Job ID = 2009040 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,265,360 reads read : 35,265,360 reads written : 35,265,360 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: 00:07:28 35265360 reads; of these: 35265360 (100.00%) were unpaired; of these: 6322495 (17.93%) aligned 0 times 22005188 (62.40%) aligned exactly 1 time 6937677 (19.67%) aligned >1 times 82.07% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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_sort_core] merging from 12 files... [bam_rmdupse_core] 27464236 / 28942865 = 0.9489 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 19:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.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 19:45:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:45:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:45:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.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 19:45:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:45:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:45:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.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 19:45:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:45:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:45:25: 1000000 INFO @ Fri, 05 Jul 2019 19:45:27: 1000000 INFO @ Fri, 05 Jul 2019 19:45:27: 1000000 INFO @ Fri, 05 Jul 2019 19:45:29: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:45:29: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:45:29: #1 total tags in treatment: 1478629 INFO @ Fri, 05 Jul 2019 19:45:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:45:29: #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 19:45:29: #1 tags after filtering in treatment: 1478629 INFO @ Fri, 05 Jul 2019 19:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:45:29: #1 finished! INFO @ Fri, 05 Jul 2019 19:45:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:45:29: #2 number of paired peaks: 622 WARNING @ Fri, 05 Jul 2019 19:45:29: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Fri, 05 Jul 2019 19:45:29: start model_add_line... INFO @ Fri, 05 Jul 2019 19:45:29: start X-correlation... INFO @ Fri, 05 Jul 2019 19:45:29: end of X-cor INFO @ Fri, 05 Jul 2019 19:45:29: #2 finished! INFO @ Fri, 05 Jul 2019 19:45:29: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 19:45:29: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 05 Jul 2019 19:45:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.05_model.r INFO @ Fri, 05 Jul 2019 19:45:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:45:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:45:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:45:31: #1 total tags in treatment: 1478629 INFO @ Fri, 05 Jul 2019 19:45:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:45:31: #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 19:45:31: #1 tags after filtering in treatment: 1478629 INFO @ Fri, 05 Jul 2019 19:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:45:31: #1 finished! INFO @ Fri, 05 Jul 2019 19:45:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:45:31: #2 number of paired peaks: 622 WARNING @ Fri, 05 Jul 2019 19:45:31: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Fri, 05 Jul 2019 19:45:31: start model_add_line... INFO @ Fri, 05 Jul 2019 19:45:31: start X-correlation... INFO @ Fri, 05 Jul 2019 19:45:31: end of X-cor INFO @ Fri, 05 Jul 2019 19:45:31: #2 finished! INFO @ Fri, 05 Jul 2019 19:45:31: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 19:45:31: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 05 Jul 2019 19:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.20_model.r INFO @ Fri, 05 Jul 2019 19:45:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:45:32: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:45:32: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:45:32: #1 total tags in treatment: 1478629 INFO @ Fri, 05 Jul 2019 19:45:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:45:32: #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 19:45:32: #1 tags after filtering in treatment: 1478629 INFO @ Fri, 05 Jul 2019 19:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:45:32: #1 finished! INFO @ Fri, 05 Jul 2019 19:45:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:45:32: #2 number of paired peaks: 622 WARNING @ Fri, 05 Jul 2019 19:45:32: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Fri, 05 Jul 2019 19:45:32: start model_add_line... INFO @ Fri, 05 Jul 2019 19:45:32: start X-correlation... INFO @ Fri, 05 Jul 2019 19:45:32: end of X-cor INFO @ Fri, 05 Jul 2019 19:45:32: #2 finished! INFO @ Fri, 05 Jul 2019 19:45:32: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 19:45:32: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 05 Jul 2019 19:45:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.10_model.r INFO @ Fri, 05 Jul 2019 19:45:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:45:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.05_summits.bed INFO @ Fri, 05 Jul 2019 19:45:39: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (952 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 19:45:39: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:45:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:45:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:45:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:45:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.20_summits.bed INFO @ Fri, 05 Jul 2019 19:45:41: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (474 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 19:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:45:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:45:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX662720/ERX662720.10_summits.bed INFO @ Fri, 05 Jul 2019 19:45:42: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (728 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。