Job ID = 11633845 sra ファイルのダウンロード中... Completed: 97327K bytes transferred in 4 seconds (180219K 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 3022363 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420462/ERR1348938.sra Written 3022363 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420462/ERR1348938.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: 00:00:31 3022363 reads; of these: 3022363 (100.00%) were unpaired; of these: 284108 (9.40%) aligned 0 times 2142394 (70.88%) aligned exactly 1 time 595861 (19.72%) aligned >1 times 90.60% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 648720 / 2738255 = 0.2369 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 09:16:42: # Command line: callpeak -t ERX1420462.bam -f BAM -g 12100000 -n ERX1420462.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420462.20 # format = BAM # ChIP-seq file = ['ERX1420462.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 09:16:42: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:16:42: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:16:42: # Command line: callpeak -t ERX1420462.bam -f BAM -g 12100000 -n ERX1420462.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420462.05 # format = BAM # ChIP-seq file = ['ERX1420462.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 09:16:42: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:16:42: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:16:42: # Command line: callpeak -t ERX1420462.bam -f BAM -g 12100000 -n ERX1420462.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420462.10 # format = BAM # ChIP-seq file = ['ERX1420462.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 09:16:42: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:16:42: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:16:48: 1000000 INFO @ Fri, 15 Feb 2019 09:16:48: 1000000 INFO @ Fri, 15 Feb 2019 09:16:48: 1000000 INFO @ Fri, 15 Feb 2019 09:16:54: 2000000 INFO @ Fri, 15 Feb 2019 09:16:54: 2000000 INFO @ Fri, 15 Feb 2019 09:16:54: 2000000 INFO @ Fri, 15 Feb 2019 09:16:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:16:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:16:55: #1 total tags in treatment: 2089535 INFO @ Fri, 15 Feb 2019 09:16:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:16:55: #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 09:16:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:16:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:16:55: #1 total tags in treatment: 2089535 INFO @ Fri, 15 Feb 2019 09:16:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:16:55: #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 09:16:55: #1 tags after filtering in treatment: 2089535 INFO @ Fri, 15 Feb 2019 09:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:16:55: #1 finished! INFO @ Fri, 15 Feb 2019 09:16:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:16:55: #1 tags after filtering in treatment: 2089535 INFO @ Fri, 15 Feb 2019 09:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:16:55: #1 finished! INFO @ Fri, 15 Feb 2019 09:16:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:16:55: #2 number of paired peaks: 112 WARNING @ Fri, 15 Feb 2019 09:16:55: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Fri, 15 Feb 2019 09:16:55: start model_add_line... INFO @ Fri, 15 Feb 2019 09:16:55: start X-correlation... INFO @ Fri, 15 Feb 2019 09:16:55: end of X-cor INFO @ Fri, 15 Feb 2019 09:16:55: #2 finished! INFO @ Fri, 15 Feb 2019 09:16:55: #2 predicted fragment length is 308 bps INFO @ Fri, 15 Feb 2019 09:16:55: #2 alternative fragment length(s) may be 308 bps INFO @ Fri, 15 Feb 2019 09:16:55: #2.2 Generate R script for model : ERX1420462.10_model.r INFO @ Fri, 15 Feb 2019 09:16:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:16:55: #2 number of paired peaks: 112 WARNING @ Fri, 15 Feb 2019 09:16:55: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Fri, 15 Feb 2019 09:16:55: start model_add_line... INFO @ Fri, 15 Feb 2019 09:16:55: start X-correlation... INFO @ Fri, 15 Feb 2019 09:16:55: end of X-cor INFO @ Fri, 15 Feb 2019 09:16:55: #2 finished! INFO @ Fri, 15 Feb 2019 09:16:55: #2 predicted fragment length is 308 bps INFO @ Fri, 15 Feb 2019 09:16:55: #2 alternative fragment length(s) may be 308 bps INFO @ Fri, 15 Feb 2019 09:16:55: #2.2 Generate R script for model : ERX1420462.05_model.r INFO @ Fri, 15 Feb 2019 09:16:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:16:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:16:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:16:55: #1 total tags in treatment: 2089535 INFO @ Fri, 15 Feb 2019 09:16:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:16:55: #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 09:16:55: #1 tags after filtering in treatment: 2089535 INFO @ Fri, 15 Feb 2019 09:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:16:55: #1 finished! INFO @ Fri, 15 Feb 2019 09:16:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:16:55: #2 number of paired peaks: 112 WARNING @ Fri, 15 Feb 2019 09:16:55: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Fri, 15 Feb 2019 09:16:55: start model_add_line... INFO @ Fri, 15 Feb 2019 09:16:55: start X-correlation... INFO @ Fri, 15 Feb 2019 09:16:55: end of X-cor INFO @ Fri, 15 Feb 2019 09:16:55: #2 finished! INFO @ Fri, 15 Feb 2019 09:16:55: #2 predicted fragment length is 308 bps INFO @ Fri, 15 Feb 2019 09:16:55: #2 alternative fragment length(s) may be 308 bps INFO @ Fri, 15 Feb 2019 09:16:55: #2.2 Generate R script for model : ERX1420462.20_model.r INFO @ Fri, 15 Feb 2019 09:16:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:17:01: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:17:01: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:17:01: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:17:03: #4 Write output xls file... ERX1420462.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:17:03: #4 Write peak in narrowPeak format file... ERX1420462.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:17:03: #4 Write summits bed file... ERX1420462.05_summits.bed INFO @ Fri, 15 Feb 2019 09:17:03: Done! INFO @ Fri, 15 Feb 2019 09:17:03: #4 Write output xls file... ERX1420462.10_peaks.xls pass1 - making usageList (8 chroms): 1 millis INFO @ Fri, 15 Feb 2019 09:17:03: #4 Write peak in narrowPeak format file... ERX1420462.10_peaks.narrowPeak pass2 - checking and writing primary data (57 records, 4 fields): 3 millis INFO @ Fri, 15 Feb 2019 09:17:03: #4 Write summits bed file... ERX1420462.10_summits.bed INFO @ Fri, 15 Feb 2019 09:17:03: Done! CompletedMACS2peakCalling pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:17:03: #4 Write output xls file... ERX1420462.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:17:03: #4 Write peak in narrowPeak format file... ERX1420462.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:17:03: #4 Write summits bed file... ERX1420462.20_summits.bed INFO @ Fri, 15 Feb 2019 09:17:03: Done! pass1 - making usageList (3 chroms): 2 millis pass2 - checking and writing primary data (31 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。