528 (19.60%) aligned exactly 1 time 13603 (3.58%) aligned >1 times 23.18% overall alignment rate Time searching: 00:00:03 Overall time: 00:00:03 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] 5242 / 88131 = 0.0595 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, 15 Feb 2019 09:07:41: # Command line: callpeak -t ERX1420298.bam -f BAM -g 12100000 -n ERX1420298.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420298.20 # format = BAM # ChIP-seq file = ['ERX1420298.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, 15 Feb 2019 09:07:41: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:07:41: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:07:41: # Command line: callpeak -t ERX1420298.bam -f BAM -g 12100000 -n ERX1420298.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420298.10 # format = BAM # ChIP-seq file = ['ERX1420298.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, 15 Feb 2019 09:07:41: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:07:41: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:07:41: # Command line: callpeak -t ERX1420298.bam -f BAM -g 12100000 -n ERX1420298.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420298.05 # format = BAM # ChIP-seq file = ['ERX1420298.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, 15 Feb 2019 09:07:41: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:07:41: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:07:42: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:07:42: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:07:42: #1 total tags in treatment: 82889 INFO @ Fri, 15 Feb 2019 09:07:42: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:07:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:07:42: #1 tags after filtering in treatment: 82889 INFO @ Fri, 15 Feb 2019 09:07:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:07:42: #1 finished! INFO @ Fri, 15 Feb 2019 09:07:42: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:07:42: #2 number of paired peaks: 265 WARNING @ Fri, 15 Feb 2019 09:07:42: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Fri, 15 Feb 2019 09:07:42: start model_add_line... INFO @ Fri, 15 Feb 2019 09:07:42: start X-correlation... INFO @ Fri, 15 Feb 2019 09:07:42: end of X-cor INFO @ Fri, 15 Feb 2019 09:07:42: #2 finished! INFO @ Fri, 15 Feb 2019 09:07:42: #2 predicted fragment length is 213 bps INFO @ Fri, 15 Feb 2019 09:07:42: #2 alternative fragment length(s) may be 188,213 bps INFO @ Fri, 15 Feb 2019 09:07:42: #2.2 Generate R script for model : ERX1420298.20_model.r INFO @ Fri, 15 Feb 2019 09:07:42: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:07:42: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:07:42: #1 total tags in treatment: 82889 INFO @ Fri, 15 Feb 2019 09:07:42: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:07:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:07:42: #1 tags after filtering in treatment: 82889 INFO @ Fri, 15 Feb 2019 09:07:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:07:42: #1 finished! INFO @ Fri, 15 Feb 2019 09:07:42: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:07:42: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:07:42: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:07:42: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:07:42: #1 total tags in treatment: 82889 INFO @ Fri, 15 Feb 2019 09:07:42: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:07:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:07:42: #2 number of paired peaks: 265 WARNING @ Fri, 15 Feb 2019 09:07:42: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Fri, 15 Feb 2019 09:07:42: start model_add_line... INFO @ Fri, 15 Feb 2019 09:07:42: #1 tags after filtering in treatment: 82889 INFO @ Fri, 15 Feb 2019 09:07:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:07:42: #1 finished! INFO @ Fri, 15 Feb 2019 09:07:42: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:07:42: start X-correlation... INFO @ Fri, 15 Feb 2019 09:07:42: end of X-cor INFO @ Fri, 15 Feb 2019 09:07:42: #2 finished! INFO @ Fri, 15 Feb 2019 09:07:42: #2 predicted fragment length is 213 bps INFO @ Fri, 15 Feb 2019 09:07:42: #2 alternative fragment length(s) may be 188,213 bps INFO @ Fri, 15 Feb 2019 09:07:42: #2.2 Generate R script for model : ERX1420298.10_model.r INFO @ Fri, 15 Feb 2019 09:07:42: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:07:42: #2 number of paired peaks: 265 WARNING @ Fri, 15 Feb 2019 09:07:42: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Fri, 15 Feb 2019 09:07:42: start model_add_line... INFO @ Fri, 15 Feb 2019 09:07:42: start X-correlation... INFO @ Fri, 15 Feb 2019 09:07:42: end of X-cor INFO @ Fri, 15 Feb 2019 09:07:42: #2 finished! INFO @ Fri, 15 Feb 2019 09:07:42: #2 predicted fragment length is 213 bps INFO @ Fri, 15 Feb 2019 09:07:42: #2 alternative fragment length(s) may be 188,213 bps INFO @ Fri, 15 Feb 2019 09:07:42: #2.2 Generate R script for model : ERX1420298.05_model.r INFO @ Fri, 15 Feb 2019 09:07:42: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:07:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:07:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:07:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:07:42: #4 Write output xls file... ERX1420298.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:07:42: #4 Write peak in narrowPeak format file... ERX1420298.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:07:42: #4 Write summits bed file... ERX1420298.20_summits.bed INFO @ Fri, 15 Feb 2019 09:07:42: Done! INFO @ Fri, 15 Feb 2019 09:07:42: #4 Write output xls file... ERX1420298.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:07:42: #4 Write output xls file... ERX1420298.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:07:42: #4 Write peak in narrowPeak format file... ERX1420298.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:07:42: #4 Write peak in narrowPeak format file... ERX1420298.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:07:42: #4 Write summits bed file... ERX1420298.10_summits.bed INFO @ Fri, 15 Feb 2019 09:07:42: #4 Write summits bed file... ERX1420298.05_summits.bed INFO @ Fri, 15 Feb 2019 09:07:42: Done! INFO @ Fri, 15 Feb 2019 09:07:42: Done! pass1 - making usageList (1 chroms): 9 millis pass2 - checking and writing primary data (1 records, 4 fields): 5 millis pass1 - making usageList (1 chroms): 21 millis pass2 - checking and writing primary data (2 records, 4 fields): 14 millis CompletedMACS2peakCalling pass1 - making usageList (10 chroms): 17 millis pass2 - checking and writing primary data (27 records, 4 fields): 10 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。