Job ID = 2008080 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,681,878 reads read : 3,363,756 reads written : 3,363,756 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: 00:02:09 1681878 reads; of these: 1681878 (100.00%) were paired; of these: 197989 (11.77%) aligned concordantly 0 times 1363741 (81.08%) aligned concordantly exactly 1 time 120148 (7.14%) aligned concordantly >1 times ---- 197989 pairs aligned concordantly 0 times; of these: 115487 (58.33%) aligned discordantly 1 time ---- 82502 pairs aligned 0 times concordantly or discordantly; of these: 165004 mates make up the pairs; of these: 104061 (63.07%) aligned 0 times 34263 (20.76%) aligned exactly 1 time 26680 (16.17%) aligned >1 times 96.91% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 46746 / 1575052 = 0.0297 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 17:32:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.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 17:32:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.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 17:32:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.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 17:32:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:33:08: 1000000 INFO @ Fri, 05 Jul 2019 17:33:08: 1000000 INFO @ Fri, 05 Jul 2019 17:33:09: 1000000 INFO @ Fri, 05 Jul 2019 17:33:17: 2000000 INFO @ Fri, 05 Jul 2019 17:33:18: 2000000 INFO @ Fri, 05 Jul 2019 17:33:22: 2000000 INFO @ Fri, 05 Jul 2019 17:33:25: 3000000 INFO @ Fri, 05 Jul 2019 17:33:27: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:33:27: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:33:27: #1 total tags in treatment: 1438887 INFO @ Fri, 05 Jul 2019 17:33:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:27: #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 17:33:27: #1 tags after filtering in treatment: 1344615 INFO @ Fri, 05 Jul 2019 17:33:27: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:33:27: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:27: #2 number of paired peaks: 145 WARNING @ Fri, 05 Jul 2019 17:33:27: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:27: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:27: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:27: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:27: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:27: #2 predicted fragment length is 210 bps INFO @ Fri, 05 Jul 2019 17:33:27: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 05 Jul 2019 17:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.20_model.r INFO @ Fri, 05 Jul 2019 17:33:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:29: 3000000 INFO @ Fri, 05 Jul 2019 17:33:31: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:33:31: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:33:31: #1 total tags in treatment: 1438887 INFO @ Fri, 05 Jul 2019 17:33:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:31: #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 17:33:31: #1 tags after filtering in treatment: 1344615 INFO @ Fri, 05 Jul 2019 17:33:31: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:33:31: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:31: #2 number of paired peaks: 145 WARNING @ Fri, 05 Jul 2019 17:33:31: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:31: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:31: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:31: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:31: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:31: #2 predicted fragment length is 210 bps INFO @ Fri, 05 Jul 2019 17:33:31: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 05 Jul 2019 17:33:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.10_model.r INFO @ Fri, 05 Jul 2019 17:33:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.20_summits.bed INFO @ Fri, 05 Jul 2019 17:33:34: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:33:36: 3000000 INFO @ Fri, 05 Jul 2019 17:33:36: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:33:38: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:33:38: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:33:38: #1 total tags in treatment: 1438887 INFO @ Fri, 05 Jul 2019 17:33:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:38: #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 17:33:38: #1 tags after filtering in treatment: 1344615 INFO @ Fri, 05 Jul 2019 17:33:38: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:33:38: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:38: #2 number of paired peaks: 145 WARNING @ Fri, 05 Jul 2019 17:33:38: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:38: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.10_summits.bed INFO @ Fri, 05 Jul 2019 17:33:38: Done! INFO @ Fri, 05 Jul 2019 17:33:38: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:38: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:38: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:38: #2 predicted fragment length is 210 bps INFO @ Fri, 05 Jul 2019 17:33:38: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 05 Jul 2019 17:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.05_model.r INFO @ Fri, 05 Jul 2019 17:33:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:38: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (425 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:33:43: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:33:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471858/ERX471858.05_summits.bed INFO @ Fri, 05 Jul 2019 17:33:45: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (729 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。