Job ID = 2006288 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,146,031 reads read : 9,146,031 reads written : 9,146,031 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: 00:04:32 9146031 reads; of these: 9146031 (100.00%) were unpaired; of these: 301226 (3.29%) aligned 0 times 7226332 (79.01%) aligned exactly 1 time 1618473 (17.70%) aligned >1 times 96.71% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 8810999 / 8844805 = 0.9962 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 15:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.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 15:25:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:25:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:25:35: #1 tag size is determined as 58 bps INFO @ Fri, 05 Jul 2019 15:25:35: #1 tag size = 58 INFO @ Fri, 05 Jul 2019 15:25:35: #1 total tags in treatment: 33806 INFO @ Fri, 05 Jul 2019 15:25:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:25:35: #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 15:25:35: #1 tags after filtering in treatment: 33806 INFO @ Fri, 05 Jul 2019 15:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:25:35: #1 finished! INFO @ Fri, 05 Jul 2019 15:25:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:25:35: #2 number of paired peaks: 362 WARNING @ Fri, 05 Jul 2019 15:25:35: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Fri, 05 Jul 2019 15:25:35: start model_add_line... INFO @ Fri, 05 Jul 2019 15:25:35: start X-correlation... INFO @ Fri, 05 Jul 2019 15:25:35: end of X-cor INFO @ Fri, 05 Jul 2019 15:25:35: #2 finished! INFO @ Fri, 05 Jul 2019 15:25:35: #2 predicted fragment length is 293 bps INFO @ Fri, 05 Jul 2019 15:25:35: #2 alternative fragment length(s) may be 2,22,40,61,76,99,132,150,182,199,236,261,293,328,348,411,451,481,518,566 bps INFO @ Fri, 05 Jul 2019 15:25:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.05_model.r INFO @ Fri, 05 Jul 2019 15:25:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:25:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:25:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:25:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:25:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:25:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.05_summits.bed INFO @ Fri, 05 Jul 2019 15:25:35: Done! BigWig に変換しました。 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (37 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:25:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.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 15:25:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:25:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:25:36: #1 tag size is determined as 58 bps INFO @ Fri, 05 Jul 2019 15:25:36: #1 tag size = 58 INFO @ Fri, 05 Jul 2019 15:25:36: #1 total tags in treatment: 33806 INFO @ Fri, 05 Jul 2019 15:25:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:25:36: #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 15:25:36: #1 tags after filtering in treatment: 33806 INFO @ Fri, 05 Jul 2019 15:25:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:25:36: #1 finished! INFO @ Fri, 05 Jul 2019 15:25:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:25:36: #2 number of paired peaks: 362 WARNING @ Fri, 05 Jul 2019 15:25:36: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Fri, 05 Jul 2019 15:25:36: start model_add_line... INFO @ Fri, 05 Jul 2019 15:25:36: start X-correlation... INFO @ Fri, 05 Jul 2019 15:25:36: end of X-cor INFO @ Fri, 05 Jul 2019 15:25:36: #2 finished! INFO @ Fri, 05 Jul 2019 15:25:36: #2 predicted fragment length is 293 bps INFO @ Fri, 05 Jul 2019 15:25:36: #2 alternative fragment length(s) may be 2,22,40,61,76,99,132,150,182,199,236,261,293,328,348,411,451,481,518,566 bps INFO @ Fri, 05 Jul 2019 15:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.10_model.r INFO @ Fri, 05 Jul 2019 15:25:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:25:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.10_summits.bed INFO @ Fri, 05 Jul 2019 15:25:36: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.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 15:25:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:25:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:25:37: #1 tag size is determined as 58 bps INFO @ Fri, 05 Jul 2019 15:25:37: #1 tag size = 58 INFO @ Fri, 05 Jul 2019 15:25:37: #1 total tags in treatment: 33806 INFO @ Fri, 05 Jul 2019 15:25:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:25:37: #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 15:25:37: #1 tags after filtering in treatment: 33806 INFO @ Fri, 05 Jul 2019 15:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:25:37: #1 finished! INFO @ Fri, 05 Jul 2019 15:25:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:25:37: #2 number of paired peaks: 362 WARNING @ Fri, 05 Jul 2019 15:25:37: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Fri, 05 Jul 2019 15:25:37: start model_add_line... INFO @ Fri, 05 Jul 2019 15:25:37: start X-correlation... INFO @ Fri, 05 Jul 2019 15:25:37: end of X-cor INFO @ Fri, 05 Jul 2019 15:25:37: #2 finished! INFO @ Fri, 05 Jul 2019 15:25:37: #2 predicted fragment length is 293 bps INFO @ Fri, 05 Jul 2019 15:25:37: #2 alternative fragment length(s) may be 2,22,40,61,76,99,132,150,182,199,236,261,293,328,348,411,451,481,518,566 bps INFO @ Fri, 05 Jul 2019 15:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.20_model.r INFO @ Fri, 05 Jul 2019 15:25:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:25:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:25:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:25:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:25:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548137/ERX2548137.20_summits.bed INFO @ Fri, 05 Jul 2019 15:25:37: Done! CompletedMACS2peakCalling pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling