Job ID = 2641226 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,634,825 reads read : 51,269,650 reads written : 51,269,650 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: 00:21:05 25634825 reads; of these: 25634825 (100.00%) were paired; of these: 21924604 (85.53%) aligned concordantly 0 times 1670671 (6.52%) aligned concordantly exactly 1 time 2039550 (7.96%) aligned concordantly >1 times ---- 21924604 pairs aligned concordantly 0 times; of these: 787693 (3.59%) aligned discordantly 1 time ---- 21136911 pairs aligned 0 times concordantly or discordantly; of these: 42273822 mates make up the pairs; of these: 32200447 (76.17%) aligned 0 times 5312737 (12.57%) aligned exactly 1 time 4760638 (11.26%) aligned >1 times 37.19% overall alignment rate Time searching: 00:21:05 Overall time: 00:21:05 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_sort_core] merging from 8 files... [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] 2349428 / 4136854 = 0.5679 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:42:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.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 22:42:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:42:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:42:31: 1000000 INFO @ Sat, 24 Aug 2019 22:42:38: 2000000 INFO @ Sat, 24 Aug 2019 22:42:45: 3000000 INFO @ Sat, 24 Aug 2019 22:42:52: 4000000 INFO @ Sat, 24 Aug 2019 22:42:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.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 22:42:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:42:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:43:00: 1000000 INFO @ Sat, 24 Aug 2019 22:43:01: 5000000 INFO @ Sat, 24 Aug 2019 22:43:08: 2000000 INFO @ Sat, 24 Aug 2019 22:43:09: 6000000 INFO @ Sat, 24 Aug 2019 22:43:15: 3000000 INFO @ Sat, 24 Aug 2019 22:43:17: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:43:21: 4000000 INFO @ Sat, 24 Aug 2019 22:43:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.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 22:43:23: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:43:23: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:43:25: 8000000 INFO @ Sat, 24 Aug 2019 22:43:28: 5000000 INFO @ Sat, 24 Aug 2019 22:43:30: 1000000 INFO @ Sat, 24 Aug 2019 22:43:32: 9000000 INFO @ Sat, 24 Aug 2019 22:43:35: 6000000 INFO @ Sat, 24 Aug 2019 22:43:38: 2000000 INFO @ Sat, 24 Aug 2019 22:43:40: 10000000 INFO @ Sat, 24 Aug 2019 22:43:42: 7000000 INFO @ Sat, 24 Aug 2019 22:43:45: 3000000 INFO @ Sat, 24 Aug 2019 22:43:48: 11000000 INFO @ Sat, 24 Aug 2019 22:43:49: 8000000 INFO @ Sat, 24 Aug 2019 22:43:52: 4000000 INFO @ Sat, 24 Aug 2019 22:43:56: 12000000 INFO @ Sat, 24 Aug 2019 22:43:56: 9000000 INFO @ Sat, 24 Aug 2019 22:43:58: 5000000 INFO @ Sat, 24 Aug 2019 22:44:03: 10000000 INFO @ Sat, 24 Aug 2019 22:44:04: 13000000 INFO @ Sat, 24 Aug 2019 22:44:05: 6000000 INFO @ Sat, 24 Aug 2019 22:44:09: 11000000 INFO @ Sat, 24 Aug 2019 22:44:12: 7000000 INFO @ Sat, 24 Aug 2019 22:44:12: 14000000 INFO @ Sat, 24 Aug 2019 22:44:15: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 22:44:15: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 22:44:15: #1 total tags in treatment: 1567353 INFO @ Sat, 24 Aug 2019 22:44:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:44:15: #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 22:44:15: #1 tags after filtering in treatment: 531500 INFO @ Sat, 24 Aug 2019 22:44:15: #1 Redundant rate of treatment: 0.66 INFO @ Sat, 24 Aug 2019 22:44:15: #1 finished! INFO @ Sat, 24 Aug 2019 22:44:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:44:15: #2 number of paired peaks: 424 WARNING @ Sat, 24 Aug 2019 22:44:15: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 24 Aug 2019 22:44:15: start model_add_line... INFO @ Sat, 24 Aug 2019 22:44:15: start X-correlation... INFO @ Sat, 24 Aug 2019 22:44:15: end of X-cor INFO @ Sat, 24 Aug 2019 22:44:15: #2 finished! INFO @ Sat, 24 Aug 2019 22:44:15: #2 predicted fragment length is 217 bps INFO @ Sat, 24 Aug 2019 22:44:15: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 24 Aug 2019 22:44:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.05_model.r INFO @ Sat, 24 Aug 2019 22:44:16: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:44:16: 12000000 INFO @ Sat, 24 Aug 2019 22:44:18: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:44:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.05_peaks.xls INFO @ Sat, 24 Aug 2019 22:44:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:44:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.05_summits.bed INFO @ Sat, 24 Aug 2019 22:44:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:44:19: 8000000 INFO @ Sat, 24 Aug 2019 22:44:22: 13000000 INFO @ Sat, 24 Aug 2019 22:44:26: 9000000 INFO @ Sat, 24 Aug 2019 22:44:29: 14000000 INFO @ Sat, 24 Aug 2019 22:44:31: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 22:44:31: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 22:44:31: #1 total tags in treatment: 1567353 INFO @ Sat, 24 Aug 2019 22:44:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:44:31: #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 22:44:31: #1 tags after filtering in treatment: 531500 INFO @ Sat, 24 Aug 2019 22:44:31: #1 Redundant rate of treatment: 0.66 INFO @ Sat, 24 Aug 2019 22:44:31: #1 finished! INFO @ Sat, 24 Aug 2019 22:44:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:44:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:44:31: #2 number of paired peaks: 424 WARNING @ Sat, 24 Aug 2019 22:44:31: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 24 Aug 2019 22:44:31: start model_add_line... INFO @ Sat, 24 Aug 2019 22:44:31: start X-correlation... INFO @ Sat, 24 Aug 2019 22:44:31: end of X-cor INFO @ Sat, 24 Aug 2019 22:44:31: #2 finished! INFO @ Sat, 24 Aug 2019 22:44:31: #2 predicted fragment length is 217 bps INFO @ Sat, 24 Aug 2019 22:44:31: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 24 Aug 2019 22:44:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.10_model.r INFO @ Sat, 24 Aug 2019 22:44:31: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:44:33: 10000000 INFO @ Sat, 24 Aug 2019 22:44:34: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:44:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.10_peaks.xls INFO @ Sat, 24 Aug 2019 22:44:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:44:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.10_summits.bed INFO @ Sat, 24 Aug 2019 22:44:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:44:39: 11000000 INFO @ Sat, 24 Aug 2019 22:44:46: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:44:52: 13000000 INFO @ Sat, 24 Aug 2019 22:44:58: 14000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:45:01: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 22:45:01: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 22:45:01: #1 total tags in treatment: 1567353 INFO @ Sat, 24 Aug 2019 22:45:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:45:01: #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 22:45:01: #1 tags after filtering in treatment: 531500 INFO @ Sat, 24 Aug 2019 22:45:01: #1 Redundant rate of treatment: 0.66 INFO @ Sat, 24 Aug 2019 22:45:01: #1 finished! INFO @ Sat, 24 Aug 2019 22:45:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:45:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:45:01: #2 number of paired peaks: 424 WARNING @ Sat, 24 Aug 2019 22:45:01: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 24 Aug 2019 22:45:01: start model_add_line... INFO @ Sat, 24 Aug 2019 22:45:01: start X-correlation... INFO @ Sat, 24 Aug 2019 22:45:01: end of X-cor INFO @ Sat, 24 Aug 2019 22:45:01: #2 finished! INFO @ Sat, 24 Aug 2019 22:45:01: #2 predicted fragment length is 217 bps INFO @ Sat, 24 Aug 2019 22:45:01: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 24 Aug 2019 22:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.20_model.r INFO @ Sat, 24 Aug 2019 22:45:01: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:45:04: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:45:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.20_peaks.xls INFO @ Sat, 24 Aug 2019 22:45:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:45:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5820060/SRX5820060.20_summits.bed INFO @ Sat, 24 Aug 2019 22:45:04: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 3 millis CompletedMACS2peakCalling