Job ID = 2640736 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,785,704 reads read : 17,571,408 reads written : 17,571,408 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: 00:01:30 8785704 reads; of these: 8785704 (100.00%) were paired; of these: 8630953 (98.24%) aligned concordantly 0 times 121595 (1.38%) aligned concordantly exactly 1 time 33156 (0.38%) aligned concordantly >1 times ---- 8630953 pairs aligned concordantly 0 times; of these: 29846 (0.35%) aligned discordantly 1 time ---- 8601107 pairs aligned 0 times concordantly or discordantly; of these: 17202214 mates make up the pairs; of these: 16695404 (97.05%) aligned 0 times 397380 (2.31%) aligned exactly 1 time 109430 (0.64%) aligned >1 times 4.99% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 27053 / 183463 = 0.1475 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:49:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.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 @ Sat, 24 Aug 2019 18:49:10: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:49:10: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:49:16: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:49:16: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:49:16: #1 total tags in treatment: 132885 INFO @ Sat, 24 Aug 2019 18:49:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:49:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:49:16: #1 tags after filtering in treatment: 129455 INFO @ Sat, 24 Aug 2019 18:49:16: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 24 Aug 2019 18:49:16: #1 finished! INFO @ Sat, 24 Aug 2019 18:49:16: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:49:16: #2 number of paired peaks: 180 WARNING @ Sat, 24 Aug 2019 18:49:16: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 24 Aug 2019 18:49:16: start model_add_line... INFO @ Sat, 24 Aug 2019 18:49:16: start X-correlation... INFO @ Sat, 24 Aug 2019 18:49:16: end of X-cor INFO @ Sat, 24 Aug 2019 18:49:16: #2 finished! INFO @ Sat, 24 Aug 2019 18:49:16: #2 predicted fragment length is 193 bps INFO @ Sat, 24 Aug 2019 18:49:16: #2 alternative fragment length(s) may be 14,62,110,164,193,256,274,298 bps INFO @ Sat, 24 Aug 2019 18:49:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.05_model.r INFO @ Sat, 24 Aug 2019 18:49:16: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:49:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:49:16: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:49:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:49:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:49:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.05_summits.bed INFO @ Sat, 24 Aug 2019 18:49:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:49:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.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 @ Sat, 24 Aug 2019 18:49:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:49:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:49:48: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:49:48: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:49:48: #1 total tags in treatment: 132885 INFO @ Sat, 24 Aug 2019 18:49:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:49:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:49:48: #1 tags after filtering in treatment: 129455 INFO @ Sat, 24 Aug 2019 18:49:48: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 24 Aug 2019 18:49:48: #1 finished! INFO @ Sat, 24 Aug 2019 18:49:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:49:48: #2 number of paired peaks: 180 WARNING @ Sat, 24 Aug 2019 18:49:48: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 24 Aug 2019 18:49:48: start model_add_line... INFO @ Sat, 24 Aug 2019 18:49:48: start X-correlation... INFO @ Sat, 24 Aug 2019 18:49:48: end of X-cor INFO @ Sat, 24 Aug 2019 18:49:48: #2 finished! INFO @ Sat, 24 Aug 2019 18:49:48: #2 predicted fragment length is 193 bps INFO @ Sat, 24 Aug 2019 18:49:48: #2 alternative fragment length(s) may be 14,62,110,164,193,256,274,298 bps INFO @ Sat, 24 Aug 2019 18:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.10_model.r INFO @ Sat, 24 Aug 2019 18:49:48: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:49:49: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:49:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:49:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:49:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.10_summits.bed INFO @ Sat, 24 Aug 2019 18:49:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.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 @ Sat, 24 Aug 2019 18:50:10: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:50:10: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:50:18: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:50:18: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:50:18: #1 total tags in treatment: 132885 INFO @ Sat, 24 Aug 2019 18:50:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:50:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:50:18: #1 tags after filtering in treatment: 129455 INFO @ Sat, 24 Aug 2019 18:50:18: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 24 Aug 2019 18:50:18: #1 finished! INFO @ Sat, 24 Aug 2019 18:50:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:50:18: #2 number of paired peaks: 180 WARNING @ Sat, 24 Aug 2019 18:50:18: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 24 Aug 2019 18:50:18: start model_add_line... INFO @ Sat, 24 Aug 2019 18:50:18: start X-correlation... INFO @ Sat, 24 Aug 2019 18:50:18: end of X-cor INFO @ Sat, 24 Aug 2019 18:50:18: #2 finished! INFO @ Sat, 24 Aug 2019 18:50:18: #2 predicted fragment length is 193 bps INFO @ Sat, 24 Aug 2019 18:50:18: #2 alternative fragment length(s) may be 14,62,110,164,193,256,274,298 bps INFO @ Sat, 24 Aug 2019 18:50:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.20_model.r INFO @ Sat, 24 Aug 2019 18:50:18: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:50:18: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2070729/ERX2070729.20_summits.bed INFO @ Sat, 24 Aug 2019 18:50:19: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。