Job ID = 11193098 sra ファイルのダウンロード中... Completed: 46711K bytes transferred in 3 seconds (97205K 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 2385333 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234068/SRR7361033.sra Written 2385333 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234068/SRR7361033.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 2385333 reads; of these: 2385333 (100.00%) were unpaired; of these: 54474 (2.28%) aligned 0 times 2042159 (85.61%) aligned exactly 1 time 288700 (12.10%) aligned >1 times 97.72% 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] 291672 / 2330859 = 0.1251 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 @ Sat, 15 Sep 2018 10:56:16: # Command line: callpeak -t SRX4234068.bam -f BAM -g 12100000 -n SRX4234068.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4234068.10 # format = BAM # ChIP-seq file = ['SRX4234068.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 @ Sat, 15 Sep 2018 10:56:16: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:56:16: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:56:16: # Command line: callpeak -t SRX4234068.bam -f BAM -g 12100000 -n SRX4234068.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4234068.05 # format = BAM # ChIP-seq file = ['SRX4234068.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 @ Sat, 15 Sep 2018 10:56:16: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:56:16: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:56:16: # Command line: callpeak -t SRX4234068.bam -f BAM -g 12100000 -n SRX4234068.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4234068.20 # format = BAM # ChIP-seq file = ['SRX4234068.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 @ Sat, 15 Sep 2018 10:56:16: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:56:16: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:56:24: 1000000 INFO @ Sat, 15 Sep 2018 10:56:24: 1000000 INFO @ Sat, 15 Sep 2018 10:56:25: 1000000 INFO @ Sat, 15 Sep 2018 10:56:33: 2000000 INFO @ Sat, 15 Sep 2018 10:56:33: 2000000 INFO @ Sat, 15 Sep 2018 10:56:33: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 10:56:33: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 10:56:33: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 10:56:33: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 10:56:33: #1 total tags in treatment: 2039187 INFO @ Sat, 15 Sep 2018 10:56:33: #1 total tags in treatment: 2039187 INFO @ Sat, 15 Sep 2018 10:56:33: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:56:33: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:56:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:56:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:56:33: #1 tags after filtering in treatment: 2039187 INFO @ Sat, 15 Sep 2018 10:56:33: #1 tags after filtering in treatment: 2039187 INFO @ Sat, 15 Sep 2018 10:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:56:33: #1 finished! INFO @ Sat, 15 Sep 2018 10:56:33: #1 finished! INFO @ Sat, 15 Sep 2018 10:56:33: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:56:33: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:56:33: #2 number of paired peaks: 115 WARNING @ Sat, 15 Sep 2018 10:56:33: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 15 Sep 2018 10:56:33: start model_add_line... INFO @ Sat, 15 Sep 2018 10:56:33: #2 number of paired peaks: 115 WARNING @ Sat, 15 Sep 2018 10:56:33: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 15 Sep 2018 10:56:33: start model_add_line... INFO @ Sat, 15 Sep 2018 10:56:33: start X-correlation... INFO @ Sat, 15 Sep 2018 10:56:33: start X-correlation... INFO @ Sat, 15 Sep 2018 10:56:33: end of X-cor INFO @ Sat, 15 Sep 2018 10:56:33: end of X-cor INFO @ Sat, 15 Sep 2018 10:56:33: #2 finished! INFO @ Sat, 15 Sep 2018 10:56:33: #2 finished! INFO @ Sat, 15 Sep 2018 10:56:33: #2 predicted fragment length is 337 bps INFO @ Sat, 15 Sep 2018 10:56:33: #2 predicted fragment length is 337 bps INFO @ Sat, 15 Sep 2018 10:56:33: #2 alternative fragment length(s) may be 4,337 bps INFO @ Sat, 15 Sep 2018 10:56:33: #2 alternative fragment length(s) may be 4,337 bps INFO @ Sat, 15 Sep 2018 10:56:33: #2.2 Generate R script for model : SRX4234068.05_model.r INFO @ Sat, 15 Sep 2018 10:56:33: #2.2 Generate R script for model : SRX4234068.10_model.r INFO @ Sat, 15 Sep 2018 10:56:33: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:56:33: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:56:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:56:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:56:33: 2000000 INFO @ Sat, 15 Sep 2018 10:56:34: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 10:56:34: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 10:56:34: #1 total tags in treatment: 2039187 INFO @ Sat, 15 Sep 2018 10:56:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:56:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:56:34: #1 tags after filtering in treatment: 2039187 INFO @ Sat, 15 Sep 2018 10:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:56:34: #1 finished! INFO @ Sat, 15 Sep 2018 10:56:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:56:34: #2 number of paired peaks: 115 WARNING @ Sat, 15 Sep 2018 10:56:34: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 15 Sep 2018 10:56:34: start model_add_line... INFO @ Sat, 15 Sep 2018 10:56:34: start X-correlation... INFO @ Sat, 15 Sep 2018 10:56:34: end of X-cor INFO @ Sat, 15 Sep 2018 10:56:34: #2 finished! INFO @ Sat, 15 Sep 2018 10:56:34: #2 predicted fragment length is 337 bps INFO @ Sat, 15 Sep 2018 10:56:34: #2 alternative fragment length(s) may be 4,337 bps INFO @ Sat, 15 Sep 2018 10:56:34: #2.2 Generate R script for model : SRX4234068.20_model.r INFO @ Sat, 15 Sep 2018 10:56:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:56:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:56:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:56:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:56:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:56:42: #4 Write output xls file... SRX4234068.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:56:42: #4 Write peak in narrowPeak format file... SRX4234068.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:56:42: #4 Write summits bed file... SRX4234068.10_summits.bed INFO @ Sat, 15 Sep 2018 10:56:42: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (33 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:56:42: #4 Write output xls file... SRX4234068.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:56:42: #4 Write peak in narrowPeak format file... SRX4234068.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:56:42: #4 Write summits bed file... SRX4234068.05_summits.bed INFO @ Sat, 15 Sep 2018 10:56:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:56:43: #4 Write output xls file... SRX4234068.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:56:43: #4 Write peak in narrowPeak format file... SRX4234068.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:56:43: #4 Write summits bed file... SRX4234068.20_summits.bed INFO @ Sat, 15 Sep 2018 10:56:43: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。