Job ID = 2008245 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,492,465 reads read : 8,984,930 reads written : 8,984,930 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628976.sra.cache’: 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: 00:03:37 4492465 reads; of these: 4492465 (100.00%) were paired; of these: 374269 (8.33%) aligned concordantly 0 times 3694721 (82.24%) aligned concordantly exactly 1 time 423475 (9.43%) aligned concordantly >1 times ---- 374269 pairs aligned concordantly 0 times; of these: 23580 (6.30%) aligned discordantly 1 time ---- 350689 pairs aligned 0 times concordantly or discordantly; of these: 701378 mates make up the pairs; of these: 674191 (96.12%) aligned 0 times 16636 (2.37%) aligned exactly 1 time 10551 (1.50%) aligned >1 times 92.50% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 2323204 / 4136858 = 0.5616 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 18:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.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 18:10:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:10:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.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 18:10:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:10:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.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 18:10:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:10:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:10:20: 1000000 INFO @ Fri, 05 Jul 2019 18:10:21: 1000000 INFO @ Fri, 05 Jul 2019 18:10:21: 1000000 INFO @ Fri, 05 Jul 2019 18:10:27: 2000000 INFO @ Fri, 05 Jul 2019 18:10:28: 2000000 INFO @ Fri, 05 Jul 2019 18:10:28: 2000000 INFO @ Fri, 05 Jul 2019 18:10:34: 3000000 INFO @ Fri, 05 Jul 2019 18:10:35: 3000000 INFO @ Fri, 05 Jul 2019 18:10:36: 3000000 INFO @ Fri, 05 Jul 2019 18:10:38: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:10:38: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:10:38: #1 total tags in treatment: 1798427 INFO @ Fri, 05 Jul 2019 18:10:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:10:38: #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 18:10:38: #1 tags after filtering in treatment: 1187061 INFO @ Fri, 05 Jul 2019 18:10:38: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 18:10:38: #1 finished! INFO @ Fri, 05 Jul 2019 18:10:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:10:38: #2 number of paired peaks: 110 WARNING @ Fri, 05 Jul 2019 18:10:38: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 05 Jul 2019 18:10:38: start model_add_line... INFO @ Fri, 05 Jul 2019 18:10:38: start X-correlation... INFO @ Fri, 05 Jul 2019 18:10:38: end of X-cor INFO @ Fri, 05 Jul 2019 18:10:38: #2 finished! INFO @ Fri, 05 Jul 2019 18:10:38: #2 predicted fragment length is 105 bps INFO @ Fri, 05 Jul 2019 18:10:38: #2 alternative fragment length(s) may be 1,105,499,544,569 bps INFO @ Fri, 05 Jul 2019 18:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.05_model.r INFO @ Fri, 05 Jul 2019 18:10:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:10:40: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:10:40: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:10:40: #1 total tags in treatment: 1798427 INFO @ Fri, 05 Jul 2019 18:10:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:10:40: #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 18:10:40: #1 tags after filtering in treatment: 1187061 INFO @ Fri, 05 Jul 2019 18:10:40: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 18:10:40: #1 finished! INFO @ Fri, 05 Jul 2019 18:10:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:10:40: #2 number of paired peaks: 110 WARNING @ Fri, 05 Jul 2019 18:10:40: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 05 Jul 2019 18:10:40: start model_add_line... INFO @ Fri, 05 Jul 2019 18:10:40: start X-correlation... INFO @ Fri, 05 Jul 2019 18:10:40: end of X-cor INFO @ Fri, 05 Jul 2019 18:10:40: #2 finished! INFO @ Fri, 05 Jul 2019 18:10:40: #2 predicted fragment length is 105 bps INFO @ Fri, 05 Jul 2019 18:10:40: #2 alternative fragment length(s) may be 1,105,499,544,569 bps INFO @ Fri, 05 Jul 2019 18:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.10_model.r INFO @ Fri, 05 Jul 2019 18:10:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:10:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:10:40: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:10:40: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:10:40: #1 total tags in treatment: 1798427 INFO @ Fri, 05 Jul 2019 18:10:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:10:40: #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 18:10:40: #1 tags after filtering in treatment: 1187061 INFO @ Fri, 05 Jul 2019 18:10:40: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 18:10:40: #1 finished! INFO @ Fri, 05 Jul 2019 18:10:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:10:41: #2 number of paired peaks: 110 WARNING @ Fri, 05 Jul 2019 18:10:41: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 05 Jul 2019 18:10:41: start model_add_line... INFO @ Fri, 05 Jul 2019 18:10:41: start X-correlation... INFO @ Fri, 05 Jul 2019 18:10:41: end of X-cor INFO @ Fri, 05 Jul 2019 18:10:41: #2 finished! INFO @ Fri, 05 Jul 2019 18:10:41: #2 predicted fragment length is 105 bps INFO @ Fri, 05 Jul 2019 18:10:41: #2 alternative fragment length(s) may be 1,105,499,544,569 bps INFO @ Fri, 05 Jul 2019 18:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.20_model.r INFO @ Fri, 05 Jul 2019 18:10:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:10:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:10:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:10:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:10:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.05_summits.bed INFO @ Fri, 05 Jul 2019 18:10:43: Done! pass1 - making usageList (17 chroms): 1 millis INFO @ Fri, 05 Jul 2019 18:10:44: #3 Call peaks for each chromosome... pass2 - checking and writing primary data (411 records, 4 fields): 154 millis INFO @ Fri, 05 Jul 2019 18:10:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.10_summits.bed INFO @ Fri, 05 Jul 2019 18:10:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 18:10:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:10:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:10:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585769/ERX585769.20_summits.bed INFO @ Fri, 05 Jul 2019 18:10:46: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。