Job ID = 2010634 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,222,880 reads read : 2,445,760 reads written : 2,445,760 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: 00:00:43 1222880 reads; of these: 1222880 (100.00%) were paired; of these: 774732 (63.35%) aligned concordantly 0 times 295088 (24.13%) aligned concordantly exactly 1 time 153060 (12.52%) aligned concordantly >1 times ---- 774732 pairs aligned concordantly 0 times; of these: 7870 (1.02%) aligned discordantly 1 time ---- 766862 pairs aligned 0 times concordantly or discordantly; of these: 1533724 mates make up the pairs; of these: 1422830 (92.77%) aligned 0 times 80473 (5.25%) aligned exactly 1 time 30421 (1.98%) aligned >1 times 41.82% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 106019 / 453463 = 0.2338 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 23:42:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.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 23:42:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:42:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.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 23:42:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:42:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:42:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.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 23:42:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:42:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:43:01: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:43:01: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:43:01: #1 total tags in treatment: 345329 INFO @ Fri, 05 Jul 2019 23:43:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:43:01: #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 23:43:01: #1 tags after filtering in treatment: 266462 INFO @ Fri, 05 Jul 2019 23:43:01: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 05 Jul 2019 23:43:01: #1 finished! INFO @ Fri, 05 Jul 2019 23:43:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:43:01: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 23:43:01: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 23:43:01: start model_add_line... INFO @ Fri, 05 Jul 2019 23:43:01: start X-correlation... INFO @ Fri, 05 Jul 2019 23:43:01: end of X-cor INFO @ Fri, 05 Jul 2019 23:43:01: #2 finished! INFO @ Fri, 05 Jul 2019 23:43:01: #2 predicted fragment length is 219 bps INFO @ Fri, 05 Jul 2019 23:43:01: #2 alternative fragment length(s) may be 174,206,219 bps INFO @ Fri, 05 Jul 2019 23:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.05_model.r INFO @ Fri, 05 Jul 2019 23:43:02: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:43:02: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:43:02: #1 total tags in treatment: 345329 INFO @ Fri, 05 Jul 2019 23:43:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:43:02: #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 23:43:02: #1 tags after filtering in treatment: 266462 INFO @ Fri, 05 Jul 2019 23:43:02: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 05 Jul 2019 23:43:02: #1 finished! INFO @ Fri, 05 Jul 2019 23:43:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:43:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:43:02: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 23:43:02: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 23:43:02: start model_add_line... INFO @ Fri, 05 Jul 2019 23:43:02: start X-correlation... INFO @ Fri, 05 Jul 2019 23:43:02: end of X-cor INFO @ Fri, 05 Jul 2019 23:43:02: #2 finished! INFO @ Fri, 05 Jul 2019 23:43:02: #2 predicted fragment length is 219 bps INFO @ Fri, 05 Jul 2019 23:43:02: #2 alternative fragment length(s) may be 174,206,219 bps INFO @ Fri, 05 Jul 2019 23:43:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.10_model.r INFO @ Fri, 05 Jul 2019 23:43:02: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:43:02: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:43:02: #1 total tags in treatment: 345329 INFO @ Fri, 05 Jul 2019 23:43:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:43:02: #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 23:43:02: #1 tags after filtering in treatment: 266462 INFO @ Fri, 05 Jul 2019 23:43:02: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 05 Jul 2019 23:43:02: #1 finished! INFO @ Fri, 05 Jul 2019 23:43:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:43:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:43:02: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 23:43:02: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 23:43:02: start model_add_line... INFO @ Fri, 05 Jul 2019 23:43:02: start X-correlation... INFO @ Fri, 05 Jul 2019 23:43:02: end of X-cor INFO @ Fri, 05 Jul 2019 23:43:02: #2 finished! INFO @ Fri, 05 Jul 2019 23:43:02: #2 predicted fragment length is 219 bps INFO @ Fri, 05 Jul 2019 23:43:02: #2 alternative fragment length(s) may be 174,206,219 bps INFO @ Fri, 05 Jul 2019 23:43:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.20_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:43:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:43:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:43:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:43:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:43:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:43:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:43:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:43:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:43:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:43:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:43:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:43:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:43:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.10_summits.bed INFO @ Fri, 05 Jul 2019 23:43:30: Done! INFO @ Fri, 05 Jul 2019 23:43:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:43:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.05_summits.bed INFO @ Fri, 05 Jul 2019 23:43:30: Done! INFO @ Fri, 05 Jul 2019 23:43:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:43:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:43:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386340/SRX386340.20_summits.bed INFO @ Fri, 05 Jul 2019 23:43:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 3 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。