Job ID = 2008335 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,653,483 reads read : 33,306,966 reads written : 33,306,966 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: 00:12:15 16653483 reads; of these: 16653483 (100.00%) were paired; of these: 639980 (3.84%) aligned concordantly 0 times 14730849 (88.46%) aligned concordantly exactly 1 time 1282654 (7.70%) aligned concordantly >1 times ---- 639980 pairs aligned concordantly 0 times; of these: 136121 (21.27%) aligned discordantly 1 time ---- 503859 pairs aligned 0 times concordantly or discordantly; of these: 1007718 mates make up the pairs; of these: 915507 (90.85%) aligned 0 times 54956 (5.45%) aligned exactly 1 time 37255 (3.70%) aligned >1 times 97.25% overall alignment rate Time searching: 00:12:15 Overall time: 00:12:15 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 12 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] 15457584 / 16130379 = 0.9583 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 19:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.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 19:12:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:12:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.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 19:12:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:12:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:12:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.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 19:12:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:12:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:12:26: 1000000 INFO @ Fri, 05 Jul 2019 19:12:27: 1000000 INFO @ Fri, 05 Jul 2019 19:12:28: 1000000 INFO @ Fri, 05 Jul 2019 19:12:29: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 19:12:29: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 19:12:29: #1 total tags in treatment: 627902 INFO @ Fri, 05 Jul 2019 19:12:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:12:29: #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 19:12:29: #1 tags after filtering in treatment: 499495 INFO @ Fri, 05 Jul 2019 19:12:29: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 19:12:29: #1 finished! INFO @ Fri, 05 Jul 2019 19:12:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:12:29: #2 number of paired peaks: 290 WARNING @ Fri, 05 Jul 2019 19:12:29: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 05 Jul 2019 19:12:29: start model_add_line... INFO @ Fri, 05 Jul 2019 19:12:29: start X-correlation... INFO @ Fri, 05 Jul 2019 19:12:29: end of X-cor INFO @ Fri, 05 Jul 2019 19:12:29: #2 finished! INFO @ Fri, 05 Jul 2019 19:12:29: #2 predicted fragment length is 268 bps INFO @ Fri, 05 Jul 2019 19:12:29: #2 alternative fragment length(s) may be 40,83,105,171,194,239,268,298,349,373,408,449,541,570 bps INFO @ Fri, 05 Jul 2019 19:12:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.05_model.r INFO @ Fri, 05 Jul 2019 19:12:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:12:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:12:30: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 19:12:30: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 19:12:30: #1 total tags in treatment: 627902 INFO @ Fri, 05 Jul 2019 19:12:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:12:30: #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 19:12:30: #1 tags after filtering in treatment: 499495 INFO @ Fri, 05 Jul 2019 19:12:30: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 19:12:30: #1 finished! INFO @ Fri, 05 Jul 2019 19:12:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:12:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:12:30: #2 number of paired peaks: 290 WARNING @ Fri, 05 Jul 2019 19:12:30: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 05 Jul 2019 19:12:30: start model_add_line... INFO @ Fri, 05 Jul 2019 19:12:30: start X-correlation... INFO @ Fri, 05 Jul 2019 19:12:30: end of X-cor INFO @ Fri, 05 Jul 2019 19:12:30: #2 finished! INFO @ Fri, 05 Jul 2019 19:12:30: #2 predicted fragment length is 268 bps INFO @ Fri, 05 Jul 2019 19:12:30: #2 alternative fragment length(s) may be 40,83,105,171,194,239,268,298,349,373,408,449,541,570 bps INFO @ Fri, 05 Jul 2019 19:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.10_model.r INFO @ Fri, 05 Jul 2019 19:12:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:12:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:12:31: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 19:12:31: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 19:12:31: #1 total tags in treatment: 627902 INFO @ Fri, 05 Jul 2019 19:12:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:12:31: #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 19:12:31: #1 tags after filtering in treatment: 499495 INFO @ Fri, 05 Jul 2019 19:12:31: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 19:12:31: #1 finished! INFO @ Fri, 05 Jul 2019 19:12:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:12:31: #2 number of paired peaks: 290 WARNING @ Fri, 05 Jul 2019 19:12:31: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Fri, 05 Jul 2019 19:12:31: start model_add_line... INFO @ Fri, 05 Jul 2019 19:12:31: start X-correlation... INFO @ Fri, 05 Jul 2019 19:12:31: end of X-cor INFO @ Fri, 05 Jul 2019 19:12:31: #2 finished! INFO @ Fri, 05 Jul 2019 19:12:31: #2 predicted fragment length is 268 bps INFO @ Fri, 05 Jul 2019 19:12:31: #2 alternative fragment length(s) may be 40,83,105,171,194,239,268,298,349,373,408,449,541,570 bps INFO @ Fri, 05 Jul 2019 19:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.20_model.r INFO @ Fri, 05 Jul 2019 19:12:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.05_summits.bed INFO @ Fri, 05 Jul 2019 19:12:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 19:12:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.10_summits.bed INFO @ Fri, 05 Jul 2019 19:12:33: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 19:12:33: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:12:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:12:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:12:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585843/ERX585843.20_summits.bed INFO @ Fri, 05 Jul 2019 19:12:34: 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。