Job ID = 2010075 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,073,804 reads read : 10,147,608 reads written : 5,073,804 reads 0-length : 5,073,804 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: 00:01:31 5073804 reads; of these: 5073804 (100.00%) were unpaired; of these: 695837 (13.71%) aligned 0 times 3787679 (74.65%) aligned exactly 1 time 590288 (11.63%) aligned >1 times 86.29% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 1028554 / 4377967 = 0.2349 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 21:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.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 21:15:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:15:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:15:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.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 21:15:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:15:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.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 21:15:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:15:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:15:15: 1000000 INFO @ Fri, 05 Jul 2019 21:15:16: 1000000 INFO @ Fri, 05 Jul 2019 21:15:18: 1000000 INFO @ Fri, 05 Jul 2019 21:15:25: 2000000 INFO @ Fri, 05 Jul 2019 21:15:29: 2000000 INFO @ Fri, 05 Jul 2019 21:15:32: 2000000 INFO @ Fri, 05 Jul 2019 21:15:36: 3000000 INFO @ Fri, 05 Jul 2019 21:15:40: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 21:15:40: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 21:15:40: #1 total tags in treatment: 3349413 INFO @ Fri, 05 Jul 2019 21:15:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:15:40: #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 21:15:40: #1 tags after filtering in treatment: 3349413 INFO @ Fri, 05 Jul 2019 21:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:15:40: #1 finished! INFO @ Fri, 05 Jul 2019 21:15:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:15:40: #2 number of paired peaks: 116 WARNING @ Fri, 05 Jul 2019 21:15:40: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Fri, 05 Jul 2019 21:15:40: start model_add_line... INFO @ Fri, 05 Jul 2019 21:15:40: start X-correlation... INFO @ Fri, 05 Jul 2019 21:15:40: end of X-cor INFO @ Fri, 05 Jul 2019 21:15:40: #2 finished! INFO @ Fri, 05 Jul 2019 21:15:40: #2 predicted fragment length is 3 bps INFO @ Fri, 05 Jul 2019 21:15:40: #2 alternative fragment length(s) may be 3,20,41,62,92 bps INFO @ Fri, 05 Jul 2019 21:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.10_model.r WARNING @ Fri, 05 Jul 2019 21:15:40: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:15:40: #2 You may need to consider one of the other alternative d(s): 3,20,41,62,92 WARNING @ Fri, 05 Jul 2019 21:15:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 21:15:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:15:42: 3000000 INFO @ Fri, 05 Jul 2019 21:15:45: 3000000 INFO @ Fri, 05 Jul 2019 21:15:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:15:47: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 21:15:47: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 21:15:47: #1 total tags in treatment: 3349413 INFO @ Fri, 05 Jul 2019 21:15:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:15:47: #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 21:15:47: #1 tags after filtering in treatment: 3349413 INFO @ Fri, 05 Jul 2019 21:15:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:15:47: #1 finished! INFO @ Fri, 05 Jul 2019 21:15:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:15:47: #2 number of paired peaks: 116 WARNING @ Fri, 05 Jul 2019 21:15:47: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Fri, 05 Jul 2019 21:15:47: start model_add_line... INFO @ Fri, 05 Jul 2019 21:15:47: start X-correlation... INFO @ Fri, 05 Jul 2019 21:15:47: end of X-cor INFO @ Fri, 05 Jul 2019 21:15:47: #2 finished! INFO @ Fri, 05 Jul 2019 21:15:47: #2 predicted fragment length is 3 bps INFO @ Fri, 05 Jul 2019 21:15:47: #2 alternative fragment length(s) may be 3,20,41,62,92 bps INFO @ Fri, 05 Jul 2019 21:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.05_model.r WARNING @ Fri, 05 Jul 2019 21:15:47: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:15:47: #2 You may need to consider one of the other alternative d(s): 3,20,41,62,92 WARNING @ Fri, 05 Jul 2019 21:15:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 21:15:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:15:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:15:49: #1 tag size is determined as 101 bps INFO @ Fri, 05 Jul 2019 21:15:49: #1 tag size = 101 INFO @ Fri, 05 Jul 2019 21:15:49: #1 total tags in treatment: 3349413 INFO @ Fri, 05 Jul 2019 21:15:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:15:49: #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 21:15:49: #1 tags after filtering in treatment: 3349413 INFO @ Fri, 05 Jul 2019 21:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 21:15:49: #1 finished! INFO @ Fri, 05 Jul 2019 21:15:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:15:49: #2 number of paired peaks: 116 WARNING @ Fri, 05 Jul 2019 21:15:49: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Fri, 05 Jul 2019 21:15:49: start model_add_line... INFO @ Fri, 05 Jul 2019 21:15:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:15:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:15:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.10_summits.bed INFO @ Fri, 05 Jul 2019 21:15:49: Done! INFO @ Fri, 05 Jul 2019 21:15:49: start X-correlation... INFO @ Fri, 05 Jul 2019 21:15:49: end of X-cor INFO @ Fri, 05 Jul 2019 21:15:49: #2 finished! INFO @ Fri, 05 Jul 2019 21:15:49: #2 predicted fragment length is 3 bps INFO @ Fri, 05 Jul 2019 21:15:49: #2 alternative fragment length(s) may be 3,20,41,62,92 bps INFO @ Fri, 05 Jul 2019 21:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.20_model.r WARNING @ Fri, 05 Jul 2019 21:15:49: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:15:49: #2 You may need to consider one of the other alternative d(s): 3,20,41,62,92 WARNING @ Fri, 05 Jul 2019 21:15:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 21:15:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:15:49: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BedGraph に変換しました。 CompletedMACS2peakCalling BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:15:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:15:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:15:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:15:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:15:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.05_summits.bed INFO @ Fri, 05 Jul 2019 21:15:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 21:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2737667/SRX2737667.20_summits.bed INFO @ Fri, 05 Jul 2019 21:15:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。