Job ID = 4289550 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,547,080 reads read : 5,547,080 reads written : 5,547,080 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: 00:01:02 5547080 reads; of these: 5547080 (100.00%) were unpaired; of these: 744614 (13.42%) aligned 0 times 4048511 (72.98%) aligned exactly 1 time 753955 (13.59%) aligned >1 times 86.58% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 3982976 / 4802466 = 0.8294 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:48:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.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 14:48:21: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:48:21: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:48:28: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:48:28: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:48:28: #1 total tags in treatment: 819490 INFO @ Tue, 10 Dec 2019 14:48:28: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:48:28: #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 14:48:28: #1 tags after filtering in treatment: 819490 INFO @ Tue, 10 Dec 2019 14:48:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:48:28: #1 finished! INFO @ Tue, 10 Dec 2019 14:48:28: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:48:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:48:28: #2 number of paired peaks: 153 WARNING @ Tue, 10 Dec 2019 14:48:28: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 10 Dec 2019 14:48:28: start model_add_line... INFO @ Tue, 10 Dec 2019 14:48:28: start X-correlation... INFO @ Tue, 10 Dec 2019 14:48:28: end of X-cor INFO @ Tue, 10 Dec 2019 14:48:28: #2 finished! INFO @ Tue, 10 Dec 2019 14:48:28: #2 predicted fragment length is 168 bps INFO @ Tue, 10 Dec 2019 14:48:28: #2 alternative fragment length(s) may be 0,28,48,87,111,129,149,168,194,207,236,257,272,275,292,332,359,422,441,458,476,548,563,570,587 bps INFO @ Tue, 10 Dec 2019 14:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.05_model.r INFO @ Tue, 10 Dec 2019 14:48:28: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:48:31: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.05_peaks.xls INFO @ Tue, 10 Dec 2019 14:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.05_summits.bed INFO @ Tue, 10 Dec 2019 14:48:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:48:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.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 14:48:51: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:48:51: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:48:57: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:48:57: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:48:57: #1 total tags in treatment: 819490 INFO @ Tue, 10 Dec 2019 14:48:57: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:48:57: #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 14:48:57: #1 tags after filtering in treatment: 819490 INFO @ Tue, 10 Dec 2019 14:48:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:48:57: #1 finished! INFO @ Tue, 10 Dec 2019 14:48:57: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:48:57: #2 number of paired peaks: 153 WARNING @ Tue, 10 Dec 2019 14:48:57: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 10 Dec 2019 14:48:57: start model_add_line... INFO @ Tue, 10 Dec 2019 14:48:57: start X-correlation... INFO @ Tue, 10 Dec 2019 14:48:57: end of X-cor INFO @ Tue, 10 Dec 2019 14:48:57: #2 finished! INFO @ Tue, 10 Dec 2019 14:48:57: #2 predicted fragment length is 168 bps INFO @ Tue, 10 Dec 2019 14:48:57: #2 alternative fragment length(s) may be 0,28,48,87,111,129,149,168,194,207,236,257,272,275,292,332,359,422,441,458,476,548,563,570,587 bps INFO @ Tue, 10 Dec 2019 14:48:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.10_model.r INFO @ Tue, 10 Dec 2019 14:48:57: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:48:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:49:00: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.10_peaks.xls INFO @ Tue, 10 Dec 2019 14:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.10_summits.bed INFO @ Tue, 10 Dec 2019 14:49:01: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.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 14:49:21: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:49:21: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:49:27: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:49:27: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:49:27: #1 total tags in treatment: 819490 INFO @ Tue, 10 Dec 2019 14:49:27: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:49:27: #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 14:49:27: #1 tags after filtering in treatment: 819490 INFO @ Tue, 10 Dec 2019 14:49:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:49:27: #1 finished! INFO @ Tue, 10 Dec 2019 14:49:27: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:49:27: #2 number of paired peaks: 153 WARNING @ Tue, 10 Dec 2019 14:49:27: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Tue, 10 Dec 2019 14:49:27: start model_add_line... INFO @ Tue, 10 Dec 2019 14:49:27: start X-correlation... INFO @ Tue, 10 Dec 2019 14:49:27: end of X-cor INFO @ Tue, 10 Dec 2019 14:49:27: #2 finished! INFO @ Tue, 10 Dec 2019 14:49:27: #2 predicted fragment length is 168 bps INFO @ Tue, 10 Dec 2019 14:49:27: #2 alternative fragment length(s) may be 0,28,48,87,111,129,149,168,194,207,236,257,272,275,292,332,359,422,441,458,476,548,563,570,587 bps INFO @ Tue, 10 Dec 2019 14:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.20_model.r INFO @ Tue, 10 Dec 2019 14:49:27: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:49:30: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:49:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.20_peaks.xls INFO @ Tue, 10 Dec 2019 14:49:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:49:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932540/SRX6932540.20_summits.bed INFO @ Tue, 10 Dec 2019 14:49:31: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (4 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。