Job ID = 2009665 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 182,125 reads read : 182,125 reads written : 182,125 spots read : 3,655,170 reads read : 3,655,170 reads written : 3,655,170 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: 00:00:39 3837295 reads; of these: 3837295 (100.00%) were unpaired; of these: 1879254 (48.97%) aligned 0 times 1613247 (42.04%) aligned exactly 1 time 344794 (8.99%) aligned >1 times 51.03% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 1412106 / 1958041 = 0.7212 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, 05 Jul 2019 19:34:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.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, 05 Jul 2019 19:34:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:34:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.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, 05 Jul 2019 19:34:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:34:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:34:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.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, 05 Jul 2019 19:34:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:34:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:34:39: #1 tag size is determined as 37 bps INFO @ Fri, 05 Jul 2019 19:34:39: #1 tag size = 37 INFO @ Fri, 05 Jul 2019 19:34:39: #1 total tags in treatment: 545935 INFO @ Fri, 05 Jul 2019 19:34:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:34:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:34:39: #1 tags after filtering in treatment: 545935 INFO @ Fri, 05 Jul 2019 19:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:34:39: #1 finished! INFO @ Fri, 05 Jul 2019 19:34:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:34:39: #2 number of paired peaks: 109 WARNING @ Fri, 05 Jul 2019 19:34:39: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Fri, 05 Jul 2019 19:34:39: start model_add_line... INFO @ Fri, 05 Jul 2019 19:34:39: start X-correlation... INFO @ Fri, 05 Jul 2019 19:34:39: end of X-cor INFO @ Fri, 05 Jul 2019 19:34:39: #2 finished! INFO @ Fri, 05 Jul 2019 19:34:39: #2 predicted fragment length is 171 bps INFO @ Fri, 05 Jul 2019 19:34:39: #2 alternative fragment length(s) may be 151,171 bps INFO @ Fri, 05 Jul 2019 19:34:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.05_model.r INFO @ Fri, 05 Jul 2019 19:34:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:34:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:34:40: #1 tag size is determined as 37 bps INFO @ Fri, 05 Jul 2019 19:34:40: #1 tag size = 37 INFO @ Fri, 05 Jul 2019 19:34:40: #1 total tags in treatment: 545935 INFO @ Fri, 05 Jul 2019 19:34:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:34:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:34:40: #1 tags after filtering in treatment: 545935 INFO @ Fri, 05 Jul 2019 19:34:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:34:40: #1 finished! INFO @ Fri, 05 Jul 2019 19:34:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:34:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:34:40: #2 number of paired peaks: 109 WARNING @ Fri, 05 Jul 2019 19:34:40: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Fri, 05 Jul 2019 19:34:40: start model_add_line... INFO @ Fri, 05 Jul 2019 19:34:40: start X-correlation... INFO @ Fri, 05 Jul 2019 19:34:40: end of X-cor INFO @ Fri, 05 Jul 2019 19:34:40: #2 finished! INFO @ Fri, 05 Jul 2019 19:34:40: #2 predicted fragment length is 171 bps INFO @ Fri, 05 Jul 2019 19:34:40: #2 alternative fragment length(s) may be 151,171 bps INFO @ Fri, 05 Jul 2019 19:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.10_model.r INFO @ Fri, 05 Jul 2019 19:34:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:34:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:34:41: #1 tag size is determined as 37 bps INFO @ Fri, 05 Jul 2019 19:34:41: #1 tag size = 37 INFO @ Fri, 05 Jul 2019 19:34:41: #1 total tags in treatment: 545935 INFO @ Fri, 05 Jul 2019 19:34:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:34:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:34:41: #1 tags after filtering in treatment: 545935 INFO @ Fri, 05 Jul 2019 19:34:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:34:41: #1 finished! INFO @ Fri, 05 Jul 2019 19:34:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:34:41: #2 number of paired peaks: 109 WARNING @ Fri, 05 Jul 2019 19:34:41: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Fri, 05 Jul 2019 19:34:41: start model_add_line... INFO @ Fri, 05 Jul 2019 19:34:41: start X-correlation... INFO @ Fri, 05 Jul 2019 19:34:41: end of X-cor INFO @ Fri, 05 Jul 2019 19:34:41: #2 finished! INFO @ Fri, 05 Jul 2019 19:34:41: #2 predicted fragment length is 171 bps INFO @ Fri, 05 Jul 2019 19:34:41: #2 alternative fragment length(s) may be 151,171 bps INFO @ Fri, 05 Jul 2019 19:34:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.20_model.r INFO @ Fri, 05 Jul 2019 19:34:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.05_summits.bed INFO @ Fri, 05 Jul 2019 19:34:42: Done! INFO @ Fri, 05 Jul 2019 19:34:42: #3 Call peaks for each chromosome... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 19:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.10_summits.bed INFO @ Fri, 05 Jul 2019 19:34:43: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (209 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 19:34:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:34:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX100855/SRX100855.20_summits.bed INFO @ Fri, 05 Jul 2019 19:34:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (94 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。