Job ID = 2006292 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,674,446 reads read : 2,674,446 reads written : 2,674,446 spots read : 2,600,427 reads read : 2,600,427 reads written : 2,600,427 spots read : 2,683,179 reads read : 2,683,179 reads written : 2,683,179 spots read : 2,503,168 reads read : 2,503,168 reads written : 2,503,168 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529444.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529446.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529447.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: 00:06:06 10461220 reads; of these: 10461220 (100.00%) were unpaired; of these: 589369 (5.63%) aligned 0 times 8024865 (76.71%) aligned exactly 1 time 1846986 (17.66%) aligned >1 times 94.37% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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 8 files... [bam_rmdupse_core] 9679396 / 9871851 = 0.9805 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 15:41:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.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 15:41:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:41:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:41:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.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 15:41:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:41:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:41:30: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:41:30: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:41:30: #1 total tags in treatment: 192455 INFO @ Fri, 05 Jul 2019 15:41:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:41:30: #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 15:41:30: #1 tags after filtering in treatment: 192455 INFO @ Fri, 05 Jul 2019 15:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:41:30: #1 finished! INFO @ Fri, 05 Jul 2019 15:41:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:41:30: #2 number of paired peaks: 463 WARNING @ Fri, 05 Jul 2019 15:41:30: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Fri, 05 Jul 2019 15:41:30: start model_add_line... INFO @ Fri, 05 Jul 2019 15:41:30: start X-correlation... INFO @ Fri, 05 Jul 2019 15:41:30: end of X-cor INFO @ Fri, 05 Jul 2019 15:41:30: #2 finished! INFO @ Fri, 05 Jul 2019 15:41:30: #2 predicted fragment length is 224 bps INFO @ Fri, 05 Jul 2019 15:41:30: #2 alternative fragment length(s) may be 29,79,101,133,161,182,224,246,271,301,415,491,547,573,591 bps INFO @ Fri, 05 Jul 2019 15:41:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.05_model.r INFO @ Fri, 05 Jul 2019 15:41:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:41:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.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 15:41:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:41:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:41:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:41:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:41:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.05_summits.bed INFO @ Fri, 05 Jul 2019 15:41:31: Done! INFO @ Fri, 05 Jul 2019 15:41:31: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:41:31: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:41:31: #1 total tags in treatment: 192455 INFO @ Fri, 05 Jul 2019 15:41:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:41:31: #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 15:41:31: #1 tags after filtering in treatment: 192455 INFO @ Fri, 05 Jul 2019 15:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:41:31: #1 finished! INFO @ Fri, 05 Jul 2019 15:41:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:41:31: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:41:31: #2 number of paired peaks: 463 WARNING @ Fri, 05 Jul 2019 15:41:31: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Fri, 05 Jul 2019 15:41:31: start model_add_line... INFO @ Fri, 05 Jul 2019 15:41:31: start X-correlation... INFO @ Fri, 05 Jul 2019 15:41:31: end of X-cor INFO @ Fri, 05 Jul 2019 15:41:31: #2 finished! INFO @ Fri, 05 Jul 2019 15:41:31: #2 predicted fragment length is 224 bps INFO @ Fri, 05 Jul 2019 15:41:31: #2 alternative fragment length(s) may be 29,79,101,133,161,182,224,246,271,301,415,491,547,573,591 bps INFO @ Fri, 05 Jul 2019 15:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.10_model.r INFO @ Fri, 05 Jul 2019 15:41:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:41:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:41:32: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:41:32: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:41:32: #1 total tags in treatment: 192455 INFO @ Fri, 05 Jul 2019 15:41:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:41:32: #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 15:41:32: #1 tags after filtering in treatment: 192455 INFO @ Fri, 05 Jul 2019 15:41:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:41:32: #1 finished! INFO @ Fri, 05 Jul 2019 15:41:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:41:32: #2 number of paired peaks: 463 WARNING @ Fri, 05 Jul 2019 15:41:32: Fewer paired peaks (463) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 463 pairs to build model! INFO @ Fri, 05 Jul 2019 15:41:32: start model_add_line... INFO @ Fri, 05 Jul 2019 15:41:32: start X-correlation... INFO @ Fri, 05 Jul 2019 15:41:32: end of X-cor INFO @ Fri, 05 Jul 2019 15:41:32: #2 finished! INFO @ Fri, 05 Jul 2019 15:41:32: #2 predicted fragment length is 224 bps INFO @ Fri, 05 Jul 2019 15:41:32: #2 alternative fragment length(s) may be 29,79,101,133,161,182,224,246,271,301,415,491,547,573,591 bps INFO @ Fri, 05 Jul 2019 15:41:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.20_model.r INFO @ Fri, 05 Jul 2019 15:41:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:41:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.10_summits.bed INFO @ Fri, 05 Jul 2019 15:41:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:41:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:41:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:41:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:41:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548140/ERX2548140.20_summits.bed INFO @ Fri, 05 Jul 2019 15:41:33: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling