Job ID = 11633812 sra ファイルのダウンロード中... Completed: 11632K bytes transferred in 2 seconds (33369K 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 343242 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420430/ERR1348906.sra Written 343242 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420430/ERR1348906.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: 00:00:03 343242 reads; of these: 343242 (100.00%) were unpaired; of these: 33225 (9.68%) aligned 0 times 253529 (73.86%) aligned exactly 1 time 56488 (16.46%) aligned >1 times 90.32% overall alignment rate Time searching: 00:00:03 Overall time: 00:00:04 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] 23110 / 310017 = 0.0745 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 09:13:01: # Command line: callpeak -t ERX1420430.bam -f BAM -g 12100000 -n ERX1420430.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420430.20 # format = BAM # ChIP-seq file = ['ERX1420430.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 09:13:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:13:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:13:01: # Command line: callpeak -t ERX1420430.bam -f BAM -g 12100000 -n ERX1420430.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420430.05 # format = BAM # ChIP-seq file = ['ERX1420430.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 09:13:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:13:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:13:01: # Command line: callpeak -t ERX1420430.bam -f BAM -g 12100000 -n ERX1420430.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420430.10 # format = BAM # ChIP-seq file = ['ERX1420430.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 09:13:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:13:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:13:03: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:13:03: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:13:03: #1 total tags in treatment: 286907 INFO @ Fri, 15 Feb 2019 09:13:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:13:03: #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 09:13:03: #1 tags after filtering in treatment: 286907 INFO @ Fri, 15 Feb 2019 09:13:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:13:03: #1 finished! INFO @ Fri, 15 Feb 2019 09:13:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:13:03: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:13:03: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:13:03: #1 total tags in treatment: 286907 INFO @ Fri, 15 Feb 2019 09:13:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:13:03: #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 09:13:03: #1 tags after filtering in treatment: 286907 INFO @ Fri, 15 Feb 2019 09:13:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:13:03: #1 finished! INFO @ Fri, 15 Feb 2019 09:13:03: #2 number of paired peaks: 158 INFO @ Fri, 15 Feb 2019 09:13:03: #2 Build Peak Model... WARNING @ Fri, 15 Feb 2019 09:13:03: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 15 Feb 2019 09:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:13:03: start model_add_line... INFO @ Fri, 15 Feb 2019 09:13:03: start X-correlation... INFO @ Fri, 15 Feb 2019 09:13:03: end of X-cor INFO @ Fri, 15 Feb 2019 09:13:03: #2 finished! INFO @ Fri, 15 Feb 2019 09:13:03: #2 predicted fragment length is 207 bps INFO @ Fri, 15 Feb 2019 09:13:03: #2 alternative fragment length(s) may be 3,141,207,243,266,343,495,533,551,586 bps INFO @ Fri, 15 Feb 2019 09:13:03: #2.2 Generate R script for model : ERX1420430.05_model.r INFO @ Fri, 15 Feb 2019 09:13:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:13:03: #2 number of paired peaks: 158 WARNING @ Fri, 15 Feb 2019 09:13:03: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 15 Feb 2019 09:13:03: start model_add_line... INFO @ Fri, 15 Feb 2019 09:13:03: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:13:03: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:13:03: #1 total tags in treatment: 286907 INFO @ Fri, 15 Feb 2019 09:13:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:13:03: #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 09:13:03: start X-correlation... INFO @ Fri, 15 Feb 2019 09:13:03: end of X-cor INFO @ Fri, 15 Feb 2019 09:13:03: #2 finished! INFO @ Fri, 15 Feb 2019 09:13:03: #2 predicted fragment length is 207 bps INFO @ Fri, 15 Feb 2019 09:13:03: #2 alternative fragment length(s) may be 3,141,207,243,266,343,495,533,551,586 bps INFO @ Fri, 15 Feb 2019 09:13:03: #2.2 Generate R script for model : ERX1420430.20_model.r INFO @ Fri, 15 Feb 2019 09:13:03: #1 tags after filtering in treatment: 286907 INFO @ Fri, 15 Feb 2019 09:13:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:13:03: #1 finished! INFO @ Fri, 15 Feb 2019 09:13:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:13:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:13:03: #2 number of paired peaks: 158 WARNING @ Fri, 15 Feb 2019 09:13:03: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 15 Feb 2019 09:13:03: start model_add_line... INFO @ Fri, 15 Feb 2019 09:13:03: start X-correlation... INFO @ Fri, 15 Feb 2019 09:13:03: end of X-cor INFO @ Fri, 15 Feb 2019 09:13:03: #2 finished! INFO @ Fri, 15 Feb 2019 09:13:03: #2 predicted fragment length is 207 bps INFO @ Fri, 15 Feb 2019 09:13:03: #2 alternative fragment length(s) may be 3,141,207,243,266,343,495,533,551,586 bps INFO @ Fri, 15 Feb 2019 09:13:03: #2.2 Generate R script for model : ERX1420430.10_model.r INFO @ Fri, 15 Feb 2019 09:13:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:13:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:13:04: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:13:04: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:13:04: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:13:04: #4 Write output xls file... ERX1420430.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:13:04: #4 Write peak in narrowPeak format file... ERX1420430.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:13:04: #4 Write summits bed file... ERX1420430.05_summits.bed INFO @ Fri, 15 Feb 2019 09:13:04: Done! INFO @ Fri, 15 Feb 2019 09:13:04: #4 Write output xls file... ERX1420430.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:13:04: #4 Write peak in narrowPeak format file... ERX1420430.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:13:04: #4 Write summits bed file... ERX1420430.20_summits.bed pass1 - making usageList (4 chroms): 8 millis INFO @ Fri, 15 Feb 2019 09:13:04: Done! pass2 - checking and writing primary data (11 records, 4 fields): 6 millis INFO @ Fri, 15 Feb 2019 09:13:04: #4 Write output xls file... ERX1420430.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:13:04: #4 Write peak in narrowPeak format file... ERX1420430.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:13:04: #4 Write summits bed file... ERX1420430.10_summits.bed INFO @ Fri, 15 Feb 2019 09:13:04: Done! CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 8 millis pass2 - checking and writing primary data (2 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 6 millis pass2 - checking and writing primary data (3 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。