Job ID = 2006322 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,845,526 reads read : 2,845,526 reads written : 2,845,526 spots read : 2,715,472 reads read : 2,715,472 reads written : 2,715,472 spots read : 2,772,849 reads read : 2,772,849 reads written : 2,772,849 spots read : 2,653,480 reads read : 2,653,480 reads written : 2,653,480 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529486.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529487.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529488.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529489.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: 00:02:43 10987327 reads; of these: 10987327 (100.00%) were unpaired; of these: 472172 (4.30%) aligned 0 times 8946085 (81.42%) aligned exactly 1 time 1569070 (14.28%) aligned >1 times 95.70% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 9981507 / 10515155 = 0.9492 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 15:42:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.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 15:42:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:42:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.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 15:42:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:42:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.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 15:42:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:42:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:42:29: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:42:29: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:42:29: #1 total tags in treatment: 533648 INFO @ Fri, 05 Jul 2019 15:42:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:42:29: #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 15:42:29: #1 tags after filtering in treatment: 533648 INFO @ Fri, 05 Jul 2019 15:42:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:42:29: #1 finished! INFO @ Fri, 05 Jul 2019 15:42:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:42:29: #2 number of paired peaks: 531 WARNING @ Fri, 05 Jul 2019 15:42:29: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Fri, 05 Jul 2019 15:42:29: start model_add_line... INFO @ Fri, 05 Jul 2019 15:42:29: start X-correlation... INFO @ Fri, 05 Jul 2019 15:42:29: end of X-cor INFO @ Fri, 05 Jul 2019 15:42:29: #2 finished! INFO @ Fri, 05 Jul 2019 15:42:29: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 15:42:29: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 15:42:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.05_model.r INFO @ Fri, 05 Jul 2019 15:42:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:42:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:42:31: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:42:31: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:42:31: #1 total tags in treatment: 533648 INFO @ Fri, 05 Jul 2019 15:42:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:42:31: #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 15:42:31: #1 tags after filtering in treatment: 533648 INFO @ Fri, 05 Jul 2019 15:42:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:42:31: #1 finished! INFO @ Fri, 05 Jul 2019 15:42:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:42:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:42:31: #2 number of paired peaks: 531 WARNING @ Fri, 05 Jul 2019 15:42:31: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Fri, 05 Jul 2019 15:42:31: start model_add_line... INFO @ Fri, 05 Jul 2019 15:42:31: start X-correlation... INFO @ Fri, 05 Jul 2019 15:42:31: end of X-cor INFO @ Fri, 05 Jul 2019 15:42:31: #2 finished! INFO @ Fri, 05 Jul 2019 15:42:31: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 15:42:31: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 15:42:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.10_model.r INFO @ Fri, 05 Jul 2019 15:42:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:42:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:42:32: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:42:32: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:42:32: #1 total tags in treatment: 533648 INFO @ Fri, 05 Jul 2019 15:42:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:42:32: #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 15:42:32: #1 tags after filtering in treatment: 533648 INFO @ Fri, 05 Jul 2019 15:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:42:32: #1 finished! INFO @ Fri, 05 Jul 2019 15:42:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:42:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:42:32: #2 number of paired peaks: 531 WARNING @ Fri, 05 Jul 2019 15:42:32: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Fri, 05 Jul 2019 15:42:32: start model_add_line... INFO @ Fri, 05 Jul 2019 15:42:32: start X-correlation... INFO @ Fri, 05 Jul 2019 15:42:32: end of X-cor INFO @ Fri, 05 Jul 2019 15:42:32: #2 finished! INFO @ Fri, 05 Jul 2019 15:42:32: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 15:42:32: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 15:42:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.20_model.r INFO @ Fri, 05 Jul 2019 15:42:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:42:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:42:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:42:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:42:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.05_summits.bed INFO @ Fri, 05 Jul 2019 15:42:32: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (365 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:42:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:42:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:42:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:42:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.10_summits.bed INFO @ Fri, 05 Jul 2019 15:42:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (233 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:42:34: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548155/ERX2548155.20_summits.bed INFO @ Fri, 05 Jul 2019 15:42:35: Done! pass1 - making usageList (17 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (131 records, 4 fields): 356 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。