Job ID = 11633924 sra ファイルのダウンロード中... Completed: 165856K bytes transferred in 5 seconds (265710K 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 4421380 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1424511/ERR1353036.sra Written 4421380 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1424511/ERR1353036.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 4421380 reads; of these: 4421380 (100.00%) were unpaired; of these: 2921657 (66.08%) aligned 0 times 1059276 (23.96%) aligned exactly 1 time 440447 (9.96%) aligned >1 times 33.92% 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] 663294 / 1499723 = 0.4423 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 09:18:49: # Command line: callpeak -t ERX1424511.bam -f BAM -g 12100000 -n ERX1424511.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1424511.20 # format = BAM # ChIP-seq file = ['ERX1424511.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 09:18:49: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:18:49: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:18:49: # Command line: callpeak -t ERX1424511.bam -f BAM -g 12100000 -n ERX1424511.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1424511.10 # format = BAM # ChIP-seq file = ['ERX1424511.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 09:18:49: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:18:49: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:18:49: # Command line: callpeak -t ERX1424511.bam -f BAM -g 12100000 -n ERX1424511.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1424511.05 # format = BAM # ChIP-seq file = ['ERX1424511.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 09:18:49: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:18:49: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:18:54: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:18:54: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:18:54: #1 total tags in treatment: 836429 INFO @ Fri, 15 Feb 2019 09:18:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:18:54: #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 09:18:54: #1 tags after filtering in treatment: 836429 INFO @ Fri, 15 Feb 2019 09:18:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:18:54: #1 finished! INFO @ Fri, 15 Feb 2019 09:18:54: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:18:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:18:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:18:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:18:55: #1 total tags in treatment: 836429 INFO @ Fri, 15 Feb 2019 09:18:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:18:55: #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 09:18:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:18:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:18:55: #2 number of paired peaks: 654 INFO @ Fri, 15 Feb 2019 09:18:55: #1 total tags in treatment: 836429 WARNING @ Fri, 15 Feb 2019 09:18:55: Fewer paired peaks (654) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 654 pairs to build model! INFO @ Fri, 15 Feb 2019 09:18:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:18:55: #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 09:18:55: start model_add_line... INFO @ Fri, 15 Feb 2019 09:18:55: #1 tags after filtering in treatment: 836429 INFO @ Fri, 15 Feb 2019 09:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:18:55: #1 finished! INFO @ Fri, 15 Feb 2019 09:18:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:18:55: start X-correlation... INFO @ Fri, 15 Feb 2019 09:18:55: #1 tags after filtering in treatment: 836429 INFO @ Fri, 15 Feb 2019 09:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:18:55: #1 finished! INFO @ Fri, 15 Feb 2019 09:18:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:18:55: end of X-cor INFO @ Fri, 15 Feb 2019 09:18:55: #2 finished! INFO @ Fri, 15 Feb 2019 09:18:55: #2 predicted fragment length is 176 bps INFO @ Fri, 15 Feb 2019 09:18:55: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 15 Feb 2019 09:18:55: #2.2 Generate R script for model : ERX1424511.20_model.r INFO @ Fri, 15 Feb 2019 09:18:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:18:55: #2 number of paired peaks: 654 WARNING @ Fri, 15 Feb 2019 09:18:55: Fewer paired peaks (654) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 654 pairs to build model! INFO @ Fri, 15 Feb 2019 09:18:55: start model_add_line... INFO @ Fri, 15 Feb 2019 09:18:55: #2 number of paired peaks: 654 WARNING @ Fri, 15 Feb 2019 09:18:55: Fewer paired peaks (654) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 654 pairs to build model! INFO @ Fri, 15 Feb 2019 09:18:55: start model_add_line... INFO @ Fri, 15 Feb 2019 09:18:55: start X-correlation... INFO @ Fri, 15 Feb 2019 09:18:55: end of X-cor INFO @ Fri, 15 Feb 2019 09:18:55: #2 finished! INFO @ Fri, 15 Feb 2019 09:18:55: #2 predicted fragment length is 176 bps INFO @ Fri, 15 Feb 2019 09:18:55: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 15 Feb 2019 09:18:55: #2.2 Generate R script for model : ERX1424511.10_model.r INFO @ Fri, 15 Feb 2019 09:18:55: start X-correlation... INFO @ Fri, 15 Feb 2019 09:18:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:18:55: end of X-cor INFO @ Fri, 15 Feb 2019 09:18:55: #2 finished! INFO @ Fri, 15 Feb 2019 09:18:55: #2 predicted fragment length is 176 bps INFO @ Fri, 15 Feb 2019 09:18:55: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 15 Feb 2019 09:18:55: #2.2 Generate R script for model : ERX1424511.05_model.r INFO @ Fri, 15 Feb 2019 09:18:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:18:58: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:18:58: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:18:58: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:18:59: #4 Write output xls file... ERX1424511.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:18:59: #4 Write peak in narrowPeak format file... ERX1424511.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:18:59: #4 Write summits bed file... ERX1424511.20_summits.bed INFO @ Fri, 15 Feb 2019 09:18:59: Done! pass1 - making usageList (16 chroms): 6 millis pass2 - checking and writing primary data (1004 records, 4 fields): 6 millis INFO @ Fri, 15 Feb 2019 09:18:59: #4 Write output xls file... ERX1424511.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:18:59: #4 Write output xls file... ERX1424511.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:18:59: #4 Write peak in narrowPeak format file... ERX1424511.10_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:18:59: #4 Write summits bed file... ERX1424511.10_summits.bed INFO @ Fri, 15 Feb 2019 09:18:59: #4 Write peak in narrowPeak format file... ERX1424511.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:18:59: Done! INFO @ Fri, 15 Feb 2019 09:18:59: #4 Write summits bed file... ERX1424511.05_summits.bed INFO @ Fri, 15 Feb 2019 09:18:59: Done! pass1 - making usageList (16 chroms): 6 millis pass2 - checking and writing primary data (1599 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 15 millis pass2 - checking and writing primary data (2372 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。