Job ID = 2010275 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,724,471 reads read : 8,724,471 reads written : 8,724,471 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: 00:01:23 8724471 reads; of these: 8724471 (100.00%) were unpaired; of these: 213393 (2.45%) aligned 0 times 7472692 (85.65%) aligned exactly 1 time 1038386 (11.90%) aligned >1 times 97.55% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 8239593 / 8511078 = 0.9681 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 22:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.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 22:04:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:04:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.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 22:04:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:04:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:04:27: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 22:04:27: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 22:04:27: #1 total tags in treatment: 271485 INFO @ Fri, 05 Jul 2019 22:04:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:04:27: #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 22:04:27: #1 tags after filtering in treatment: 271485 INFO @ Fri, 05 Jul 2019 22:04:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:04:27: #1 finished! INFO @ Fri, 05 Jul 2019 22:04:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:04:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:04:27: #2 number of paired peaks: 150 WARNING @ Fri, 05 Jul 2019 22:04:27: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Fri, 05 Jul 2019 22:04:27: start model_add_line... INFO @ Fri, 05 Jul 2019 22:04:27: start X-correlation... INFO @ Fri, 05 Jul 2019 22:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.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 22:04:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:04:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:04:27: end of X-cor INFO @ Fri, 05 Jul 2019 22:04:27: #2 finished! INFO @ Fri, 05 Jul 2019 22:04:27: #2 predicted fragment length is 123 bps INFO @ Fri, 05 Jul 2019 22:04:27: #2 alternative fragment length(s) may be 4,36,67,99,123,159,190,209,239,245,279,331,391,439,476,492,547,589 bps INFO @ Fri, 05 Jul 2019 22:04:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.05_model.r INFO @ Fri, 05 Jul 2019 22:04:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:04:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.05_peaks.xls INFO @ Fri, 05 Jul 2019 22:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.05_summits.bed INFO @ Fri, 05 Jul 2019 22:04:28: Done! INFO @ Fri, 05 Jul 2019 22:04:28: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 22:04:28: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 22:04:28: #1 total tags in treatment: 271485 INFO @ Fri, 05 Jul 2019 22:04:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:04:28: #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 22:04:28: #1 tags after filtering in treatment: 271485 INFO @ Fri, 05 Jul 2019 22:04:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:04:28: #1 finished! INFO @ Fri, 05 Jul 2019 22:04:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:04:28: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (144 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 22:04:28: #2 number of paired peaks: 150 WARNING @ Fri, 05 Jul 2019 22:04:28: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Fri, 05 Jul 2019 22:04:28: start model_add_line... INFO @ Fri, 05 Jul 2019 22:04:28: start X-correlation... INFO @ Fri, 05 Jul 2019 22:04:28: end of X-cor INFO @ Fri, 05 Jul 2019 22:04:28: #2 finished! INFO @ Fri, 05 Jul 2019 22:04:28: #2 predicted fragment length is 123 bps INFO @ Fri, 05 Jul 2019 22:04:28: #2 alternative fragment length(s) may be 4,36,67,99,123,159,190,209,239,245,279,331,391,439,476,492,547,589 bps INFO @ Fri, 05 Jul 2019 22:04:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.10_model.r INFO @ Fri, 05 Jul 2019 22:04:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:04:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:04:29: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 22:04:29: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 22:04:29: #1 total tags in treatment: 271485 INFO @ Fri, 05 Jul 2019 22:04:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:04:29: #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 22:04:29: #1 tags after filtering in treatment: 271485 INFO @ Fri, 05 Jul 2019 22:04:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:04:29: #1 finished! INFO @ Fri, 05 Jul 2019 22:04:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:04:29: #2 number of paired peaks: 150 WARNING @ Fri, 05 Jul 2019 22:04:29: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Fri, 05 Jul 2019 22:04:29: start model_add_line... INFO @ Fri, 05 Jul 2019 22:04:29: start X-correlation... INFO @ Fri, 05 Jul 2019 22:04:29: end of X-cor INFO @ Fri, 05 Jul 2019 22:04:29: #2 finished! INFO @ Fri, 05 Jul 2019 22:04:29: #2 predicted fragment length is 123 bps INFO @ Fri, 05 Jul 2019 22:04:29: #2 alternative fragment length(s) may be 4,36,67,99,123,159,190,209,239,245,279,331,391,439,476,492,547,589 bps INFO @ Fri, 05 Jul 2019 22:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.20_model.r INFO @ Fri, 05 Jul 2019 22:04:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:04:29: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:04:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.10_peaks.xls INFO @ Fri, 05 Jul 2019 22:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.10_summits.bed INFO @ Fri, 05 Jul 2019 22:04:30: Done! INFO @ Fri, 05 Jul 2019 22:04:30: #3 Call peaks for each chromosome... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 22:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.20_peaks.xls INFO @ Fri, 05 Jul 2019 22:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX332069/SRX332069.20_summits.bed INFO @ Fri, 05 Jul 2019 22:04:30: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。