Job ID = 2008072 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,969,512 reads read : 3,939,024 reads written : 3,939,024 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: 00:02:16 1969512 reads; of these: 1969512 (100.00%) were paired; of these: 236862 (12.03%) aligned concordantly 0 times 1598546 (81.16%) aligned concordantly exactly 1 time 134104 (6.81%) aligned concordantly >1 times ---- 236862 pairs aligned concordantly 0 times; of these: 41480 (17.51%) aligned discordantly 1 time ---- 195382 pairs aligned 0 times concordantly or discordantly; of these: 390764 mates make up the pairs; of these: 359423 (91.98%) aligned 0 times 19604 (5.02%) aligned exactly 1 time 11737 (3.00%) aligned >1 times 90.88% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 154994 / 1769391 = 0.0876 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 17:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.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 17:34:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:34:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.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 17:34:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:34:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:34:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.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 17:34:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:34:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:34:51: 1000000 INFO @ Fri, 05 Jul 2019 17:34:53: 1000000 INFO @ Fri, 05 Jul 2019 17:34:54: 1000000 INFO @ Fri, 05 Jul 2019 17:34:58: 2000000 INFO @ Fri, 05 Jul 2019 17:35:01: 2000000 INFO @ Fri, 05 Jul 2019 17:35:02: 2000000 INFO @ Fri, 05 Jul 2019 17:35:06: 3000000 INFO @ Fri, 05 Jul 2019 17:35:08: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:35:08: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:35:08: #1 total tags in treatment: 1579596 INFO @ Fri, 05 Jul 2019 17:35:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:35:08: #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 17:35:08: #1 tags after filtering in treatment: 1495598 INFO @ Fri, 05 Jul 2019 17:35:08: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:35:08: #1 finished! INFO @ Fri, 05 Jul 2019 17:35:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:35:08: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 17:35:08: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 17:35:08: start model_add_line... INFO @ Fri, 05 Jul 2019 17:35:08: start X-correlation... INFO @ Fri, 05 Jul 2019 17:35:08: end of X-cor INFO @ Fri, 05 Jul 2019 17:35:08: #2 finished! INFO @ Fri, 05 Jul 2019 17:35:08: #2 predicted fragment length is 205 bps INFO @ Fri, 05 Jul 2019 17:35:08: #2 alternative fragment length(s) may be 1,33,61,106,108,147,167,187,205,214,219,261,269,294,298,321,349,372,404,420,447,475,504,531,578 bps INFO @ Fri, 05 Jul 2019 17:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.05_model.r INFO @ Fri, 05 Jul 2019 17:35:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:35:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:35:10: 3000000 INFO @ Fri, 05 Jul 2019 17:35:10: 3000000 INFO @ Fri, 05 Jul 2019 17:35:12: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:35:12: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:35:12: #1 total tags in treatment: 1579596 INFO @ Fri, 05 Jul 2019 17:35:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:35:12: #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 17:35:12: #1 tags after filtering in treatment: 1495598 INFO @ Fri, 05 Jul 2019 17:35:12: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:35:12: #1 finished! INFO @ Fri, 05 Jul 2019 17:35:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:35:12: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:35:12: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:35:12: #1 total tags in treatment: 1579596 INFO @ Fri, 05 Jul 2019 17:35:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:35:12: #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 17:35:12: #1 tags after filtering in treatment: 1495598 INFO @ Fri, 05 Jul 2019 17:35:12: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:35:12: #1 finished! INFO @ Fri, 05 Jul 2019 17:35:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:35:12: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 17:35:12: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 17:35:12: start model_add_line... INFO @ Fri, 05 Jul 2019 17:35:12: start X-correlation... INFO @ Fri, 05 Jul 2019 17:35:12: end of X-cor INFO @ Fri, 05 Jul 2019 17:35:12: #2 finished! INFO @ Fri, 05 Jul 2019 17:35:12: #2 predicted fragment length is 205 bps INFO @ Fri, 05 Jul 2019 17:35:12: #2 alternative fragment length(s) may be 1,33,61,106,108,147,167,187,205,214,219,261,269,294,298,321,349,372,404,420,447,475,504,531,578 bps INFO @ Fri, 05 Jul 2019 17:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.20_model.r INFO @ Fri, 05 Jul 2019 17:35:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:35:12: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 17:35:12: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 17:35:12: start model_add_line... INFO @ Fri, 05 Jul 2019 17:35:12: start X-correlation... INFO @ Fri, 05 Jul 2019 17:35:12: end of X-cor INFO @ Fri, 05 Jul 2019 17:35:12: #2 finished! INFO @ Fri, 05 Jul 2019 17:35:12: #2 predicted fragment length is 205 bps INFO @ Fri, 05 Jul 2019 17:35:12: #2 alternative fragment length(s) may be 1,33,61,106,108,147,167,187,205,214,219,261,269,294,298,321,349,372,404,420,447,475,504,531,578 bps INFO @ Fri, 05 Jul 2019 17:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.10_model.r INFO @ Fri, 05 Jul 2019 17:35:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:35:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:35:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:35:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:35:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.05_summits.bed INFO @ Fri, 05 Jul 2019 17:35:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:35:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:35:17: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.20_summits.bed INFO @ Fri, 05 Jul 2019 17:35:19: Done! INFO @ Fri, 05 Jul 2019 17:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471853/ERX471853.10_summits.bed INFO @ Fri, 05 Jul 2019 17:35:19: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。