Job ID = 11633681 sra ファイルのダウンロード中... Completed: 109327K bytes transferred in 4 seconds (196313K 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 3470669 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420300/ERR1348776.sra Written 3470669 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420300/ERR1348776.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: 00:00:29 3470669 reads; of these: 3470669 (100.00%) were unpaired; of these: 1438837 (41.46%) aligned 0 times 1724723 (49.69%) aligned exactly 1 time 307109 (8.85%) aligned >1 times 58.54% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 1009328 / 2031832 = 0.4968 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 09:08:46: # Command line: callpeak -t ERX1420300.bam -f BAM -g 12100000 -n ERX1420300.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420300.20 # format = BAM # ChIP-seq file = ['ERX1420300.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 09:08:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:08:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:08:46: # Command line: callpeak -t ERX1420300.bam -f BAM -g 12100000 -n ERX1420300.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420300.10 # format = BAM # ChIP-seq file = ['ERX1420300.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 09:08:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:08:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:08:46: # Command line: callpeak -t ERX1420300.bam -f BAM -g 12100000 -n ERX1420300.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420300.05 # format = BAM # ChIP-seq file = ['ERX1420300.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 09:08:46: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:08:46: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:08:53: 1000000 INFO @ Fri, 15 Feb 2019 09:08:53: 1000000 INFO @ Fri, 15 Feb 2019 09:08:53: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:08:53: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:08:53: #1 total tags in treatment: 1022504 INFO @ Fri, 15 Feb 2019 09:08:53: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:08:53: #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 09:08:53: 1000000 INFO @ Fri, 15 Feb 2019 09:08:53: #1 tags after filtering in treatment: 1022504 INFO @ Fri, 15 Feb 2019 09:08:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:08:53: #1 finished! INFO @ Fri, 15 Feb 2019 09:08:53: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:08:54: #2 number of paired peaks: 184 WARNING @ Fri, 15 Feb 2019 09:08:54: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 15 Feb 2019 09:08:54: start model_add_line... INFO @ Fri, 15 Feb 2019 09:08:54: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:08:54: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:08:54: #1 total tags in treatment: 1022504 INFO @ Fri, 15 Feb 2019 09:08:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:08:54: #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 09:08:54: start X-correlation... INFO @ Fri, 15 Feb 2019 09:08:54: end of X-cor INFO @ Fri, 15 Feb 2019 09:08:54: #2 finished! INFO @ Fri, 15 Feb 2019 09:08:54: #2 predicted fragment length is 193 bps INFO @ Fri, 15 Feb 2019 09:08:54: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 15 Feb 2019 09:08:54: #2.2 Generate R script for model : ERX1420300.05_model.r INFO @ Fri, 15 Feb 2019 09:08:54: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:08:54: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:08:54: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:08:54: #1 total tags in treatment: 1022504 INFO @ Fri, 15 Feb 2019 09:08:54: #1 tags after filtering in treatment: 1022504 INFO @ Fri, 15 Feb 2019 09:08:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:08:54: #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 09:08:54: #1 finished! INFO @ Fri, 15 Feb 2019 09:08:54: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:08:54: #1 tags after filtering in treatment: 1022504 INFO @ Fri, 15 Feb 2019 09:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:08:54: #1 finished! INFO @ Fri, 15 Feb 2019 09:08:54: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:08:54: #2 number of paired peaks: 184 WARNING @ Fri, 15 Feb 2019 09:08:54: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 15 Feb 2019 09:08:54: start model_add_line... INFO @ Fri, 15 Feb 2019 09:08:54: start X-correlation... INFO @ Fri, 15 Feb 2019 09:08:54: end of X-cor INFO @ Fri, 15 Feb 2019 09:08:54: #2 finished! INFO @ Fri, 15 Feb 2019 09:08:54: #2 predicted fragment length is 193 bps INFO @ Fri, 15 Feb 2019 09:08:54: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 15 Feb 2019 09:08:54: #2.2 Generate R script for model : ERX1420300.10_model.r INFO @ Fri, 15 Feb 2019 09:08:54: #2 number of paired peaks: 184 WARNING @ Fri, 15 Feb 2019 09:08:54: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 15 Feb 2019 09:08:54: start model_add_line... INFO @ Fri, 15 Feb 2019 09:08:54: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:08:54: start X-correlation... INFO @ Fri, 15 Feb 2019 09:08:54: end of X-cor INFO @ Fri, 15 Feb 2019 09:08:54: #2 finished! INFO @ Fri, 15 Feb 2019 09:08:54: #2 predicted fragment length is 193 bps INFO @ Fri, 15 Feb 2019 09:08:54: #2 alternative fragment length(s) may be 193 bps INFO @ Fri, 15 Feb 2019 09:08:54: #2.2 Generate R script for model : ERX1420300.20_model.r INFO @ Fri, 15 Feb 2019 09:08:54: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:08:57: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:08:57: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:08:57: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:08:59: #4 Write output xls file... ERX1420300.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:08:59: #4 Write peak in narrowPeak format file... ERX1420300.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:08:59: #4 Write summits bed file... ERX1420300.10_summits.bed INFO @ Fri, 15 Feb 2019 09:08:59: Done! INFO @ Fri, 15 Feb 2019 09:08:59: #4 Write output xls file... ERX1420300.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:08:59: #4 Write peak in narrowPeak format file... ERX1420300.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:08:59: #4 Write summits bed file... ERX1420300.20_summits.bed INFO @ Fri, 15 Feb 2019 09:08:59: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (1016 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:08:59: #4 Write output xls file... ERX1420300.05_peaks.xls pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (382 records, 4 fields): 4 millis INFO @ Fri, 15 Feb 2019 09:08:59: #4 Write peak in narrowPeak format file... ERX1420300.05_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:08:59: #4 Write summits bed file... ERX1420300.05_summits.bed INFO @ Fri, 15 Feb 2019 09:08:59: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (1933 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。