Job ID = 11633961 sra ファイルのダウンロード中... Completed: 634341K bytes transferred in 9 seconds (556367K 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 19876774 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1424548/ERR1353073.sra Written 19876774 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1424548/ERR1353073.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: 00:02:05 19876774 reads; of these: 19876774 (100.00%) were unpaired; of these: 14508125 (72.99%) aligned 0 times 3378717 (17.00%) aligned exactly 1 time 1989932 (10.01%) aligned >1 times 27.01% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 4508541 / 5368649 = 0.8398 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 09:22:30: # Command line: callpeak -t ERX1424548.bam -f BAM -g 12100000 -n ERX1424548.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1424548.05 # format = BAM # ChIP-seq file = ['ERX1424548.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 09:22:30: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:22:30: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:22:30: # Command line: callpeak -t ERX1424548.bam -f BAM -g 12100000 -n ERX1424548.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1424548.10 # format = BAM # ChIP-seq file = ['ERX1424548.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 09:22:30: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:22:30: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:22:30: # Command line: callpeak -t ERX1424548.bam -f BAM -g 12100000 -n ERX1424548.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1424548.20 # format = BAM # ChIP-seq file = ['ERX1424548.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 09:22:30: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:22:30: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:22:35: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:22:35: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:22:35: #1 total tags in treatment: 860108 INFO @ Fri, 15 Feb 2019 09:22:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:22:35: #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 09:22:35: #1 tags after filtering in treatment: 860108 INFO @ Fri, 15 Feb 2019 09:22:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:22:35: #1 finished! INFO @ Fri, 15 Feb 2019 09:22:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:22:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:22:35: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:22:35: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:22:35: #1 total tags in treatment: 860108 INFO @ Fri, 15 Feb 2019 09:22:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:22:35: #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 09:22:35: #1 tags after filtering in treatment: 860108 INFO @ Fri, 15 Feb 2019 09:22:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:22:35: #1 finished! INFO @ Fri, 15 Feb 2019 09:22:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:22:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:22:36: #2 number of paired peaks: 556 WARNING @ Fri, 15 Feb 2019 09:22:36: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Fri, 15 Feb 2019 09:22:36: start model_add_line... INFO @ Fri, 15 Feb 2019 09:22:36: start X-correlation... INFO @ Fri, 15 Feb 2019 09:22:36: #2 number of paired peaks: 556 WARNING @ Fri, 15 Feb 2019 09:22:36: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Fri, 15 Feb 2019 09:22:36: start model_add_line... INFO @ Fri, 15 Feb 2019 09:22:36: end of X-cor INFO @ Fri, 15 Feb 2019 09:22:36: #2 finished! INFO @ Fri, 15 Feb 2019 09:22:36: #2 predicted fragment length is 174 bps INFO @ Fri, 15 Feb 2019 09:22:36: #2 alternative fragment length(s) may be 174 bps INFO @ Fri, 15 Feb 2019 09:22:36: #2.2 Generate R script for model : ERX1424548.20_model.r INFO @ Fri, 15 Feb 2019 09:22:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:22:36: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:22:36: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:22:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:22:36: #1 total tags in treatment: 860108 INFO @ Fri, 15 Feb 2019 09:22:36: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:22:36: #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 09:22:36: start X-correlation... INFO @ Fri, 15 Feb 2019 09:22:36: end of X-cor INFO @ Fri, 15 Feb 2019 09:22:36: #2 finished! INFO @ Fri, 15 Feb 2019 09:22:36: #2 predicted fragment length is 174 bps INFO @ Fri, 15 Feb 2019 09:22:36: #2 alternative fragment length(s) may be 174 bps INFO @ Fri, 15 Feb 2019 09:22:36: #2.2 Generate R script for model : ERX1424548.10_model.r INFO @ Fri, 15 Feb 2019 09:22:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:22:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:22:36: #1 tags after filtering in treatment: 860108 INFO @ Fri, 15 Feb 2019 09:22:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:22:36: #1 finished! INFO @ Fri, 15 Feb 2019 09:22:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:22:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:22:36: #2 number of paired peaks: 556 WARNING @ Fri, 15 Feb 2019 09:22:36: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Fri, 15 Feb 2019 09:22:36: start model_add_line... INFO @ Fri, 15 Feb 2019 09:22:36: start X-correlation... INFO @ Fri, 15 Feb 2019 09:22:36: end of X-cor INFO @ Fri, 15 Feb 2019 09:22:36: #2 finished! INFO @ Fri, 15 Feb 2019 09:22:36: #2 predicted fragment length is 174 bps INFO @ Fri, 15 Feb 2019 09:22:36: #2 alternative fragment length(s) may be 174 bps INFO @ Fri, 15 Feb 2019 09:22:36: #2.2 Generate R script for model : ERX1424548.05_model.r INFO @ Fri, 15 Feb 2019 09:22:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:22:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:22:39: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:22:39: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:22:39: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:22:40: #4 Write output xls file... ERX1424548.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:22:40: #4 Write peak in narrowPeak format file... ERX1424548.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:22:40: #4 Write summits bed file... ERX1424548.20_summits.bed INFO @ Fri, 15 Feb 2019 09:22:40: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (785 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:22:40: #4 Write output xls file... ERX1424548.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:22:40: #4 Write peak in narrowPeak format file... ERX1424548.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:22:40: #4 Write summits bed file... ERX1424548.10_summits.bed INFO @ Fri, 15 Feb 2019 09:22:40: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (1231 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:22:41: #4 Write output xls file... ERX1424548.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:22:41: #4 Write peak in narrowPeak format file... ERX1424548.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:22:41: #4 Write summits bed file... ERX1424548.05_summits.bed INFO @ Fri, 15 Feb 2019 09:22:41: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1751 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。