Job ID = 2640804 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,976,790 reads read : 3,953,580 reads written : 1,976,790 reads 0-length : 1,976,790 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: 00:00:48 1976790 reads; of these: 1976790 (100.00%) were unpaired; of these: 105768 (5.35%) aligned 0 times 1531040 (77.45%) aligned exactly 1 time 339982 (17.20%) aligned >1 times 94.65% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 780907 / 1871022 = 0.4174 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:21:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.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 19:21:40: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:21:40: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:21:51: 1000000 INFO @ Sat, 24 Aug 2019 19:21:52: #1 tag size is determined as 69 bps INFO @ Sat, 24 Aug 2019 19:21:52: #1 tag size = 69 INFO @ Sat, 24 Aug 2019 19:21:52: #1 total tags in treatment: 1090115 INFO @ Sat, 24 Aug 2019 19:21:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:21:52: #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 19:21:52: #1 tags after filtering in treatment: 1090115 INFO @ Sat, 24 Aug 2019 19:21:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:21:52: #1 finished! INFO @ Sat, 24 Aug 2019 19:21:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:21:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:21:52: #2 number of paired peaks: 119 WARNING @ Sat, 24 Aug 2019 19:21:52: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 24 Aug 2019 19:21:52: start model_add_line... INFO @ Sat, 24 Aug 2019 19:21:52: start X-correlation... INFO @ Sat, 24 Aug 2019 19:21:52: end of X-cor INFO @ Sat, 24 Aug 2019 19:21:52: #2 finished! INFO @ Sat, 24 Aug 2019 19:21:52: #2 predicted fragment length is 157 bps INFO @ Sat, 24 Aug 2019 19:21:52: #2 alternative fragment length(s) may be 0,51,135,157,178,212,293,318,457,507,552 bps INFO @ Sat, 24 Aug 2019 19:21:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.05_model.r INFO @ Sat, 24 Aug 2019 19:21:52: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:21:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:21:56: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:21:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:21:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:21:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.05_summits.bed INFO @ Sat, 24 Aug 2019 19:21:57: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (291 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:22:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.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 19:22:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:22:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:22:21: 1000000 INFO @ Sat, 24 Aug 2019 19:22:21: #1 tag size is determined as 69 bps INFO @ Sat, 24 Aug 2019 19:22:21: #1 tag size = 69 INFO @ Sat, 24 Aug 2019 19:22:21: #1 total tags in treatment: 1090115 INFO @ Sat, 24 Aug 2019 19:22:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:21: #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 19:22:22: #1 tags after filtering in treatment: 1090115 INFO @ Sat, 24 Aug 2019 19:22:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:22:22: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:22: #2 number of paired peaks: 119 WARNING @ Sat, 24 Aug 2019 19:22:22: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 24 Aug 2019 19:22:22: start model_add_line... INFO @ Sat, 24 Aug 2019 19:22:22: start X-correlation... INFO @ Sat, 24 Aug 2019 19:22:22: end of X-cor INFO @ Sat, 24 Aug 2019 19:22:22: #2 finished! INFO @ Sat, 24 Aug 2019 19:22:22: #2 predicted fragment length is 157 bps INFO @ Sat, 24 Aug 2019 19:22:22: #2 alternative fragment length(s) may be 0,51,135,157,178,212,293,318,457,507,552 bps INFO @ Sat, 24 Aug 2019 19:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.10_model.r INFO @ Sat, 24 Aug 2019 19:22:22: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:22:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:22:25: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.10_summits.bed INFO @ Sat, 24 Aug 2019 19:22:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:22:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.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 19:22:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:22:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:22:51: 1000000 INFO @ Sat, 24 Aug 2019 19:22:52: #1 tag size is determined as 69 bps INFO @ Sat, 24 Aug 2019 19:22:52: #1 tag size = 69 INFO @ Sat, 24 Aug 2019 19:22:52: #1 total tags in treatment: 1090115 INFO @ Sat, 24 Aug 2019 19:22:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:52: #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 19:22:52: #1 tags after filtering in treatment: 1090115 INFO @ Sat, 24 Aug 2019 19:22:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:22:52: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:52: #2 number of paired peaks: 119 WARNING @ Sat, 24 Aug 2019 19:22:52: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 24 Aug 2019 19:22:52: start model_add_line... INFO @ Sat, 24 Aug 2019 19:22:52: start X-correlation... INFO @ Sat, 24 Aug 2019 19:22:52: end of X-cor INFO @ Sat, 24 Aug 2019 19:22:52: #2 finished! INFO @ Sat, 24 Aug 2019 19:22:52: #2 predicted fragment length is 157 bps INFO @ Sat, 24 Aug 2019 19:22:52: #2 alternative fragment length(s) may be 0,51,135,157,178,212,293,318,457,507,552 bps INFO @ Sat, 24 Aug 2019 19:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.20_model.r INFO @ Sat, 24 Aug 2019 19:22:52: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:22:55: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2439292/SRX2439292.20_summits.bed INFO @ Sat, 24 Aug 2019 19:22:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (28 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。