Job ID = 2008003 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,066,499 reads read : 4,132,998 reads written : 4,132,998 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: 00:02:46 2066499 reads; of these: 2066499 (100.00%) were paired; of these: 233690 (11.31%) aligned concordantly 0 times 1664642 (80.55%) aligned concordantly exactly 1 time 168167 (8.14%) aligned concordantly >1 times ---- 233690 pairs aligned concordantly 0 times; of these: 41448 (17.74%) aligned discordantly 1 time ---- 192242 pairs aligned 0 times concordantly or discordantly; of these: 384484 mates make up the pairs; of these: 347323 (90.33%) aligned 0 times 23929 (6.22%) aligned exactly 1 time 13232 (3.44%) aligned >1 times 91.60% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:49 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] 163649 / 1862994 = 0.0878 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 17:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.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 17:09:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:09:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.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 17:09:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:09:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.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 17:09:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:09:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:09:57: 1000000 INFO @ Fri, 05 Jul 2019 17:09:59: 1000000 INFO @ Fri, 05 Jul 2019 17:09:59: 1000000 INFO @ Fri, 05 Jul 2019 17:10:05: 2000000 INFO @ Fri, 05 Jul 2019 17:10:09: 2000000 INFO @ Fri, 05 Jul 2019 17:10:11: 2000000 INFO @ Fri, 05 Jul 2019 17:10:14: 3000000 INFO @ Fri, 05 Jul 2019 17:10:17: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:10:17: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:10:17: #1 total tags in treatment: 1670683 INFO @ Fri, 05 Jul 2019 17:10:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:10:17: #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 17:10:17: #1 tags after filtering in treatment: 1560711 INFO @ Fri, 05 Jul 2019 17:10:17: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:10:17: #1 finished! INFO @ Fri, 05 Jul 2019 17:10:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:10:17: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 17:10:17: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 17:10:17: start model_add_line... INFO @ Fri, 05 Jul 2019 17:10:17: start X-correlation... INFO @ Fri, 05 Jul 2019 17:10:17: end of X-cor INFO @ Fri, 05 Jul 2019 17:10:17: #2 finished! INFO @ Fri, 05 Jul 2019 17:10:17: #2 predicted fragment length is 211 bps INFO @ Fri, 05 Jul 2019 17:10:17: #2 alternative fragment length(s) may be 1,139,166,192,211,229,258,429,494,534,562,595 bps INFO @ Fri, 05 Jul 2019 17:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.10_model.r INFO @ Fri, 05 Jul 2019 17:10:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:10:19: 3000000 INFO @ Fri, 05 Jul 2019 17:10:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:10:23: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:10:23: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:10:23: #1 total tags in treatment: 1670683 INFO @ Fri, 05 Jul 2019 17:10:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:10:23: #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 17:10:23: 3000000 INFO @ Fri, 05 Jul 2019 17:10:23: #1 tags after filtering in treatment: 1560711 INFO @ Fri, 05 Jul 2019 17:10:23: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:10:23: #1 finished! INFO @ Fri, 05 Jul 2019 17:10:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:10:23: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 17:10:23: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 17:10:23: start model_add_line... INFO @ Fri, 05 Jul 2019 17:10:23: start X-correlation... INFO @ Fri, 05 Jul 2019 17:10:23: end of X-cor INFO @ Fri, 05 Jul 2019 17:10:23: #2 finished! INFO @ Fri, 05 Jul 2019 17:10:23: #2 predicted fragment length is 211 bps INFO @ Fri, 05 Jul 2019 17:10:23: #2 alternative fragment length(s) may be 1,139,166,192,211,229,258,429,494,534,562,595 bps INFO @ Fri, 05 Jul 2019 17:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.20_model.r INFO @ Fri, 05 Jul 2019 17:10:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.10_summits.bed INFO @ Fri, 05 Jul 2019 17:10:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:10:28: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:10:28: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:10:28: #1 total tags in treatment: 1670683 INFO @ Fri, 05 Jul 2019 17:10:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:10:28: #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 17:10:28: #1 tags after filtering in treatment: 1560711 INFO @ Fri, 05 Jul 2019 17:10:28: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:10:28: #1 finished! INFO @ Fri, 05 Jul 2019 17:10:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:10:28: #2 number of paired peaks: 156 WARNING @ Fri, 05 Jul 2019 17:10:28: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 05 Jul 2019 17:10:28: start model_add_line... INFO @ Fri, 05 Jul 2019 17:10:28: start X-correlation... INFO @ Fri, 05 Jul 2019 17:10:28: end of X-cor INFO @ Fri, 05 Jul 2019 17:10:28: #2 finished! INFO @ Fri, 05 Jul 2019 17:10:28: #2 predicted fragment length is 211 bps INFO @ Fri, 05 Jul 2019 17:10:28: #2 alternative fragment length(s) may be 1,139,166,192,211,229,258,429,494,534,562,595 bps INFO @ Fri, 05 Jul 2019 17:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.05_model.r INFO @ Fri, 05 Jul 2019 17:10:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:10:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.20_summits.bed INFO @ Fri, 05 Jul 2019 17:10:32: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 17:10:33: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:10:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:10:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:10:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471792/ERX471792.05_summits.bed INFO @ Fri, 05 Jul 2019 17:10:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。