Job ID = 2010549 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,872,206 reads read : 3,744,412 reads written : 3,744,412 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: 00:01:14 1872206 reads; of these: 1872206 (100.00%) were paired; of these: 842361 (44.99%) aligned concordantly 0 times 756976 (40.43%) aligned concordantly exactly 1 time 272869 (14.57%) aligned concordantly >1 times ---- 842361 pairs aligned concordantly 0 times; of these: 69582 (8.26%) aligned discordantly 1 time ---- 772779 pairs aligned 0 times concordantly or discordantly; of these: 1545558 mates make up the pairs; of these: 1467336 (94.94%) aligned 0 times 23121 (1.50%) aligned exactly 1 time 55101 (3.57%) aligned >1 times 60.81% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 25633 / 1089538 = 0.0235 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 22:59:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.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 22:59:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:59:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:59:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.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 22:59:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:59:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.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 22:59:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:59:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:59:36: 1000000 INFO @ Fri, 05 Jul 2019 22:59:37: 1000000 INFO @ Fri, 05 Jul 2019 22:59:38: 1000000 INFO @ Fri, 05 Jul 2019 22:59:43: 2000000 INFO @ Fri, 05 Jul 2019 22:59:44: 2000000 INFO @ Fri, 05 Jul 2019 22:59:45: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:59:45: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:59:45: #1 total tags in treatment: 1006850 INFO @ Fri, 05 Jul 2019 22:59:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:59:45: #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 22:59:45: #1 tags after filtering in treatment: 734909 INFO @ Fri, 05 Jul 2019 22:59:45: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 05 Jul 2019 22:59:45: #1 finished! INFO @ Fri, 05 Jul 2019 22:59:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:59:45: #2 number of paired peaks: 951 WARNING @ Fri, 05 Jul 2019 22:59:45: Fewer paired peaks (951) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 951 pairs to build model! INFO @ Fri, 05 Jul 2019 22:59:45: start model_add_line... INFO @ Fri, 05 Jul 2019 22:59:45: start X-correlation... INFO @ Fri, 05 Jul 2019 22:59:45: end of X-cor INFO @ Fri, 05 Jul 2019 22:59:45: #2 finished! INFO @ Fri, 05 Jul 2019 22:59:45: #2 predicted fragment length is 2 bps INFO @ Fri, 05 Jul 2019 22:59:45: #2 alternative fragment length(s) may be 2,25,52 bps INFO @ Fri, 05 Jul 2019 22:59:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.05_model.r WARNING @ Fri, 05 Jul 2019 22:59:45: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 22:59:45: #2 You may need to consider one of the other alternative d(s): 2,25,52 WARNING @ Fri, 05 Jul 2019 22:59:45: #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 22:59:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:59:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:59:45: 2000000 INFO @ Fri, 05 Jul 2019 22:59:46: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:59:46: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:59:46: #1 total tags in treatment: 1006850 INFO @ Fri, 05 Jul 2019 22:59:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:59:46: #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 22:59:46: #1 tags after filtering in treatment: 734909 INFO @ Fri, 05 Jul 2019 22:59:46: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 05 Jul 2019 22:59:46: #1 finished! INFO @ Fri, 05 Jul 2019 22:59:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:59:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:59:46: #2 number of paired peaks: 951 WARNING @ Fri, 05 Jul 2019 22:59:46: Fewer paired peaks (951) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 951 pairs to build model! INFO @ Fri, 05 Jul 2019 22:59:46: start model_add_line... INFO @ Fri, 05 Jul 2019 22:59:46: start X-correlation... INFO @ Fri, 05 Jul 2019 22:59:46: end of X-cor INFO @ Fri, 05 Jul 2019 22:59:46: #2 finished! INFO @ Fri, 05 Jul 2019 22:59:46: #2 predicted fragment length is 2 bps INFO @ Fri, 05 Jul 2019 22:59:46: #2 alternative fragment length(s) may be 2,25,52 bps INFO @ Fri, 05 Jul 2019 22:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.10_model.r WARNING @ Fri, 05 Jul 2019 22:59:46: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 22:59:46: #2 You may need to consider one of the other alternative d(s): 2,25,52 WARNING @ Fri, 05 Jul 2019 22:59:46: #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 22:59:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:59:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:59:47: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 22:59:47: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 22:59:47: #1 total tags in treatment: 1006850 INFO @ Fri, 05 Jul 2019 22:59:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:59:47: #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 22:59:47: #1 tags after filtering in treatment: 734909 INFO @ Fri, 05 Jul 2019 22:59:47: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 05 Jul 2019 22:59:47: #1 finished! INFO @ Fri, 05 Jul 2019 22:59:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:59:47: #2 number of paired peaks: 951 WARNING @ Fri, 05 Jul 2019 22:59:47: Fewer paired peaks (951) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 951 pairs to build model! INFO @ Fri, 05 Jul 2019 22:59:47: start model_add_line... INFO @ Fri, 05 Jul 2019 22:59:47: start X-correlation... INFO @ Fri, 05 Jul 2019 22:59:47: end of X-cor INFO @ Fri, 05 Jul 2019 22:59:47: #2 finished! INFO @ Fri, 05 Jul 2019 22:59:47: #2 predicted fragment length is 2 bps INFO @ Fri, 05 Jul 2019 22:59:47: #2 alternative fragment length(s) may be 2,25,52 bps INFO @ Fri, 05 Jul 2019 22:59:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.20_model.r WARNING @ Fri, 05 Jul 2019 22:59:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 22:59:47: #2 You may need to consider one of the other alternative d(s): 2,25,52 WARNING @ Fri, 05 Jul 2019 22:59:47: #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 22:59:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.05_peaks.xls INFO @ Fri, 05 Jul 2019 22:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.05_summits.bed INFO @ Fri, 05 Jul 2019 22:59:48: Done! INFO @ Fri, 05 Jul 2019 22:59:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.10_peaks.xls INFO @ Fri, 05 Jul 2019 22:59:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:59:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.20_peaks.xls BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 23:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.10_summits.bed BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:00:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381250/SRX381250.20_summits.bed INFO @ Fri, 05 Jul 2019 23:00:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。