Job ID = 2007637 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,134,786 reads read : 3,134,786 reads written : 3,134,786 spots read : 3,012,651 reads read : 3,012,651 reads written : 3,012,651 spots read : 3,056,159 reads read : 3,056,159 reads written : 3,056,159 spots read : 2,988,864 reads read : 2,988,864 reads written : 2,988,864 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529766.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529767.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529768.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529769.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: 00:02:56 12192460 reads; of these: 12192460 (100.00%) were unpaired; of these: 430108 (3.53%) aligned 0 times 9660317 (79.23%) aligned exactly 1 time 2102035 (17.24%) aligned >1 times 96.47% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 11284525 / 11762352 = 0.9594 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 16:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.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 16:13:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.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 16:13:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.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 16:13:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:13:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:13:34: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:34: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:34: #1 total tags in treatment: 477827 INFO @ Fri, 05 Jul 2019 16:13:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:34: #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 16:13:34: #1 tags after filtering in treatment: 477827 INFO @ Fri, 05 Jul 2019 16:13:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:34: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:34: #2 number of paired peaks: 505 WARNING @ Fri, 05 Jul 2019 16:13:34: Fewer paired peaks (505) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 505 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:34: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:34: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:34: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:34: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:34: #2 predicted fragment length is 157 bps INFO @ Fri, 05 Jul 2019 16:13:34: #2 alternative fragment length(s) may be 135,157 bps INFO @ Fri, 05 Jul 2019 16:13:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.05_model.r INFO @ Fri, 05 Jul 2019 16:13:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:34: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:34: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:34: #1 total tags in treatment: 477827 INFO @ Fri, 05 Jul 2019 16:13:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:34: #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 16:13:34: #1 tags after filtering in treatment: 477827 INFO @ Fri, 05 Jul 2019 16:13:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:34: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:34: #2 number of paired peaks: 505 WARNING @ Fri, 05 Jul 2019 16:13:34: Fewer paired peaks (505) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 505 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:34: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:34: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:34: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:34: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:34: #2 predicted fragment length is 157 bps INFO @ Fri, 05 Jul 2019 16:13:34: #2 alternative fragment length(s) may be 135,157 bps INFO @ Fri, 05 Jul 2019 16:13:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.10_model.r INFO @ Fri, 05 Jul 2019 16:13:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:36: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:13:36: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:13:36: #1 total tags in treatment: 477827 INFO @ Fri, 05 Jul 2019 16:13:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:13:36: #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 16:13:36: #1 tags after filtering in treatment: 477827 INFO @ Fri, 05 Jul 2019 16:13:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:13:36: #1 finished! INFO @ Fri, 05 Jul 2019 16:13:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:13:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:13:36: #2 number of paired peaks: 505 WARNING @ Fri, 05 Jul 2019 16:13:36: Fewer paired peaks (505) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 505 pairs to build model! INFO @ Fri, 05 Jul 2019 16:13:36: start model_add_line... INFO @ Fri, 05 Jul 2019 16:13:36: start X-correlation... INFO @ Fri, 05 Jul 2019 16:13:36: end of X-cor INFO @ Fri, 05 Jul 2019 16:13:36: #2 finished! INFO @ Fri, 05 Jul 2019 16:13:36: #2 predicted fragment length is 157 bps INFO @ Fri, 05 Jul 2019 16:13:36: #2 alternative fragment length(s) may be 135,157 bps INFO @ Fri, 05 Jul 2019 16:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.20_model.r INFO @ Fri, 05 Jul 2019 16:13:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:13:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:13:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.05_summits.bed INFO @ Fri, 05 Jul 2019 16:13:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.10_summits.bed INFO @ Fri, 05 Jul 2019 16:13:37: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:13:38: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:13:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:13:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:13:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548237/ERX2548237.20_summits.bed INFO @ Fri, 05 Jul 2019 16:13:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling