Job ID = 2008008 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,733,895 reads read : 3,467,790 reads written : 3,467,790 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: 00:01:51 1733895 reads; of these: 1733895 (100.00%) were paired; of these: 282516 (16.29%) aligned concordantly 0 times 1327387 (76.56%) aligned concordantly exactly 1 time 123992 (7.15%) aligned concordantly >1 times ---- 282516 pairs aligned concordantly 0 times; of these: 26591 (9.41%) aligned discordantly 1 time ---- 255925 pairs aligned 0 times concordantly or discordantly; of these: 511850 mates make up the pairs; of these: 487318 (95.21%) aligned 0 times 16438 (3.21%) aligned exactly 1 time 8094 (1.58%) aligned >1 times 85.95% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 279003 / 1474793 = 0.1892 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 17:14:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.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 17:14:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:14:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.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 17:14:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:14:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:14:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.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 17:14:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:14:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:14:49: 1000000 INFO @ Fri, 05 Jul 2019 17:14:49: 1000000 INFO @ Fri, 05 Jul 2019 17:14:50: 1000000 INFO @ Fri, 05 Jul 2019 17:15:05: 2000000 INFO @ Fri, 05 Jul 2019 17:15:06: 2000000 INFO @ Fri, 05 Jul 2019 17:15:07: 2000000 INFO @ Fri, 05 Jul 2019 17:15:11: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:15:11: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:15:11: #1 total tags in treatment: 1174775 INFO @ Fri, 05 Jul 2019 17:15:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:15:11: #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 17:15:11: #1 tags after filtering in treatment: 1117975 INFO @ Fri, 05 Jul 2019 17:15:11: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:15:11: #1 finished! INFO @ Fri, 05 Jul 2019 17:15:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:15:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:15:11: #2 number of paired peaks: 174 WARNING @ Fri, 05 Jul 2019 17:15:11: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 05 Jul 2019 17:15:11: start model_add_line... INFO @ Fri, 05 Jul 2019 17:15:11: start X-correlation... INFO @ Fri, 05 Jul 2019 17:15:11: end of X-cor INFO @ Fri, 05 Jul 2019 17:15:11: #2 finished! INFO @ Fri, 05 Jul 2019 17:15:11: #2 predicted fragment length is 190 bps INFO @ Fri, 05 Jul 2019 17:15:11: #2 alternative fragment length(s) may be 1,105,148,154,190,210,236,490,555,586 bps INFO @ Fri, 05 Jul 2019 17:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.20_model.r WARNING @ Fri, 05 Jul 2019 17:15:11: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:15:11: #2 You may need to consider one of the other alternative d(s): 1,105,148,154,190,210,236,490,555,586 WARNING @ Fri, 05 Jul 2019 17:15:11: #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 17:15:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:15:12: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:15:12: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:15:12: #1 total tags in treatment: 1174775 INFO @ Fri, 05 Jul 2019 17:15:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:15:12: #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 17:15:12: #1 tags after filtering in treatment: 1117975 INFO @ Fri, 05 Jul 2019 17:15:12: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:15:12: #1 finished! INFO @ Fri, 05 Jul 2019 17:15:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:15:12: #2 number of paired peaks: 174 WARNING @ Fri, 05 Jul 2019 17:15:12: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 05 Jul 2019 17:15:12: start model_add_line... INFO @ Fri, 05 Jul 2019 17:15:12: start X-correlation... INFO @ Fri, 05 Jul 2019 17:15:12: end of X-cor INFO @ Fri, 05 Jul 2019 17:15:12: #2 finished! INFO @ Fri, 05 Jul 2019 17:15:12: #2 predicted fragment length is 190 bps INFO @ Fri, 05 Jul 2019 17:15:12: #2 alternative fragment length(s) may be 1,105,148,154,190,210,236,490,555,586 bps INFO @ Fri, 05 Jul 2019 17:15:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.05_model.r WARNING @ Fri, 05 Jul 2019 17:15:12: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:15:12: #2 You may need to consider one of the other alternative d(s): 1,105,148,154,190,210,236,490,555,586 WARNING @ Fri, 05 Jul 2019 17:15:12: #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 17:15:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:15:13: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:15:13: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:15:13: #1 total tags in treatment: 1174775 INFO @ Fri, 05 Jul 2019 17:15:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:15:13: #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 17:15:13: #1 tags after filtering in treatment: 1117975 INFO @ Fri, 05 Jul 2019 17:15:13: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:15:13: #1 finished! INFO @ Fri, 05 Jul 2019 17:15:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:15:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:15:13: #2 number of paired peaks: 174 WARNING @ Fri, 05 Jul 2019 17:15:13: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 05 Jul 2019 17:15:13: start model_add_line... INFO @ Fri, 05 Jul 2019 17:15:13: start X-correlation... INFO @ Fri, 05 Jul 2019 17:15:13: end of X-cor INFO @ Fri, 05 Jul 2019 17:15:13: #2 finished! INFO @ Fri, 05 Jul 2019 17:15:13: #2 predicted fragment length is 190 bps INFO @ Fri, 05 Jul 2019 17:15:13: #2 alternative fragment length(s) may be 1,105,148,154,190,210,236,490,555,586 bps INFO @ Fri, 05 Jul 2019 17:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.10_model.r WARNING @ Fri, 05 Jul 2019 17:15:13: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:15:13: #2 You may need to consider one of the other alternative d(s): 1,105,148,154,190,210,236,490,555,586 WARNING @ Fri, 05 Jul 2019 17:15:13: #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 17:15:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:15:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:15:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.20_summits.bed INFO @ Fri, 05 Jul 2019 17:15:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 17:15:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:15:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:15:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:15:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.05_summits.bed INFO @ Fri, 05 Jul 2019 17:15:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 59 millis INFO @ Fri, 05 Jul 2019 17:15:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:15:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:15:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471796/ERX471796.10_summits.bed INFO @ Fri, 05 Jul 2019 17:15:18: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。