Job ID = 2006049 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,027,994 reads read : 1,027,994 reads written : 1,027,994 spots read : 995,712 reads read : 995,712 reads written : 995,712 spots read : 1,029,885 reads read : 1,029,885 reads written : 1,029,885 spots read : 960,320 reads read : 960,320 reads written : 960,320 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529300.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529302.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: 00:01:58 4013911 reads; of these: 4013911 (100.00%) were unpaired; of these: 194169 (4.84%) aligned 0 times 3156930 (78.65%) aligned exactly 1 time 662812 (16.51%) aligned >1 times 95.16% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 3740809 / 3819742 = 0.9793 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 14:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.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 14:59:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:59:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:59:01: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:59:01: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:59:01: #1 total tags in treatment: 78933 INFO @ Fri, 05 Jul 2019 14:59:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:59:01: #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 14:59:01: #1 tags after filtering in treatment: 78933 INFO @ Fri, 05 Jul 2019 14:59:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:59:01: #1 finished! INFO @ Fri, 05 Jul 2019 14:59:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:59:01: #2 number of paired peaks: 394 WARNING @ Fri, 05 Jul 2019 14:59:01: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Fri, 05 Jul 2019 14:59:01: start model_add_line... INFO @ Fri, 05 Jul 2019 14:59:01: start X-correlation... INFO @ Fri, 05 Jul 2019 14:59:01: end of X-cor INFO @ Fri, 05 Jul 2019 14:59:01: #2 finished! INFO @ Fri, 05 Jul 2019 14:59:01: #2 predicted fragment length is 163 bps INFO @ Fri, 05 Jul 2019 14:59:01: #2 alternative fragment length(s) may be 25,60,87,125,163,186,230,260,297,327,343,408,425,460,497,546,564 bps INFO @ Fri, 05 Jul 2019 14:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.05_model.r INFO @ Fri, 05 Jul 2019 14:59:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:59:01: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 14:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.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 14:59:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:59:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:59:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:59:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:59:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:59:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.05_summits.bed INFO @ Fri, 05 Jul 2019 14:59:02: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 14:59:02: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:59:02: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:59:02: #1 total tags in treatment: 78933 INFO @ Fri, 05 Jul 2019 14:59:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:59:02: #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 14:59:02: #1 tags after filtering in treatment: 78933 INFO @ Fri, 05 Jul 2019 14:59:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:59:02: #1 finished! INFO @ Fri, 05 Jul 2019 14:59:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:59:02: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 14:59:02: #2 number of paired peaks: 394 WARNING @ Fri, 05 Jul 2019 14:59:02: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Fri, 05 Jul 2019 14:59:02: start model_add_line... INFO @ Fri, 05 Jul 2019 14:59:02: start X-correlation... INFO @ Fri, 05 Jul 2019 14:59:02: end of X-cor INFO @ Fri, 05 Jul 2019 14:59:02: #2 finished! INFO @ Fri, 05 Jul 2019 14:59:02: #2 predicted fragment length is 163 bps INFO @ Fri, 05 Jul 2019 14:59:02: #2 alternative fragment length(s) may be 25,60,87,125,163,186,230,260,297,327,343,408,425,460,497,546,564 bps INFO @ Fri, 05 Jul 2019 14:59:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.10_model.r INFO @ Fri, 05 Jul 2019 14:59:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.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 14:59:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:59:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:59:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:59:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:59:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:59:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.10_summits.bed INFO @ Fri, 05 Jul 2019 14:59:02: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 14:59:03: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:59:03: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:59:03: #1 total tags in treatment: 78933 INFO @ Fri, 05 Jul 2019 14:59:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:59:03: #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 14:59:03: #1 tags after filtering in treatment: 78933 INFO @ Fri, 05 Jul 2019 14:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:59:03: #1 finished! INFO @ Fri, 05 Jul 2019 14:59:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:59:03: #2 number of paired peaks: 394 WARNING @ Fri, 05 Jul 2019 14:59:03: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Fri, 05 Jul 2019 14:59:03: start model_add_line... INFO @ Fri, 05 Jul 2019 14:59:03: start X-correlation... INFO @ Fri, 05 Jul 2019 14:59:03: end of X-cor INFO @ Fri, 05 Jul 2019 14:59:03: #2 finished! INFO @ Fri, 05 Jul 2019 14:59:03: #2 predicted fragment length is 163 bps INFO @ Fri, 05 Jul 2019 14:59:03: #2 alternative fragment length(s) may be 25,60,87,125,163,186,230,260,297,327,343,408,425,460,497,546,564 bps INFO @ Fri, 05 Jul 2019 14:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.20_model.r INFO @ Fri, 05 Jul 2019 14:59:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:59:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:59:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548098/ERX2548098.20_summits.bed INFO @ Fri, 05 Jul 2019 14:59:04: Done! CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling