Job ID = 2010865 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,534,688 reads read : 11,069,376 reads written : 5,534,688 reads 0-length : 5,534,688 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: 00:02:12 5534688 reads; of these: 5534688 (100.00%) were unpaired; of these: 459819 (8.31%) aligned 0 times 4461854 (80.62%) aligned exactly 1 time 613015 (11.08%) aligned >1 times 91.69% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 1401954 / 5074869 = 0.2763 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 01:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.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 01:09:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:09:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.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 01:09:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:09:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.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 01:09:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:09:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:09:50: 1000000 INFO @ Sat, 06 Jul 2019 01:09:51: 1000000 INFO @ Sat, 06 Jul 2019 01:09:52: 1000000 INFO @ Sat, 06 Jul 2019 01:09:58: 2000000 INFO @ Sat, 06 Jul 2019 01:10:02: 2000000 INFO @ Sat, 06 Jul 2019 01:10:02: 2000000 INFO @ Sat, 06 Jul 2019 01:10:06: 3000000 INFO @ Sat, 06 Jul 2019 01:10:11: 3000000 INFO @ Sat, 06 Jul 2019 01:10:11: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:10:11: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:10:11: #1 total tags in treatment: 3672915 INFO @ Sat, 06 Jul 2019 01:10:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:10:11: #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 01:10:11: #1 tags after filtering in treatment: 3672915 INFO @ Sat, 06 Jul 2019 01:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:10:11: #1 finished! INFO @ Sat, 06 Jul 2019 01:10:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:10:11: #2 number of paired peaks: 112 WARNING @ Sat, 06 Jul 2019 01:10:11: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 06 Jul 2019 01:10:11: start model_add_line... INFO @ Sat, 06 Jul 2019 01:10:11: start X-correlation... INFO @ Sat, 06 Jul 2019 01:10:11: end of X-cor INFO @ Sat, 06 Jul 2019 01:10:11: #2 finished! INFO @ Sat, 06 Jul 2019 01:10:11: #2 predicted fragment length is 1 bps INFO @ Sat, 06 Jul 2019 01:10:11: #2 alternative fragment length(s) may be 1,11,60,95,127,176,205,252,308,433,575,593 bps INFO @ Sat, 06 Jul 2019 01:10:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.10_model.r INFO @ Sat, 06 Jul 2019 01:10:12: 3000000 INFO @ Sat, 06 Jul 2019 01:10:16: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:10:16: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:10:16: #1 total tags in treatment: 3672915 INFO @ Sat, 06 Jul 2019 01:10:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:10:16: #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 01:10:16: #1 tags after filtering in treatment: 3672915 INFO @ Sat, 06 Jul 2019 01:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:10:16: #1 finished! INFO @ Sat, 06 Jul 2019 01:10:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:10:16: #2 number of paired peaks: 112 WARNING @ Sat, 06 Jul 2019 01:10:16: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 06 Jul 2019 01:10:16: start model_add_line... INFO @ Sat, 06 Jul 2019 01:10:16: start X-correlation... INFO @ Sat, 06 Jul 2019 01:10:16: end of X-cor INFO @ Sat, 06 Jul 2019 01:10:16: #2 finished! INFO @ Sat, 06 Jul 2019 01:10:16: #2 predicted fragment length is 1 bps INFO @ Sat, 06 Jul 2019 01:10:16: #2 alternative fragment length(s) may be 1,11,60,95,127,176,205,252,308,433,575,593 bps INFO @ Sat, 06 Jul 2019 01:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.20_model.r INFO @ Sat, 06 Jul 2019 01:10:19: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:10:19: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:10:19: #1 total tags in treatment: 3672915 INFO @ Sat, 06 Jul 2019 01:10:19: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:10:19: #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 01:10:19: #1 tags after filtering in treatment: 3672915 INFO @ Sat, 06 Jul 2019 01:10:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:10:19: #1 finished! INFO @ Sat, 06 Jul 2019 01:10:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:10:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:10:19: #2 number of paired peaks: 112 WARNING @ Sat, 06 Jul 2019 01:10:19: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 06 Jul 2019 01:10:19: start model_add_line... INFO @ Sat, 06 Jul 2019 01:10:19: start X-correlation... INFO @ Sat, 06 Jul 2019 01:10:19: end of X-cor INFO @ Sat, 06 Jul 2019 01:10:19: #2 finished! INFO @ Sat, 06 Jul 2019 01:10:19: #2 predicted fragment length is 1 bps INFO @ Sat, 06 Jul 2019 01:10:19: #2 alternative fragment length(s) may be 1,11,60,95,127,176,205,252,308,433,575,593 bps INFO @ Sat, 06 Jul 2019 01:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.05_model.r BedGraph に変換しました。 BigWig に変換中... WARNING @ Sat, 06 Jul 2019 01:10:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 01:10:52: #2 You may need to consider one of the other alternative d(s): 1,11,60,95,127,176,205,252,308,433,575,593 WARNING @ Sat, 06 Jul 2019 01:10:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 01:10:52: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:10:52: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 06 Jul 2019 01:10:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 01:10:52: #2 You may need to consider one of the other alternative d(s): 1,11,60,95,127,176,205,252,308,433,575,593 WARNING @ Sat, 06 Jul 2019 01:10:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 01:10:52: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:10:52: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 06 Jul 2019 01:10:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 01:10:52: #2 You may need to consider one of the other alternative d(s): 1,11,60,95,127,176,205,252,308,433,575,593 WARNING @ Sat, 06 Jul 2019 01:10:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 01:10:52: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:10:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:10:58: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:10:58: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:10:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 01:11:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.10_peaks.xls INFO @ Sat, 06 Jul 2019 01:11:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:11:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.10_summits.bed INFO @ Sat, 06 Jul 2019 01:11:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.05_peaks.xls INFO @ Sat, 06 Jul 2019 01:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.05_summits.bed INFO @ Sat, 06 Jul 2019 01:11:02: Done! INFO @ Sat, 06 Jul 2019 01:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.20_peaks.xls INFO @ Sat, 06 Jul 2019 01:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4140966/SRX4140966.20_summits.bed INFO @ Sat, 06 Jul 2019 01:11:02: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling