Job ID = 2641222 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,127,081 reads read : 20,254,162 reads written : 20,254,162 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: 00:02:58 10127081 reads; of these: 10127081 (100.00%) were paired; of these: 9519947 (94.00%) aligned concordantly 0 times 545040 (5.38%) aligned concordantly exactly 1 time 62094 (0.61%) aligned concordantly >1 times ---- 9519947 pairs aligned concordantly 0 times; of these: 316661 (3.33%) aligned discordantly 1 time ---- 9203286 pairs aligned 0 times concordantly or discordantly; of these: 18406572 mates make up the pairs; of these: 15226604 (82.72%) aligned 0 times 2882120 (15.66%) aligned exactly 1 time 297848 (1.62%) aligned >1 times 24.82% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 288274 / 886981 = 0.3250 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:00:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.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, 24 Aug 2019 22:00:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:00:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:00:26: 1000000 INFO @ Sat, 24 Aug 2019 22:00:31: 2000000 INFO @ Sat, 24 Aug 2019 22:00:38: 3000000 INFO @ Sat, 24 Aug 2019 22:00:45: 4000000 INFO @ Sat, 24 Aug 2019 22:00:48: #1 tag size is determined as 40 bps INFO @ Sat, 24 Aug 2019 22:00:48: #1 tag size = 40 INFO @ Sat, 24 Aug 2019 22:00:48: #1 total tags in treatment: 421226 INFO @ Sat, 24 Aug 2019 22:00:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:00:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:00:48: #1 tags after filtering in treatment: 398122 INFO @ Sat, 24 Aug 2019 22:00:48: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 24 Aug 2019 22:00:48: #1 finished! INFO @ Sat, 24 Aug 2019 22:00:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:00:48: #2 number of paired peaks: 134 WARNING @ Sat, 24 Aug 2019 22:00:48: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 24 Aug 2019 22:00:48: start model_add_line... INFO @ Sat, 24 Aug 2019 22:00:48: start X-correlation... INFO @ Sat, 24 Aug 2019 22:00:48: end of X-cor INFO @ Sat, 24 Aug 2019 22:00:48: #2 finished! INFO @ Sat, 24 Aug 2019 22:00:48: #2 predicted fragment length is 166 bps INFO @ Sat, 24 Aug 2019 22:00:48: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 24 Aug 2019 22:00:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.05_model.r INFO @ Sat, 24 Aug 2019 22:00:48: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:00:50: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:00:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.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, 24 Aug 2019 22:00:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:00:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:00:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.05_peaks.xls INFO @ Sat, 24 Aug 2019 22:00:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:00:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.05_summits.bed INFO @ Sat, 24 Aug 2019 22:00:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (764 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:00:56: 1000000 INFO @ Sat, 24 Aug 2019 22:01:01: 2000000 INFO @ Sat, 24 Aug 2019 22:01:07: 3000000 INFO @ Sat, 24 Aug 2019 22:01:12: 4000000 INFO @ Sat, 24 Aug 2019 22:01:15: #1 tag size is determined as 40 bps INFO @ Sat, 24 Aug 2019 22:01:15: #1 tag size = 40 INFO @ Sat, 24 Aug 2019 22:01:15: #1 total tags in treatment: 421226 INFO @ Sat, 24 Aug 2019 22:01:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:01:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:01:15: #1 tags after filtering in treatment: 398122 INFO @ Sat, 24 Aug 2019 22:01:15: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 24 Aug 2019 22:01:15: #1 finished! INFO @ Sat, 24 Aug 2019 22:01:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:01:15: #2 number of paired peaks: 134 WARNING @ Sat, 24 Aug 2019 22:01:15: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 24 Aug 2019 22:01:15: start model_add_line... INFO @ Sat, 24 Aug 2019 22:01:15: start X-correlation... INFO @ Sat, 24 Aug 2019 22:01:15: end of X-cor INFO @ Sat, 24 Aug 2019 22:01:15: #2 finished! INFO @ Sat, 24 Aug 2019 22:01:15: #2 predicted fragment length is 166 bps INFO @ Sat, 24 Aug 2019 22:01:15: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 24 Aug 2019 22:01:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.10_model.r INFO @ Sat, 24 Aug 2019 22:01:15: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:01:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:01:16: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:01:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.10_peaks.xls INFO @ Sat, 24 Aug 2019 22:01:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:01:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.10_summits.bed INFO @ Sat, 24 Aug 2019 22:01:17: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (314 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:01:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.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, 24 Aug 2019 22:01:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:01:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:01:26: 1000000 INFO @ Sat, 24 Aug 2019 22:01:32: 2000000 INFO @ Sat, 24 Aug 2019 22:01:37: 3000000 INFO @ Sat, 24 Aug 2019 22:01:43: 4000000 INFO @ Sat, 24 Aug 2019 22:01:46: #1 tag size is determined as 40 bps INFO @ Sat, 24 Aug 2019 22:01:46: #1 tag size = 40 INFO @ Sat, 24 Aug 2019 22:01:46: #1 total tags in treatment: 421226 INFO @ Sat, 24 Aug 2019 22:01:46: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:01:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:01:46: #1 tags after filtering in treatment: 398122 INFO @ Sat, 24 Aug 2019 22:01:46: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 24 Aug 2019 22:01:46: #1 finished! INFO @ Sat, 24 Aug 2019 22:01:46: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:01:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:01:46: #2 number of paired peaks: 134 WARNING @ Sat, 24 Aug 2019 22:01:46: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Sat, 24 Aug 2019 22:01:46: start model_add_line... INFO @ Sat, 24 Aug 2019 22:01:46: start X-correlation... INFO @ Sat, 24 Aug 2019 22:01:46: end of X-cor INFO @ Sat, 24 Aug 2019 22:01:46: #2 finished! INFO @ Sat, 24 Aug 2019 22:01:46: #2 predicted fragment length is 166 bps INFO @ Sat, 24 Aug 2019 22:01:46: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 24 Aug 2019 22:01:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.20_model.r INFO @ Sat, 24 Aug 2019 22:01:46: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:01:47: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:01:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.20_peaks.xls INFO @ Sat, 24 Aug 2019 22:01:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:01:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5820056/SRX5820056.20_summits.bed INFO @ Sat, 24 Aug 2019 22:01:48: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (88 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。