Job ID = 2008037 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,675,703 reads read : 3,351,406 reads written : 3,351,406 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: 00:02:35 1675703 reads; of these: 1675703 (100.00%) were paired; of these: 167612 (10.00%) aligned concordantly 0 times 1372482 (81.90%) aligned concordantly exactly 1 time 135609 (8.09%) aligned concordantly >1 times ---- 167612 pairs aligned concordantly 0 times; of these: 31456 (18.77%) aligned discordantly 1 time ---- 136156 pairs aligned 0 times concordantly or discordantly; of these: 272312 mates make up the pairs; of these: 246922 (90.68%) aligned 0 times 15961 (5.86%) aligned exactly 1 time 9429 (3.46%) aligned >1 times 92.63% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 47161 / 1535499 = 0.0307 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 17:21:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.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 17:21:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:21:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.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 17:21:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:21:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.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 17:21:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:21:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:21:24: 1000000 INFO @ Fri, 05 Jul 2019 17:21:25: 1000000 INFO @ Fri, 05 Jul 2019 17:21:26: 1000000 INFO @ Fri, 05 Jul 2019 17:21:34: 2000000 INFO @ Fri, 05 Jul 2019 17:21:38: 2000000 INFO @ Fri, 05 Jul 2019 17:21:40: 2000000 INFO @ Fri, 05 Jul 2019 17:21:43: 3000000 INFO @ Fri, 05 Jul 2019 17:21:44: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:21:44: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:21:44: #1 total tags in treatment: 1461432 INFO @ Fri, 05 Jul 2019 17:21:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:21:44: #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 17:21:44: #1 tags after filtering in treatment: 1368402 INFO @ Fri, 05 Jul 2019 17:21:44: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:21:44: #1 finished! INFO @ Fri, 05 Jul 2019 17:21:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:21:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:21:44: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 17:21:44: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 17:21:44: start model_add_line... INFO @ Fri, 05 Jul 2019 17:21:44: start X-correlation... INFO @ Fri, 05 Jul 2019 17:21:44: end of X-cor INFO @ Fri, 05 Jul 2019 17:21:44: #2 finished! INFO @ Fri, 05 Jul 2019 17:21:44: #2 predicted fragment length is 231 bps INFO @ Fri, 05 Jul 2019 17:21:44: #2 alternative fragment length(s) may be 1,84,106,144,183,201,205,214,231,248,274,286,305,455,479,500,566,581 bps INFO @ Fri, 05 Jul 2019 17:21:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.20_model.r INFO @ Fri, 05 Jul 2019 17:21:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:21:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:21:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:21:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:21:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:21:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.20_summits.bed INFO @ Fri, 05 Jul 2019 17:21:51: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 17:21:51: 3000000 INFO @ Fri, 05 Jul 2019 17:21:51: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:21:51: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:21:51: #1 total tags in treatment: 1461432 INFO @ Fri, 05 Jul 2019 17:21:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:21:51: #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 17:21:51: #1 tags after filtering in treatment: 1368402 INFO @ Fri, 05 Jul 2019 17:21:51: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:21:51: #1 finished! INFO @ Fri, 05 Jul 2019 17:21:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:21:51: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 17:21:51: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 17:21:51: start model_add_line... INFO @ Fri, 05 Jul 2019 17:21:51: start X-correlation... INFO @ Fri, 05 Jul 2019 17:21:51: end of X-cor INFO @ Fri, 05 Jul 2019 17:21:51: #2 finished! INFO @ Fri, 05 Jul 2019 17:21:51: #2 predicted fragment length is 231 bps INFO @ Fri, 05 Jul 2019 17:21:51: #2 alternative fragment length(s) may be 1,84,106,144,183,201,205,214,231,248,274,286,305,455,479,500,566,581 bps INFO @ Fri, 05 Jul 2019 17:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.05_model.r INFO @ Fri, 05 Jul 2019 17:21:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:21:51: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:21:53: 3000000 INFO @ Fri, 05 Jul 2019 17:21:53: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:21:53: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:21:53: #1 total tags in treatment: 1461432 INFO @ Fri, 05 Jul 2019 17:21:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:21:53: #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 17:21:53: #1 tags after filtering in treatment: 1368402 INFO @ Fri, 05 Jul 2019 17:21:53: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:21:53: #1 finished! INFO @ Fri, 05 Jul 2019 17:21:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:21:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:21:53: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 17:21:53: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 17:21:53: start model_add_line... INFO @ Fri, 05 Jul 2019 17:21:53: start X-correlation... INFO @ Fri, 05 Jul 2019 17:21:53: end of X-cor INFO @ Fri, 05 Jul 2019 17:21:53: #2 finished! INFO @ Fri, 05 Jul 2019 17:21:53: #2 predicted fragment length is 231 bps INFO @ Fri, 05 Jul 2019 17:21:53: #2 alternative fragment length(s) may be 1,84,106,144,183,201,205,214,231,248,274,286,305,455,479,500,566,581 bps INFO @ Fri, 05 Jul 2019 17:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.10_model.r INFO @ Fri, 05 Jul 2019 17:21:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:21:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.05_summits.bed INFO @ Fri, 05 Jul 2019 17:21:58: Done! INFO @ Fri, 05 Jul 2019 17:21:59: #3 Call peaks for each chromosome... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (73 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471822/ERX471822.10_summits.bed INFO @ Fri, 05 Jul 2019 17:22:01: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (26 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。