Job ID = 2640744 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,500,183 reads read : 22,500,183 reads written : 22,500,183 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: 00:02:57 22500183 reads; of these: 22500183 (100.00%) were unpaired; of these: 19407813 (86.26%) aligned 0 times 2372789 (10.55%) aligned exactly 1 time 719581 (3.20%) aligned >1 times 13.74% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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_rmdupse_core] 2720826 / 3092370 = 0.8799 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:00:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.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 19:00:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:00:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:00:31: #1 tag size is determined as 52 bps INFO @ Sat, 24 Aug 2019 19:00:31: #1 tag size = 52 INFO @ Sat, 24 Aug 2019 19:00:31: #1 total tags in treatment: 371544 INFO @ Sat, 24 Aug 2019 19:00:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:00:31: #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 19:00:31: #1 tags after filtering in treatment: 371544 INFO @ Sat, 24 Aug 2019 19:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:00:31: #1 finished! INFO @ Sat, 24 Aug 2019 19:00:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:00:31: #2 number of paired peaks: 238 WARNING @ Sat, 24 Aug 2019 19:00:31: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Sat, 24 Aug 2019 19:00:31: start model_add_line... INFO @ Sat, 24 Aug 2019 19:00:31: start X-correlation... INFO @ Sat, 24 Aug 2019 19:00:32: end of X-cor INFO @ Sat, 24 Aug 2019 19:00:32: #2 finished! INFO @ Sat, 24 Aug 2019 19:00:32: #2 predicted fragment length is 161 bps INFO @ Sat, 24 Aug 2019 19:00:32: #2 alternative fragment length(s) may be 4,91,141,161,180 bps INFO @ Sat, 24 Aug 2019 19:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.05_model.r INFO @ Sat, 24 Aug 2019 19:00:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:00:33: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.05_summits.bed INFO @ Sat, 24 Aug 2019 19:00:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.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 19:00:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:00:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:01:01: #1 tag size is determined as 52 bps INFO @ Sat, 24 Aug 2019 19:01:01: #1 tag size = 52 INFO @ Sat, 24 Aug 2019 19:01:01: #1 total tags in treatment: 371544 INFO @ Sat, 24 Aug 2019 19:01:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:01:01: #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 19:01:01: #1 tags after filtering in treatment: 371544 INFO @ Sat, 24 Aug 2019 19:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:01:01: #1 finished! INFO @ Sat, 24 Aug 2019 19:01:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:01:01: #2 number of paired peaks: 238 WARNING @ Sat, 24 Aug 2019 19:01:01: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Sat, 24 Aug 2019 19:01:01: start model_add_line... INFO @ Sat, 24 Aug 2019 19:01:01: start X-correlation... INFO @ Sat, 24 Aug 2019 19:01:01: end of X-cor INFO @ Sat, 24 Aug 2019 19:01:01: #2 finished! INFO @ Sat, 24 Aug 2019 19:01:01: #2 predicted fragment length is 161 bps INFO @ Sat, 24 Aug 2019 19:01:01: #2 alternative fragment length(s) may be 4,91,141,161,180 bps INFO @ Sat, 24 Aug 2019 19:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.10_model.r INFO @ Sat, 24 Aug 2019 19:01:01: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:01:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.10_summits.bed INFO @ Sat, 24 Aug 2019 19:01:03: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (64 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.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 19:01:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:01:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:01:31: #1 tag size is determined as 52 bps INFO @ Sat, 24 Aug 2019 19:01:31: #1 tag size = 52 INFO @ Sat, 24 Aug 2019 19:01:31: #1 total tags in treatment: 371544 INFO @ Sat, 24 Aug 2019 19:01:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:01:31: #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 19:01:31: #1 tags after filtering in treatment: 371544 INFO @ Sat, 24 Aug 2019 19:01:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:01:31: #1 finished! INFO @ Sat, 24 Aug 2019 19:01:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:01:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:01:31: #2 number of paired peaks: 238 WARNING @ Sat, 24 Aug 2019 19:01:31: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Sat, 24 Aug 2019 19:01:31: start model_add_line... INFO @ Sat, 24 Aug 2019 19:01:31: start X-correlation... INFO @ Sat, 24 Aug 2019 19:01:31: end of X-cor INFO @ Sat, 24 Aug 2019 19:01:31: #2 finished! INFO @ Sat, 24 Aug 2019 19:01:31: #2 predicted fragment length is 161 bps INFO @ Sat, 24 Aug 2019 19:01:31: #2 alternative fragment length(s) may be 4,91,141,161,180 bps INFO @ Sat, 24 Aug 2019 19:01:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.20_model.r INFO @ Sat, 24 Aug 2019 19:01:31: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:01:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 19:01:33: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:01:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:01:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:01:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2732435/ERX2732435.20_summits.bed INFO @ Sat, 24 Aug 2019 19:01:33: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling