Job ID = 2007798 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 587,665 reads read : 1,175,330 reads written : 1,175,330 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: 00:00:35 587665 reads; of these: 587665 (100.00%) were paired; of these: 48580 (8.27%) aligned concordantly 0 times 494576 (84.16%) aligned concordantly exactly 1 time 44509 (7.57%) aligned concordantly >1 times ---- 48580 pairs aligned concordantly 0 times; of these: 19814 (40.79%) aligned discordantly 1 time ---- 28766 pairs aligned 0 times concordantly or discordantly; of these: 57532 mates make up the pairs; of these: 46602 (81.00%) aligned 0 times 6259 (10.88%) aligned exactly 1 time 4671 (8.12%) aligned >1 times 96.03% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 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] 544 / 558685 = 0.0010 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 16:30:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.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 16:30:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:30:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.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 16:30:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:30:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:30:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.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 16:30:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:30:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:30:39: 1000000 INFO @ Fri, 05 Jul 2019 16:30:40: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:30:40: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:30:40: #1 total tags in treatment: 538554 INFO @ Fri, 05 Jul 2019 16:30:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:30:40: #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 16:30:40: #1 tags after filtering in treatment: 525461 INFO @ Fri, 05 Jul 2019 16:30:40: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 05 Jul 2019 16:30:40: #1 finished! INFO @ Fri, 05 Jul 2019 16:30:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:30:40: #2 number of paired peaks: 173 WARNING @ Fri, 05 Jul 2019 16:30:40: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Fri, 05 Jul 2019 16:30:40: start model_add_line... INFO @ Fri, 05 Jul 2019 16:30:40: start X-correlation... INFO @ Fri, 05 Jul 2019 16:30:40: end of X-cor INFO @ Fri, 05 Jul 2019 16:30:40: #2 finished! INFO @ Fri, 05 Jul 2019 16:30:40: #2 predicted fragment length is 291 bps INFO @ Fri, 05 Jul 2019 16:30:40: #2 alternative fragment length(s) may be 0,56,95,131,148,181,187,215,237,262,291,319,340,369,393,427,455,522,565 bps INFO @ Fri, 05 Jul 2019 16:30:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.05_model.r INFO @ Fri, 05 Jul 2019 16:30:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:30:41: 1000000 INFO @ Fri, 05 Jul 2019 16:30:42: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:30:42: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:30:42: #1 total tags in treatment: 538554 INFO @ Fri, 05 Jul 2019 16:30:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:30:42: #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 16:30:42: #1 tags after filtering in treatment: 525461 INFO @ Fri, 05 Jul 2019 16:30:42: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 05 Jul 2019 16:30:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:30:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:30:42: 1000000 INFO @ Fri, 05 Jul 2019 16:30:42: #2 number of paired peaks: 173 WARNING @ Fri, 05 Jul 2019 16:30:42: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Fri, 05 Jul 2019 16:30:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:30:42: start X-correlation... INFO @ Fri, 05 Jul 2019 16:30:42: end of X-cor INFO @ Fri, 05 Jul 2019 16:30:42: #2 finished! INFO @ Fri, 05 Jul 2019 16:30:42: #2 predicted fragment length is 291 bps INFO @ Fri, 05 Jul 2019 16:30:42: #2 alternative fragment length(s) may be 0,56,95,131,148,181,187,215,237,262,291,319,340,369,393,427,455,522,565 bps INFO @ Fri, 05 Jul 2019 16:30:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.10_model.r INFO @ Fri, 05 Jul 2019 16:30:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:30:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:30:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:30:43: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:30:43: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:30:43: #1 total tags in treatment: 538554 INFO @ Fri, 05 Jul 2019 16:30:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:30:43: #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 16:30:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:30:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:30:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.05_summits.bed INFO @ Fri, 05 Jul 2019 16:30:43: Done! INFO @ Fri, 05 Jul 2019 16:30:43: #1 tags after filtering in treatment: 525461 INFO @ Fri, 05 Jul 2019 16:30:43: #1 Redundant rate of treatment: 0.02 INFO @ Fri, 05 Jul 2019 16:30:43: #1 finished! INFO @ Fri, 05 Jul 2019 16:30:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:30:43: #2 number of paired peaks: 173 WARNING @ Fri, 05 Jul 2019 16:30:43: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Fri, 05 Jul 2019 16:30:43: start model_add_line... INFO @ Fri, 05 Jul 2019 16:30:43: start X-correlation... pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:30:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:30:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:30:43: #2 predicted fragment length is 291 bps INFO @ Fri, 05 Jul 2019 16:30:43: #2 alternative fragment length(s) may be 0,56,95,131,148,181,187,215,237,262,291,319,340,369,393,427,455,522,565 bps INFO @ Fri, 05 Jul 2019 16:30:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.20_model.r INFO @ Fri, 05 Jul 2019 16:30:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:30:43: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:30:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:30:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.10_summits.bed INFO @ Fri, 05 Jul 2019 16:30:45: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:30:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:30:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433717/ERX433717.20_summits.bed INFO @ Fri, 05 Jul 2019 16:30:45: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。