Job ID = 2006640 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,877,554 reads read : 13,877,554 reads written : 13,877,554 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529583.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: 00:05:13 13877554 reads; of these: 13877554 (100.00%) were unpaired; of these: 459576 (3.31%) aligned 0 times 11029456 (79.48%) aligned exactly 1 time 2388522 (17.21%) aligned >1 times 96.69% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 13341456 / 13417978 = 0.9943 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 15:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.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 15:49:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:49:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:49:37: #1 tag size is determined as 67 bps INFO @ Fri, 05 Jul 2019 15:49:37: #1 tag size = 67 INFO @ Fri, 05 Jul 2019 15:49:37: #1 total tags in treatment: 76522 INFO @ Fri, 05 Jul 2019 15:49:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:49:37: #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 15:49:37: #1 tags after filtering in treatment: 76522 INFO @ Fri, 05 Jul 2019 15:49:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:49:37: #1 finished! INFO @ Fri, 05 Jul 2019 15:49:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:49:37: #2 number of paired peaks: 336 WARNING @ Fri, 05 Jul 2019 15:49:37: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Fri, 05 Jul 2019 15:49:37: start model_add_line... INFO @ Fri, 05 Jul 2019 15:49:37: start X-correlation... INFO @ Fri, 05 Jul 2019 15:49:37: end of X-cor INFO @ Fri, 05 Jul 2019 15:49:37: #2 finished! INFO @ Fri, 05 Jul 2019 15:49:37: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 15:49:37: #2 alternative fragment length(s) may be 61,116,156,199,234,274,299,351,423,474,520 bps INFO @ Fri, 05 Jul 2019 15:49:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.05_model.r INFO @ Fri, 05 Jul 2019 15:49:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:49:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:49:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.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 15:49:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:49:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:49:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 15:49:37: #1 tag size is determined as 67 bps INFO @ Fri, 05 Jul 2019 15:49:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.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 15:49:40: #1 tag size = 67 INFO @ Fri, 05 Jul 2019 15:49:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:49:40: #1 total tags in treatment: 76522 INFO @ Fri, 05 Jul 2019 15:49:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:49:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:49:40: #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 15:49:40: #1 tags after filtering in treatment: 76522 INFO @ Fri, 05 Jul 2019 15:49:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:49:40: #1 finished! INFO @ Fri, 05 Jul 2019 15:49:40: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:49:40: #2 looking for paired plus/minus strand peaks... BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:49:40: #2 number of paired peaks: 336 WARNING @ Fri, 05 Jul 2019 15:49:40: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Fri, 05 Jul 2019 15:49:40: start model_add_line... INFO @ Fri, 05 Jul 2019 15:49:40: start X-correlation... INFO @ Fri, 05 Jul 2019 15:49:40: end of X-cor INFO @ Fri, 05 Jul 2019 15:49:40: #2 finished! INFO @ Fri, 05 Jul 2019 15:49:40: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 15:49:40: #2 alternative fragment length(s) may be 61,116,156,199,234,274,299,351,423,474,520 bps INFO @ Fri, 05 Jul 2019 15:49:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.10_model.r INFO @ Fri, 05 Jul 2019 15:49:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:49:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.05_summits.bed INFO @ Fri, 05 Jul 2019 15:49:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:49:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:49:41: #1 tag size is determined as 67 bps INFO @ Fri, 05 Jul 2019 15:49:41: #1 tag size = 67 INFO @ Fri, 05 Jul 2019 15:49:41: #1 total tags in treatment: 76522 INFO @ Fri, 05 Jul 2019 15:49:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:49:41: #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 15:49:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.10_peaks.xls BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:49:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:49:42: #1 tags after filtering in treatment: 76522 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.10_summits.bed INFO @ Fri, 05 Jul 2019 15:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:49:44: #1 finished! INFO @ Fri, 05 Jul 2019 15:49:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:49:44: Done! INFO @ Fri, 05 Jul 2019 15:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:49:48: #2 number of paired peaks: 336 pass1 - making usageList (7 chroms): 1 millis WARNING @ Fri, 05 Jul 2019 15:49:50: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Fri, 05 Jul 2019 15:49:50: start model_add_line... pass2 - checking and writing primary data (9 records, 4 fields): 2098 millis INFO @ Fri, 05 Jul 2019 15:49:50: start X-correlation... INFO @ Fri, 05 Jul 2019 15:49:52: end of X-cor INFO @ Fri, 05 Jul 2019 15:49:53: #2 finished! INFO @ Fri, 05 Jul 2019 15:49:53: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 15:49:53: #2 alternative fragment length(s) may be 61,116,156,199,234,274,299,351,423,474,520 bps INFO @ Fri, 05 Jul 2019 15:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.20_model.r INFO @ Fri, 05 Jul 2019 15:49:53: #3 Call peaks... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:50:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:50:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:50:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548180/ERX2548180.20_summits.bed INFO @ Fri, 05 Jul 2019 15:50:02: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 2 millis CompletedMACS2peakCalling