Job ID = 11633844 sra ファイルのダウンロード中... Completed: 92354K bytes transferred in 4 seconds (176081K 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 2855138 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420461/ERR1348937.sra Written 2855138 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420461/ERR1348937.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 2855138 reads; of these: 2855138 (100.00%) were unpaired; of these: 337409 (11.82%) aligned 0 times 1942716 (68.04%) aligned exactly 1 time 575013 (20.14%) aligned >1 times 88.18% 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] 608220 / 2517729 = 0.2416 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 09:16:37: # Command line: callpeak -t ERX1420461.bam -f BAM -g 12100000 -n ERX1420461.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420461.20 # format = BAM # ChIP-seq file = ['ERX1420461.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 09:16:37: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:16:37: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:16:37: # Command line: callpeak -t ERX1420461.bam -f BAM -g 12100000 -n ERX1420461.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420461.10 # format = BAM # ChIP-seq file = ['ERX1420461.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 09:16:37: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:16:37: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:16:37: # Command line: callpeak -t ERX1420461.bam -f BAM -g 12100000 -n ERX1420461.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420461.05 # format = BAM # ChIP-seq file = ['ERX1420461.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 09:16:37: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:16:37: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:16:44: 1000000 INFO @ Fri, 15 Feb 2019 09:16:44: 1000000 INFO @ Fri, 15 Feb 2019 09:16:44: 1000000 INFO @ Fri, 15 Feb 2019 09:16:50: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:16:50: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:16:50: #1 total tags in treatment: 1909509 INFO @ Fri, 15 Feb 2019 09:16:50: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:16:50: #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 09:16:50: #1 tags after filtering in treatment: 1909509 INFO @ Fri, 15 Feb 2019 09:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:16:50: #1 finished! INFO @ Fri, 15 Feb 2019 09:16:50: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:16:50: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:16:50: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:16:50: #1 total tags in treatment: 1909509 INFO @ Fri, 15 Feb 2019 09:16:50: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:16:50: #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 09:16:50: #1 tags after filtering in treatment: 1909509 INFO @ Fri, 15 Feb 2019 09:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:16:50: #1 finished! INFO @ Fri, 15 Feb 2019 09:16:50: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:16:50: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:16:50: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:16:50: #1 total tags in treatment: 1909509 INFO @ Fri, 15 Feb 2019 09:16:50: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:16:50: #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 09:16:50: #1 tags after filtering in treatment: 1909509 INFO @ Fri, 15 Feb 2019 09:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:16:50: #1 finished! INFO @ Fri, 15 Feb 2019 09:16:50: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:16:50: #2 number of paired peaks: 107 WARNING @ Fri, 15 Feb 2019 09:16:50: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Fri, 15 Feb 2019 09:16:50: start model_add_line... INFO @ Fri, 15 Feb 2019 09:16:50: start X-correlation... INFO @ Fri, 15 Feb 2019 09:16:50: end of X-cor INFO @ Fri, 15 Feb 2019 09:16:50: #2 finished! INFO @ Fri, 15 Feb 2019 09:16:50: #2 predicted fragment length is 312 bps INFO @ Fri, 15 Feb 2019 09:16:50: #2 alternative fragment length(s) may be 312 bps INFO @ Fri, 15 Feb 2019 09:16:50: #2.2 Generate R script for model : ERX1420461.20_model.r INFO @ Fri, 15 Feb 2019 09:16:50: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:16:50: #2 number of paired peaks: 107 WARNING @ Fri, 15 Feb 2019 09:16:50: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Fri, 15 Feb 2019 09:16:50: start model_add_line... INFO @ Fri, 15 Feb 2019 09:16:50: start X-correlation... INFO @ Fri, 15 Feb 2019 09:16:50: end of X-cor INFO @ Fri, 15 Feb 2019 09:16:50: #2 finished! INFO @ Fri, 15 Feb 2019 09:16:50: #2 predicted fragment length is 312 bps INFO @ Fri, 15 Feb 2019 09:16:50: #2 alternative fragment length(s) may be 312 bps INFO @ Fri, 15 Feb 2019 09:16:50: #2.2 Generate R script for model : ERX1420461.05_model.r INFO @ Fri, 15 Feb 2019 09:16:50: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:16:50: #2 number of paired peaks: 107 WARNING @ Fri, 15 Feb 2019 09:16:50: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Fri, 15 Feb 2019 09:16:50: start model_add_line... INFO @ Fri, 15 Feb 2019 09:16:50: start X-correlation... INFO @ Fri, 15 Feb 2019 09:16:50: end of X-cor INFO @ Fri, 15 Feb 2019 09:16:50: #2 finished! INFO @ Fri, 15 Feb 2019 09:16:50: #2 predicted fragment length is 312 bps INFO @ Fri, 15 Feb 2019 09:16:50: #2 alternative fragment length(s) may be 312 bps INFO @ Fri, 15 Feb 2019 09:16:50: #2.2 Generate R script for model : ERX1420461.10_model.r INFO @ Fri, 15 Feb 2019 09:16:50: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:16:56: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:16:56: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:16:56: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:16:58: #4 Write output xls file... ERX1420461.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:16:58: #4 Write peak in narrowPeak format file... ERX1420461.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:16:58: #4 Write summits bed file... ERX1420461.20_summits.bed INFO @ Fri, 15 Feb 2019 09:16:58: Done! pass1 - making usageList (3 chroms): 3 millis pass2 - checking and writing primary data (30 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:16:58: #4 Write output xls file... ERX1420461.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:16:58: #4 Write peak in narrowPeak format file... ERX1420461.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:16:58: #4 Write summits bed file... ERX1420461.10_summits.bed INFO @ Fri, 15 Feb 2019 09:16:58: Done! pass1 - making usageList (5 chroms): 4 millis pass2 - checking and writing primary data (44 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:16:58: #4 Write output xls file... ERX1420461.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:16:58: #4 Write peak in narrowPeak format file... ERX1420461.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:16:58: #4 Write summits bed file... ERX1420461.05_summits.bed INFO @ Fri, 15 Feb 2019 09:16:58: Done! pass1 - making usageList (9 chroms): 3 millis pass2 - checking and writing primary data (54 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。