Job ID = 11633842 sra ファイルのダウンロード中... Completed: 17735K bytes transferred in 3 seconds (47229K 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 551422 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420459/ERR1348935.sra Written 551422 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420459/ERR1348935.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: 00:00:06 551422 reads; of these: 551422 (100.00%) were unpaired; of these: 56461 (10.24%) aligned 0 times 385469 (69.90%) aligned exactly 1 time 109492 (19.86%) aligned >1 times 89.76% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 63407 / 494961 = 0.1281 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 09:15:21: # Command line: callpeak -t ERX1420459.bam -f BAM -g 12100000 -n ERX1420459.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420459.05 # format = BAM # ChIP-seq file = ['ERX1420459.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 09:15:21: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:15:21: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:15:21: # Command line: callpeak -t ERX1420459.bam -f BAM -g 12100000 -n ERX1420459.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420459.10 # format = BAM # ChIP-seq file = ['ERX1420459.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 09:15:21: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:15:21: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:15:21: # Command line: callpeak -t ERX1420459.bam -f BAM -g 12100000 -n ERX1420459.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420459.20 # format = BAM # ChIP-seq file = ['ERX1420459.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 09:15:21: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:15:21: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:15:24: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:15:24: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:15:24: #1 total tags in treatment: 431554 INFO @ Fri, 15 Feb 2019 09:15:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:15:24: #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 09:15:24: #1 tags after filtering in treatment: 431554 INFO @ Fri, 15 Feb 2019 09:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:15:24: #1 finished! INFO @ Fri, 15 Feb 2019 09:15:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:15:24: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:15:24: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:15:24: #1 total tags in treatment: 431554 INFO @ Fri, 15 Feb 2019 09:15:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:15:24: #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 09:15:24: #1 tags after filtering in treatment: 431554 INFO @ Fri, 15 Feb 2019 09:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:15:24: #1 finished! INFO @ Fri, 15 Feb 2019 09:15:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:15:24: #2 number of paired peaks: 121 WARNING @ Fri, 15 Feb 2019 09:15:24: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Fri, 15 Feb 2019 09:15:24: start model_add_line... INFO @ Fri, 15 Feb 2019 09:15:24: start X-correlation... INFO @ Fri, 15 Feb 2019 09:15:24: end of X-cor INFO @ Fri, 15 Feb 2019 09:15:24: #2 finished! INFO @ Fri, 15 Feb 2019 09:15:24: #2 predicted fragment length is 261 bps INFO @ Fri, 15 Feb 2019 09:15:24: #2 alternative fragment length(s) may be 261 bps INFO @ Fri, 15 Feb 2019 09:15:24: #2.2 Generate R script for model : ERX1420459.20_model.r INFO @ Fri, 15 Feb 2019 09:15:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:15:24: #2 number of paired peaks: 121 WARNING @ Fri, 15 Feb 2019 09:15:24: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Fri, 15 Feb 2019 09:15:24: start model_add_line... INFO @ Fri, 15 Feb 2019 09:15:24: start X-correlation... INFO @ Fri, 15 Feb 2019 09:15:24: end of X-cor INFO @ Fri, 15 Feb 2019 09:15:24: #2 finished! INFO @ Fri, 15 Feb 2019 09:15:24: #2 predicted fragment length is 261 bps INFO @ Fri, 15 Feb 2019 09:15:24: #2 alternative fragment length(s) may be 261 bps INFO @ Fri, 15 Feb 2019 09:15:24: #2.2 Generate R script for model : ERX1420459.10_model.r INFO @ Fri, 15 Feb 2019 09:15:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:15:24: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:15:24: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:15:24: #1 total tags in treatment: 431554 INFO @ Fri, 15 Feb 2019 09:15:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:15:24: #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 09:15:24: #1 tags after filtering in treatment: 431554 INFO @ Fri, 15 Feb 2019 09:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:15:24: #1 finished! INFO @ Fri, 15 Feb 2019 09:15:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:15:24: #2 number of paired peaks: 121 WARNING @ Fri, 15 Feb 2019 09:15:24: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Fri, 15 Feb 2019 09:15:24: start model_add_line... INFO @ Fri, 15 Feb 2019 09:15:24: start X-correlation... INFO @ Fri, 15 Feb 2019 09:15:24: end of X-cor INFO @ Fri, 15 Feb 2019 09:15:24: #2 finished! INFO @ Fri, 15 Feb 2019 09:15:24: #2 predicted fragment length is 261 bps INFO @ Fri, 15 Feb 2019 09:15:24: #2 alternative fragment length(s) may be 261 bps INFO @ Fri, 15 Feb 2019 09:15:24: #2.2 Generate R script for model : ERX1420459.05_model.r INFO @ Fri, 15 Feb 2019 09:15:24: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:15:25: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:15:25: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:15:26: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:15:26: #4 Write output xls file... ERX1420459.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:15:26: #4 Write peak in narrowPeak format file... ERX1420459.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:15:26: #4 Write summits bed file... ERX1420459.20_summits.bed INFO @ Fri, 15 Feb 2019 09:15:26: Done! INFO @ Fri, 15 Feb 2019 09:15:26: #4 Write output xls file... ERX1420459.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:15:26: #4 Write peak in narrowPeak format file... ERX1420459.10_peaks.narrowPeak pass1 - making usageList (2 chroms): 1 millis INFO @ Fri, 15 Feb 2019 09:15:26: #4 Write summits bed file... ERX1420459.10_summits.bed pass2 - checking and writing primary data (15 records, 4 fields): 3 millis INFO @ Fri, 15 Feb 2019 09:15:26: Done! CompletedMACS2peakCalling pass1 - making usageList (2 chroms): 2 millis pass2 - checking and writing primary data (31 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:15:26: #4 Write output xls file... ERX1420459.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:15:26: #4 Write peak in narrowPeak format file... ERX1420459.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:15:26: #4 Write summits bed file... ERX1420459.05_summits.bed INFO @ Fri, 15 Feb 2019 09:15:26: Done! pass1 - making usageList (3 chroms): 2 millis pass2 - checking and writing primary data (45 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。