Job ID = 2008082 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,998,955 reads read : 3,997,910 reads written : 3,997,910 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: 00:02:18 1998955 reads; of these: 1998955 (100.00%) were paired; of these: 188500 (9.43%) aligned concordantly 0 times 1677871 (83.94%) aligned concordantly exactly 1 time 132584 (6.63%) aligned concordantly >1 times ---- 188500 pairs aligned concordantly 0 times; of these: 84553 (44.86%) aligned discordantly 1 time ---- 103947 pairs aligned 0 times concordantly or discordantly; of these: 207894 mates make up the pairs; of these: 168782 (81.19%) aligned 0 times 22105 (10.63%) aligned exactly 1 time 17007 (8.18%) aligned >1 times 95.78% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 11995 / 1893589 = 0.0063 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 17:34:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.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 17:34:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:34:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:34:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.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 17:34:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:34:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.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 17:34:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:34:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:34:45: 1000000 INFO @ Fri, 05 Jul 2019 17:34:47: 1000000 INFO @ Fri, 05 Jul 2019 17:34:49: 1000000 INFO @ Fri, 05 Jul 2019 17:34:54: 2000000 INFO @ Fri, 05 Jul 2019 17:35:00: 2000000 INFO @ Fri, 05 Jul 2019 17:35:03: 2000000 INFO @ Fri, 05 Jul 2019 17:35:03: 3000000 INFO @ Fri, 05 Jul 2019 17:35:10: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:35:10: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:35:10: #1 total tags in treatment: 1798689 INFO @ Fri, 05 Jul 2019 17:35:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:35:10: #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 17:35:10: #1 tags after filtering in treatment: 1678150 INFO @ Fri, 05 Jul 2019 17:35:10: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:35:10: #1 finished! INFO @ Fri, 05 Jul 2019 17:35:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:35:10: #2 number of paired peaks: 166 WARNING @ Fri, 05 Jul 2019 17:35:10: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 05 Jul 2019 17:35:10: start model_add_line... INFO @ Fri, 05 Jul 2019 17:35:10: start X-correlation... INFO @ Fri, 05 Jul 2019 17:35:10: end of X-cor INFO @ Fri, 05 Jul 2019 17:35:10: #2 finished! INFO @ Fri, 05 Jul 2019 17:35:10: #2 predicted fragment length is 174 bps INFO @ Fri, 05 Jul 2019 17:35:10: #2 alternative fragment length(s) may be 45,62,86,103,131,174,200,224,254,278,280,296,320,357,400,416,423,428,449,478,511,539,570,593 bps INFO @ Fri, 05 Jul 2019 17:35:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.10_model.r WARNING @ Fri, 05 Jul 2019 17:35:10: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:35:10: #2 You may need to consider one of the other alternative d(s): 45,62,86,103,131,174,200,224,254,278,280,296,320,357,400,416,423,428,449,478,511,539,570,593 WARNING @ Fri, 05 Jul 2019 17:35:10: #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 17:35:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:35:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:35:12: 3000000 INFO @ Fri, 05 Jul 2019 17:35:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:35:16: 3000000 INFO @ Fri, 05 Jul 2019 17:35:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:35:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:35:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.10_summits.bed INFO @ Fri, 05 Jul 2019 17:35:17: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:35:22: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:35:22: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:35:22: #1 total tags in treatment: 1798689 INFO @ Fri, 05 Jul 2019 17:35:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:35:22: #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 17:35:22: #1 tags after filtering in treatment: 1678150 INFO @ Fri, 05 Jul 2019 17:35:22: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:35:22: #1 finished! INFO @ Fri, 05 Jul 2019 17:35:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:35:22: #2 number of paired peaks: 166 WARNING @ Fri, 05 Jul 2019 17:35:22: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 05 Jul 2019 17:35:22: start model_add_line... INFO @ Fri, 05 Jul 2019 17:35:22: start X-correlation... INFO @ Fri, 05 Jul 2019 17:35:22: end of X-cor INFO @ Fri, 05 Jul 2019 17:35:22: #2 finished! INFO @ Fri, 05 Jul 2019 17:35:22: #2 predicted fragment length is 174 bps INFO @ Fri, 05 Jul 2019 17:35:22: #2 alternative fragment length(s) may be 45,62,86,103,131,174,200,224,254,278,280,296,320,357,400,416,423,428,449,478,511,539,570,593 bps INFO @ Fri, 05 Jul 2019 17:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.05_model.r WARNING @ Fri, 05 Jul 2019 17:35:22: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:35:22: #2 You may need to consider one of the other alternative d(s): 45,62,86,103,131,174,200,224,254,278,280,296,320,357,400,416,423,428,449,478,511,539,570,593 WARNING @ Fri, 05 Jul 2019 17:35:22: #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 17:35:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:35:26: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:35:26: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:35:26: #1 total tags in treatment: 1798689 INFO @ Fri, 05 Jul 2019 17:35:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:35:26: #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 17:35:26: #1 tags after filtering in treatment: 1678150 INFO @ Fri, 05 Jul 2019 17:35:26: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:35:26: #1 finished! INFO @ Fri, 05 Jul 2019 17:35:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:35:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:35:27: #2 number of paired peaks: 166 WARNING @ Fri, 05 Jul 2019 17:35:27: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 05 Jul 2019 17:35:27: start model_add_line... INFO @ Fri, 05 Jul 2019 17:35:27: start X-correlation... INFO @ Fri, 05 Jul 2019 17:35:27: end of X-cor INFO @ Fri, 05 Jul 2019 17:35:27: #2 finished! INFO @ Fri, 05 Jul 2019 17:35:27: #2 predicted fragment length is 174 bps INFO @ Fri, 05 Jul 2019 17:35:27: #2 alternative fragment length(s) may be 45,62,86,103,131,174,200,224,254,278,280,296,320,357,400,416,423,428,449,478,511,539,570,593 bps INFO @ Fri, 05 Jul 2019 17:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.20_model.r WARNING @ Fri, 05 Jul 2019 17:35:27: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:35:27: #2 You may need to consider one of the other alternative d(s): 45,62,86,103,131,174,200,224,254,278,280,296,320,357,400,416,423,428,449,478,511,539,570,593 WARNING @ Fri, 05 Jul 2019 17:35:27: #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 17:35:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:35:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.05_summits.bed INFO @ Fri, 05 Jul 2019 17:35:29: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:35:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:35:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:35:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:35:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471860/ERX471860.20_summits.bed INFO @ Fri, 05 Jul 2019 17:35:34: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。