Job ID = 2004034 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 207,448 reads read : 207,448 reads written : 207,448 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: 00:00:01 Multiseed full-index search: 00:00:01 207448 reads; of these: 207448 (100.00%) were unpaired; of these: 201579 (97.17%) aligned 0 times 5042 (2.43%) aligned exactly 1 time 827 (0.40%) aligned >1 times 2.83% overall alignment rate Time searching: 00:00:02 Overall time: 00:00:02 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] 696 / 5869 = 0.1186 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 14:18:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.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 14:18:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:18:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:18:20: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:18:20: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:18:20: #1 total tags in treatment: 5173 INFO @ Fri, 05 Jul 2019 14:18:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:18:20: #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 14:18:20: #1 tags after filtering in treatment: 5173 INFO @ Fri, 05 Jul 2019 14:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:18:20: #1 finished! INFO @ Fri, 05 Jul 2019 14:18:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:18:20: #2 number of paired peaks: 191 WARNING @ Fri, 05 Jul 2019 14:18:20: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 05 Jul 2019 14:18:20: start model_add_line... INFO @ Fri, 05 Jul 2019 14:18:20: start X-correlation... INFO @ Fri, 05 Jul 2019 14:18:20: end of X-cor INFO @ Fri, 05 Jul 2019 14:18:20: #2 finished! INFO @ Fri, 05 Jul 2019 14:18:20: #2 predicted fragment length is 297 bps INFO @ Fri, 05 Jul 2019 14:18:20: #2 alternative fragment length(s) may be 51,139,184,202,216,239,249,273,297,319,345,362 bps INFO @ Fri, 05 Jul 2019 14:18:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.05_model.r INFO @ Fri, 05 Jul 2019 14:18:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:18:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:18:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:18:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:18:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:18:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.05_summits.bed INFO @ Fri, 05 Jul 2019 14:18:20: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 14:18:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.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 14:18:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:18:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:18:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:18:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:18:21: #1 total tags in treatment: 5173 INFO @ Fri, 05 Jul 2019 14:18:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:18:21: #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 14:18:21: #1 tags after filtering in treatment: 5173 INFO @ Fri, 05 Jul 2019 14:18:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:18:21: #1 finished! INFO @ Fri, 05 Jul 2019 14:18:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:18:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:18:21: #2 number of paired peaks: 191 WARNING @ Fri, 05 Jul 2019 14:18:21: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 05 Jul 2019 14:18:21: start model_add_line... INFO @ Fri, 05 Jul 2019 14:18:21: start X-correlation... INFO @ Fri, 05 Jul 2019 14:18:21: end of X-cor INFO @ Fri, 05 Jul 2019 14:18:21: #2 finished! INFO @ Fri, 05 Jul 2019 14:18:21: #2 predicted fragment length is 297 bps INFO @ Fri, 05 Jul 2019 14:18:21: #2 alternative fragment length(s) may be 51,139,184,202,216,239,249,273,297,319,345,362 bps INFO @ Fri, 05 Jul 2019 14:18:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.10_model.r INFO @ Fri, 05 Jul 2019 14:18:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:18:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:18:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:18:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:18:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:18:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.10_summits.bed INFO @ Fri, 05 Jul 2019 14:18:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 14:18:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.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 14:18:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:18:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:18:22: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:18:22: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:18:22: #1 total tags in treatment: 5173 INFO @ Fri, 05 Jul 2019 14:18:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:18:22: #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 14:18:22: #1 tags after filtering in treatment: 5173 INFO @ Fri, 05 Jul 2019 14:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:18:22: #1 finished! INFO @ Fri, 05 Jul 2019 14:18:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:18:22: #2 number of paired peaks: 191 WARNING @ Fri, 05 Jul 2019 14:18:22: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 05 Jul 2019 14:18:22: start model_add_line... INFO @ Fri, 05 Jul 2019 14:18:22: start X-correlation... INFO @ Fri, 05 Jul 2019 14:18:22: end of X-cor INFO @ Fri, 05 Jul 2019 14:18:22: #2 finished! INFO @ Fri, 05 Jul 2019 14:18:22: #2 predicted fragment length is 297 bps INFO @ Fri, 05 Jul 2019 14:18:22: #2 alternative fragment length(s) may be 51,139,184,202,216,239,249,273,297,319,345,362 bps INFO @ Fri, 05 Jul 2019 14:18:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.20_model.r INFO @ Fri, 05 Jul 2019 14:18:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:18:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:18:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX193139/ERX193139.20_summits.bed INFO @ Fri, 05 Jul 2019 14:18:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling