Job ID = 2011870 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,618,130 reads read : 2,618,130 reads written : 2,618,130 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8433458.sra.cache’: 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: 00:00:30 2618130 reads; of these: 2618130 (100.00%) were unpaired; of these: 66059 (2.52%) aligned 0 times 1596526 (60.98%) aligned exactly 1 time 955545 (36.50%) aligned >1 times 97.48% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 864118 / 2552071 = 0.3386 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, 06 Jul 2019 02:55:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.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, 06 Jul 2019 02:55:23: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:55:23: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:55:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.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, 06 Jul 2019 02:55:24: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:55:24: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:55:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.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, 06 Jul 2019 02:55:25: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:55:25: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:55:30: 1000000 INFO @ Sat, 06 Jul 2019 02:55:32: 1000000 INFO @ Sat, 06 Jul 2019 02:55:33: 1000000 INFO @ Sat, 06 Jul 2019 02:55:35: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:55:35: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:55:35: #1 total tags in treatment: 1687953 INFO @ Sat, 06 Jul 2019 02:55:35: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:55:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:55:35: #1 tags after filtering in treatment: 1687953 INFO @ Sat, 06 Jul 2019 02:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:55:35: #1 finished! INFO @ Sat, 06 Jul 2019 02:55:35: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:55:35: #2 number of paired peaks: 139 WARNING @ Sat, 06 Jul 2019 02:55:35: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 06 Jul 2019 02:55:35: start model_add_line... INFO @ Sat, 06 Jul 2019 02:55:35: start X-correlation... INFO @ Sat, 06 Jul 2019 02:55:35: end of X-cor INFO @ Sat, 06 Jul 2019 02:55:35: #2 finished! INFO @ Sat, 06 Jul 2019 02:55:35: #2 predicted fragment length is 176 bps INFO @ Sat, 06 Jul 2019 02:55:35: #2 alternative fragment length(s) may be 4,176 bps INFO @ Sat, 06 Jul 2019 02:55:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.05_model.r INFO @ Sat, 06 Jul 2019 02:55:35: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:55:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:55:38: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:55:38: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:55:38: #1 total tags in treatment: 1687953 INFO @ Sat, 06 Jul 2019 02:55:38: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:55:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:55:38: #1 tags after filtering in treatment: 1687953 INFO @ Sat, 06 Jul 2019 02:55:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:55:38: #1 finished! INFO @ Sat, 06 Jul 2019 02:55:38: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:55:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:55:38: #2 number of paired peaks: 139 WARNING @ Sat, 06 Jul 2019 02:55:38: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 06 Jul 2019 02:55:38: start model_add_line... INFO @ Sat, 06 Jul 2019 02:55:38: start X-correlation... INFO @ Sat, 06 Jul 2019 02:55:38: end of X-cor INFO @ Sat, 06 Jul 2019 02:55:38: #2 finished! INFO @ Sat, 06 Jul 2019 02:55:38: #2 predicted fragment length is 176 bps INFO @ Sat, 06 Jul 2019 02:55:38: #2 alternative fragment length(s) may be 4,176 bps INFO @ Sat, 06 Jul 2019 02:55:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.10_model.r INFO @ Sat, 06 Jul 2019 02:55:38: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:55:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:55:39: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:55:39: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:55:39: #1 total tags in treatment: 1687953 INFO @ Sat, 06 Jul 2019 02:55:39: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:55:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:55:39: #1 tags after filtering in treatment: 1687953 INFO @ Sat, 06 Jul 2019 02:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:55:39: #1 finished! INFO @ Sat, 06 Jul 2019 02:55:39: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:55:39: #2 number of paired peaks: 139 WARNING @ Sat, 06 Jul 2019 02:55:39: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 06 Jul 2019 02:55:39: start model_add_line... INFO @ Sat, 06 Jul 2019 02:55:39: start X-correlation... INFO @ Sat, 06 Jul 2019 02:55:39: end of X-cor INFO @ Sat, 06 Jul 2019 02:55:39: #2 finished! INFO @ Sat, 06 Jul 2019 02:55:39: #2 predicted fragment length is 176 bps INFO @ Sat, 06 Jul 2019 02:55:39: #2 alternative fragment length(s) may be 4,176 bps INFO @ Sat, 06 Jul 2019 02:55:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.20_model.r INFO @ Sat, 06 Jul 2019 02:55:39: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:55:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:55:41: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:55:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:55:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.05_summits.bed INFO @ Sat, 06 Jul 2019 02:55:43: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (373 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:55:44: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:55:45: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:55:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:55:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:55:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.10_summits.bed INFO @ Sat, 06 Jul 2019 02:55:47: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5241177/SRX5241177.20_summits.bed INFO @ Sat, 06 Jul 2019 02:55:48: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。