Job ID = 4289553 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,984,811 reads read : 4,984,811 reads written : 4,984,811 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:37 4984811 reads; of these: 4984811 (100.00%) were unpaired; of these: 1611464 (32.33%) aligned 0 times 3160088 (63.39%) aligned exactly 1 time 213259 (4.28%) aligned >1 times 67.67% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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] 2040456 / 3373347 = 0.6049 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.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 @ Tue, 10 Dec 2019 14:48:45: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:48:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:48:55: 1000000 INFO @ Tue, 10 Dec 2019 14:48:57: #1 tag size is determined as 40 bps INFO @ Tue, 10 Dec 2019 14:48:57: #1 tag size = 40 INFO @ Tue, 10 Dec 2019 14:48:57: #1 total tags in treatment: 1332891 INFO @ Tue, 10 Dec 2019 14:48:57: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:48:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:48:57: #1 tags after filtering in treatment: 1332891 INFO @ Tue, 10 Dec 2019 14:48:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:48:57: #1 finished! INFO @ Tue, 10 Dec 2019 14:48:57: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:48:58: #2 number of paired peaks: 524 WARNING @ Tue, 10 Dec 2019 14:48:58: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Tue, 10 Dec 2019 14:48:58: start model_add_line... INFO @ Tue, 10 Dec 2019 14:48:58: start X-correlation... INFO @ Tue, 10 Dec 2019 14:48:58: end of X-cor INFO @ Tue, 10 Dec 2019 14:48:58: #2 finished! INFO @ Tue, 10 Dec 2019 14:48:58: #2 predicted fragment length is 115 bps INFO @ Tue, 10 Dec 2019 14:48:58: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 10 Dec 2019 14:48:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.05_model.r INFO @ Tue, 10 Dec 2019 14:48:58: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:48:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:49:02: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:49:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.05_peaks.xls INFO @ Tue, 10 Dec 2019 14:49:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:49:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.05_summits.bed INFO @ Tue, 10 Dec 2019 14:49:04: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2909 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.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 @ Tue, 10 Dec 2019 14:49:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:49:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:49:24: 1000000 INFO @ Tue, 10 Dec 2019 14:49:27: #1 tag size is determined as 40 bps INFO @ Tue, 10 Dec 2019 14:49:27: #1 tag size = 40 INFO @ Tue, 10 Dec 2019 14:49:27: #1 total tags in treatment: 1332891 INFO @ Tue, 10 Dec 2019 14:49:27: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:49:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:49:27: #1 tags after filtering in treatment: 1332891 INFO @ Tue, 10 Dec 2019 14:49:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:49:27: #1 finished! INFO @ Tue, 10 Dec 2019 14:49:27: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:49:27: #2 number of paired peaks: 524 WARNING @ Tue, 10 Dec 2019 14:49:27: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Tue, 10 Dec 2019 14:49:27: start model_add_line... INFO @ Tue, 10 Dec 2019 14:49:27: start X-correlation... INFO @ Tue, 10 Dec 2019 14:49:27: end of X-cor INFO @ Tue, 10 Dec 2019 14:49:27: #2 finished! INFO @ Tue, 10 Dec 2019 14:49:27: #2 predicted fragment length is 115 bps INFO @ Tue, 10 Dec 2019 14:49:27: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 10 Dec 2019 14:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.10_model.r INFO @ Tue, 10 Dec 2019 14:49:27: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:49:32: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:49:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.10_peaks.xls INFO @ Tue, 10 Dec 2019 14:49:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:49:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.10_summits.bed INFO @ Tue, 10 Dec 2019 14:49:34: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2287 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.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 @ Tue, 10 Dec 2019 14:49:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:49:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:49:55: 1000000 INFO @ Tue, 10 Dec 2019 14:49:58: #1 tag size is determined as 40 bps INFO @ Tue, 10 Dec 2019 14:49:58: #1 tag size = 40 INFO @ Tue, 10 Dec 2019 14:49:58: #1 total tags in treatment: 1332891 INFO @ Tue, 10 Dec 2019 14:49:58: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:49:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:49:58: #1 tags after filtering in treatment: 1332891 INFO @ Tue, 10 Dec 2019 14:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:49:58: #1 finished! INFO @ Tue, 10 Dec 2019 14:49:58: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:49:58: #2 number of paired peaks: 524 WARNING @ Tue, 10 Dec 2019 14:49:58: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Tue, 10 Dec 2019 14:49:58: start model_add_line... INFO @ Tue, 10 Dec 2019 14:49:58: start X-correlation... INFO @ Tue, 10 Dec 2019 14:49:58: end of X-cor INFO @ Tue, 10 Dec 2019 14:49:58: #2 finished! INFO @ Tue, 10 Dec 2019 14:49:58: #2 predicted fragment length is 115 bps INFO @ Tue, 10 Dec 2019 14:49:58: #2 alternative fragment length(s) may be 115 bps INFO @ Tue, 10 Dec 2019 14:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.20_model.r INFO @ Tue, 10 Dec 2019 14:49:58: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:49:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:50:02: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:50:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.20_peaks.xls INFO @ Tue, 10 Dec 2019 14:50:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:50:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932543/SRX6932543.20_summits.bed INFO @ Tue, 10 Dec 2019 14:50:04: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1445 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。