Job ID = 2009671 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,979,978 reads read : 12,979,978 reads written : 12,979,978 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR364335.sra.cache’: 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: 00:01:07 12979978 reads; of these: 12979978 (100.00%) were unpaired; of these: 9868377 (76.03%) aligned 0 times 2609023 (20.10%) aligned exactly 1 time 502578 (3.87%) aligned >1 times 23.97% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 1876806 / 3111601 = 0.6032 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 19:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.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 @ Fri, 05 Jul 2019 19:28:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:28:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:28:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.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 @ Fri, 05 Jul 2019 19:28:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:28:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.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 @ Fri, 05 Jul 2019 19:28:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:28:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:28:45: 1000000 INFO @ Fri, 05 Jul 2019 19:28:46: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:28:46: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:28:46: #1 total tags in treatment: 1234795 INFO @ Fri, 05 Jul 2019 19:28:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:28:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:28:46: #1 tags after filtering in treatment: 1234795 INFO @ Fri, 05 Jul 2019 19:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:28:46: #1 finished! INFO @ Fri, 05 Jul 2019 19:28:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:28:46: #2 number of paired peaks: 818 WARNING @ Fri, 05 Jul 2019 19:28:46: Fewer paired peaks (818) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 818 pairs to build model! INFO @ Fri, 05 Jul 2019 19:28:46: start model_add_line... INFO @ Fri, 05 Jul 2019 19:28:46: start X-correlation... INFO @ Fri, 05 Jul 2019 19:28:46: end of X-cor INFO @ Fri, 05 Jul 2019 19:28:46: #2 finished! INFO @ Fri, 05 Jul 2019 19:28:46: #2 predicted fragment length is 201 bps INFO @ Fri, 05 Jul 2019 19:28:46: #2 alternative fragment length(s) may be 2,22,64,76,107,133,156,189,201,223,250 bps INFO @ Fri, 05 Jul 2019 19:28:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.05_model.r INFO @ Fri, 05 Jul 2019 19:28:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:28:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:28:47: 1000000 INFO @ Fri, 05 Jul 2019 19:28:47: 1000000 INFO @ Fri, 05 Jul 2019 19:28:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:28:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:28:49: #1 total tags in treatment: 1234795 INFO @ Fri, 05 Jul 2019 19:28:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:28:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:28:49: #1 tags after filtering in treatment: 1234795 INFO @ Fri, 05 Jul 2019 19:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:28:49: #1 finished! INFO @ Fri, 05 Jul 2019 19:28:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:28:49: #2 number of paired peaks: 818 WARNING @ Fri, 05 Jul 2019 19:28:49: Fewer paired peaks (818) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 818 pairs to build model! INFO @ Fri, 05 Jul 2019 19:28:49: start model_add_line... INFO @ Fri, 05 Jul 2019 19:28:49: start X-correlation... INFO @ Fri, 05 Jul 2019 19:28:49: end of X-cor INFO @ Fri, 05 Jul 2019 19:28:49: #2 finished! INFO @ Fri, 05 Jul 2019 19:28:49: #2 predicted fragment length is 201 bps INFO @ Fri, 05 Jul 2019 19:28:49: #2 alternative fragment length(s) may be 2,22,64,76,107,133,156,189,201,223,250 bps INFO @ Fri, 05 Jul 2019 19:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.20_model.r INFO @ Fri, 05 Jul 2019 19:28:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:28:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:28:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:28:49: #1 total tags in treatment: 1234795 INFO @ Fri, 05 Jul 2019 19:28:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:28:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:28:49: #1 tags after filtering in treatment: 1234795 INFO @ Fri, 05 Jul 2019 19:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:28:49: #1 finished! INFO @ Fri, 05 Jul 2019 19:28:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:28:49: #2 number of paired peaks: 818 WARNING @ Fri, 05 Jul 2019 19:28:49: Fewer paired peaks (818) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 818 pairs to build model! INFO @ Fri, 05 Jul 2019 19:28:49: start model_add_line... INFO @ Fri, 05 Jul 2019 19:28:49: start X-correlation... INFO @ Fri, 05 Jul 2019 19:28:49: end of X-cor INFO @ Fri, 05 Jul 2019 19:28:49: #2 finished! INFO @ Fri, 05 Jul 2019 19:28:49: #2 predicted fragment length is 201 bps INFO @ Fri, 05 Jul 2019 19:28:49: #2 alternative fragment length(s) may be 2,22,64,76,107,133,156,189,201,223,250 bps INFO @ Fri, 05 Jul 2019 19:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.10_model.r INFO @ Fri, 05 Jul 2019 19:28:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:28:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.05_summits.bed INFO @ Fri, 05 Jul 2019 19:28:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (653 records, 4 fields): 3 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:28:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:28:57: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:28:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:28:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:29:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:29:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.20_summits.bed INFO @ Fri, 05 Jul 2019 19:29:13: Done! INFO @ Fri, 05 Jul 2019 19:29:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.10_peaks.narrowPeak BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 19:29:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105549/SRX105549.10_summits.bed INFO @ Fri, 05 Jul 2019 19:29:13: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (196 records, 4 fields): 3 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling