Job ID = 2007966 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,770,087 reads read : 3,540,174 reads written : 3,540,174 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: 00:03:17 1770087 reads; of these: 1770087 (100.00%) were paired; of these: 246047 (13.90%) aligned concordantly 0 times 1407441 (79.51%) aligned concordantly exactly 1 time 116599 (6.59%) aligned concordantly >1 times ---- 246047 pairs aligned concordantly 0 times; of these: 32840 (13.35%) aligned discordantly 1 time ---- 213207 pairs aligned 0 times concordantly or discordantly; of these: 426414 mates make up the pairs; of these: 400527 (93.93%) aligned 0 times 16986 (3.98%) aligned exactly 1 time 8901 (2.09%) aligned >1 times 88.69% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 315891 / 1554236 = 0.2032 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 17:06:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.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 17:06:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:06:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.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 17:06:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:06:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.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 17:06:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:06:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:57: 1000000 INFO @ Fri, 05 Jul 2019 17:06:58: 1000000 INFO @ Fri, 05 Jul 2019 17:07:00: 1000000 INFO @ Fri, 05 Jul 2019 17:07:06: 2000000 INFO @ Fri, 05 Jul 2019 17:07:08: 2000000 INFO @ Fri, 05 Jul 2019 17:07:10: 2000000 INFO @ Fri, 05 Jul 2019 17:07:11: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:11: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:11: #1 total tags in treatment: 1211248 INFO @ Fri, 05 Jul 2019 17:07:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:11: #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 17:07:11: #1 tags after filtering in treatment: 1158210 INFO @ Fri, 05 Jul 2019 17:07:11: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:07:11: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:11: #2 number of paired peaks: 181 WARNING @ Fri, 05 Jul 2019 17:07:11: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Fri, 05 Jul 2019 17:07:11: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:11: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:11: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:11: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:11: #2 predicted fragment length is 258 bps INFO @ Fri, 05 Jul 2019 17:07:11: #2 alternative fragment length(s) may be 0,31,53,101,142,182,204,238,258,324,378,544 bps INFO @ Fri, 05 Jul 2019 17:07:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.10_model.r INFO @ Fri, 05 Jul 2019 17:07:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:14: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:14: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:14: #1 total tags in treatment: 1211248 INFO @ Fri, 05 Jul 2019 17:07:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:14: #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 17:07:14: #1 tags after filtering in treatment: 1158210 INFO @ Fri, 05 Jul 2019 17:07:14: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:07:14: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:14: #2 number of paired peaks: 181 WARNING @ Fri, 05 Jul 2019 17:07:14: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Fri, 05 Jul 2019 17:07:14: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:14: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:14: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:14: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:14: #2 predicted fragment length is 258 bps INFO @ Fri, 05 Jul 2019 17:07:14: #2 alternative fragment length(s) may be 0,31,53,101,142,182,204,238,258,324,378,544 bps INFO @ Fri, 05 Jul 2019 17:07:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.05_model.r INFO @ Fri, 05 Jul 2019 17:07:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:07:15: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:15: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:15: #1 total tags in treatment: 1211248 INFO @ Fri, 05 Jul 2019 17:07:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:15: #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 17:07:15: #1 tags after filtering in treatment: 1158210 INFO @ Fri, 05 Jul 2019 17:07:15: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:07:15: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:16: #2 number of paired peaks: 181 WARNING @ Fri, 05 Jul 2019 17:07:16: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Fri, 05 Jul 2019 17:07:16: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:16: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:16: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:16: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:16: #2 predicted fragment length is 258 bps INFO @ Fri, 05 Jul 2019 17:07:16: #2 alternative fragment length(s) may be 0,31,53,101,142,182,204,238,258,324,378,544 bps INFO @ Fri, 05 Jul 2019 17:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.20_model.r INFO @ Fri, 05 Jul 2019 17:07:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.10_summits.bed INFO @ Fri, 05 Jul 2019 17:07:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:07:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.05_summits.bed INFO @ Fri, 05 Jul 2019 17:07:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:07:19: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:07:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471757/ERX471757.20_summits.bed INFO @ Fri, 05 Jul 2019 17:07:21: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (18 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。