Job ID = 4289552 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,727,157 reads read : 7,727,157 reads written : 7,727,157 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: 00:00:59 7727157 reads; of these: 7727157 (100.00%) were unpaired; of these: 3352014 (43.38%) aligned 0 times 4035677 (52.23%) aligned exactly 1 time 339466 (4.39%) aligned >1 times 56.62% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 2511400 / 4375143 = 0.5740 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:50:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.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 @ Tue, 10 Dec 2019 14:50:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:50:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:50:11: 1000000 INFO @ Tue, 10 Dec 2019 14:50:19: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:50:19: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:50:19: #1 total tags in treatment: 1863743 INFO @ Tue, 10 Dec 2019 14:50:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:50:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:50:20: #1 tags after filtering in treatment: 1863743 INFO @ Tue, 10 Dec 2019 14:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:50:20: #1 finished! INFO @ Tue, 10 Dec 2019 14:50:20: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:50:20: #2 number of paired peaks: 477 WARNING @ Tue, 10 Dec 2019 14:50:20: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Tue, 10 Dec 2019 14:50:20: start model_add_line... INFO @ Tue, 10 Dec 2019 14:50:20: start X-correlation... INFO @ Tue, 10 Dec 2019 14:50:20: end of X-cor INFO @ Tue, 10 Dec 2019 14:50:20: #2 finished! INFO @ Tue, 10 Dec 2019 14:50:20: #2 predicted fragment length is 106 bps INFO @ Tue, 10 Dec 2019 14:50:20: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 10 Dec 2019 14:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.05_model.r INFO @ Tue, 10 Dec 2019 14:50:20: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:50:26: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.05_peaks.xls INFO @ Tue, 10 Dec 2019 14:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.05_summits.bed INFO @ Tue, 10 Dec 2019 14:50:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2721 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:50:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.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 @ Tue, 10 Dec 2019 14:50:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:50:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:50:42: 1000000 INFO @ Tue, 10 Dec 2019 14:50:51: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:50:51: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:50:51: #1 total tags in treatment: 1863743 INFO @ Tue, 10 Dec 2019 14:50:51: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:50:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:50:51: #1 tags after filtering in treatment: 1863743 INFO @ Tue, 10 Dec 2019 14:50:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:50:51: #1 finished! INFO @ Tue, 10 Dec 2019 14:50:51: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:50:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:50:51: #2 number of paired peaks: 477 WARNING @ Tue, 10 Dec 2019 14:50:51: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Tue, 10 Dec 2019 14:50:51: start model_add_line... INFO @ Tue, 10 Dec 2019 14:50:51: start X-correlation... INFO @ Tue, 10 Dec 2019 14:50:51: end of X-cor INFO @ Tue, 10 Dec 2019 14:50:51: #2 finished! INFO @ Tue, 10 Dec 2019 14:50:51: #2 predicted fragment length is 106 bps INFO @ Tue, 10 Dec 2019 14:50:51: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 10 Dec 2019 14:50:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.10_model.r INFO @ Tue, 10 Dec 2019 14:50:51: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:50:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:50:57: #3 Call peaks for each chromosome... BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.10_peaks.xls INFO @ Tue, 10 Dec 2019 14:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.10_summits.bed INFO @ Tue, 10 Dec 2019 14:51:00: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (2182 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:51:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.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 @ Tue, 10 Dec 2019 14:51:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:51:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:51:09: 1000000 INFO @ Tue, 10 Dec 2019 14:51:16: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:51:16: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:51:16: #1 total tags in treatment: 1863743 INFO @ Tue, 10 Dec 2019 14:51:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:51:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 14:51:16: #1 tags after filtering in treatment: 1863743 INFO @ Tue, 10 Dec 2019 14:51:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:51:16: #1 finished! INFO @ Tue, 10 Dec 2019 14:51:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:51:16: #2 number of paired peaks: 477 WARNING @ Tue, 10 Dec 2019 14:51:16: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Tue, 10 Dec 2019 14:51:16: start model_add_line... INFO @ Tue, 10 Dec 2019 14:51:16: start X-correlation... INFO @ Tue, 10 Dec 2019 14:51:16: end of X-cor INFO @ Tue, 10 Dec 2019 14:51:16: #2 finished! INFO @ Tue, 10 Dec 2019 14:51:16: #2 predicted fragment length is 106 bps INFO @ Tue, 10 Dec 2019 14:51:16: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 10 Dec 2019 14:51:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.20_model.r INFO @ Tue, 10 Dec 2019 14:51:16: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:51:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:51:23: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 14:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.20_peaks.xls INFO @ Tue, 10 Dec 2019 14:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932542/SRX6932542.20_summits.bed INFO @ Tue, 10 Dec 2019 14:51:25: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1403 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。