Job ID = 2640737 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,653,675 reads read : 13,307,350 reads written : 13,307,350 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:23 6653675 reads; of these: 6653675 (100.00%) were paired; of these: 6487023 (97.50%) aligned concordantly 0 times 124795 (1.88%) aligned concordantly exactly 1 time 41857 (0.63%) aligned concordantly >1 times ---- 6487023 pairs aligned concordantly 0 times; of these: 56148 (0.87%) aligned discordantly 1 time ---- 6430875 pairs aligned 0 times concordantly or discordantly; of these: 12861750 mates make up the pairs; of these: 12355155 (96.06%) aligned 0 times 385649 (3.00%) aligned exactly 1 time 120946 (0.94%) aligned >1 times 7.16% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 71018 / 221310 = 0.3209 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.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 18:48:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:48:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:49:02: #1 tag size is determined as 47 bps INFO @ Sat, 24 Aug 2019 18:49:02: #1 tag size = 47 INFO @ Sat, 24 Aug 2019 18:49:02: #1 total tags in treatment: 114859 INFO @ Sat, 24 Aug 2019 18:49:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:49:02: #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 18:49:02: #1 tags after filtering in treatment: 109799 INFO @ Sat, 24 Aug 2019 18:49:02: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 24 Aug 2019 18:49:02: #1 finished! INFO @ Sat, 24 Aug 2019 18:49:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:49:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:49:02: #2 number of paired peaks: 149 WARNING @ Sat, 24 Aug 2019 18:49:02: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Sat, 24 Aug 2019 18:49:02: start model_add_line... INFO @ Sat, 24 Aug 2019 18:49:02: start X-correlation... INFO @ Sat, 24 Aug 2019 18:49:02: end of X-cor INFO @ Sat, 24 Aug 2019 18:49:02: #2 finished! INFO @ Sat, 24 Aug 2019 18:49:02: #2 predicted fragment length is 257 bps INFO @ Sat, 24 Aug 2019 18:49:02: #2 alternative fragment length(s) may be 79,109,129,145,169,193,215,234,257,281,320,366,393,414,438,481,505,552,571,588 bps INFO @ Sat, 24 Aug 2019 18:49:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.05_model.r INFO @ Sat, 24 Aug 2019 18:49:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:49:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:49:02: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.05_summits.bed INFO @ Sat, 24 Aug 2019 18:49:02: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:49:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.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 18:49:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:49:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:49:30: #1 tag size is determined as 47 bps INFO @ Sat, 24 Aug 2019 18:49:30: #1 tag size = 47 INFO @ Sat, 24 Aug 2019 18:49:30: #1 total tags in treatment: 114859 INFO @ Sat, 24 Aug 2019 18:49:30: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:49:30: #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 18:49:30: #1 tags after filtering in treatment: 109799 INFO @ Sat, 24 Aug 2019 18:49:30: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 24 Aug 2019 18:49:30: #1 finished! INFO @ Sat, 24 Aug 2019 18:49:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:49:31: #2 number of paired peaks: 149 WARNING @ Sat, 24 Aug 2019 18:49:31: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Sat, 24 Aug 2019 18:49:31: start model_add_line... INFO @ Sat, 24 Aug 2019 18:49:31: start X-correlation... INFO @ Sat, 24 Aug 2019 18:49:31: end of X-cor INFO @ Sat, 24 Aug 2019 18:49:31: #2 finished! INFO @ Sat, 24 Aug 2019 18:49:31: #2 predicted fragment length is 257 bps INFO @ Sat, 24 Aug 2019 18:49:31: #2 alternative fragment length(s) may be 79,109,129,145,169,193,215,234,257,281,320,366,393,414,438,481,505,552,571,588 bps INFO @ Sat, 24 Aug 2019 18:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.10_model.r INFO @ Sat, 24 Aug 2019 18:49:31: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:49:31: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.10_summits.bed INFO @ Sat, 24 Aug 2019 18:49:31: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.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 18:49:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:49:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:50:01: #1 tag size is determined as 47 bps INFO @ Sat, 24 Aug 2019 18:50:01: #1 tag size = 47 INFO @ Sat, 24 Aug 2019 18:50:01: #1 total tags in treatment: 114859 INFO @ Sat, 24 Aug 2019 18:50:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:50:01: #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 18:50:01: #1 tags after filtering in treatment: 109799 INFO @ Sat, 24 Aug 2019 18:50:01: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 24 Aug 2019 18:50:01: #1 finished! INFO @ Sat, 24 Aug 2019 18:50:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:50:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:50:01: #2 number of paired peaks: 149 WARNING @ Sat, 24 Aug 2019 18:50:01: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Sat, 24 Aug 2019 18:50:01: start model_add_line... INFO @ Sat, 24 Aug 2019 18:50:01: start X-correlation... INFO @ Sat, 24 Aug 2019 18:50:01: end of X-cor INFO @ Sat, 24 Aug 2019 18:50:01: #2 finished! INFO @ Sat, 24 Aug 2019 18:50:01: #2 predicted fragment length is 257 bps INFO @ Sat, 24 Aug 2019 18:50:01: #2 alternative fragment length(s) may be 79,109,129,145,169,193,215,234,257,281,320,366,393,414,438,481,505,552,571,588 bps INFO @ Sat, 24 Aug 2019 18:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.20_model.r INFO @ Sat, 24 Aug 2019 18:50:01: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:50:02: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:50:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:50:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:50:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2070730/ERX2070730.20_summits.bed INFO @ Sat, 24 Aug 2019 18:50:02: 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。