Job ID = 2589114 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,045,900 reads read : 2,045,900 reads written : 2,045,900 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107298.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: 00:00:19 2045900 reads; of these: 2045900 (100.00%) were unpaired; of these: 930761 (45.49%) aligned 0 times 856112 (41.85%) aligned exactly 1 time 259027 (12.66%) aligned >1 times 54.51% overall alignment rate Time searching: 00:00:19 Overall time: 00:00:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 149253 / 1115139 = 0.1338 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 @ Mon, 12 Aug 2019 16:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 16:55:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:55:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 16:55:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:55:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 16:55:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:55:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:55:54: #1 tag size is determined as 27 bps INFO @ Mon, 12 Aug 2019 16:55:54: #1 tag size = 27 INFO @ Mon, 12 Aug 2019 16:55:54: #1 total tags in treatment: 965886 INFO @ Mon, 12 Aug 2019 16:55:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 16:55:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 16:55:54: #1 tags after filtering in treatment: 965886 INFO @ Mon, 12 Aug 2019 16:55:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 16:55:54: #1 finished! INFO @ Mon, 12 Aug 2019 16:55:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 16:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 16:55:54: #2 number of paired peaks: 371 WARNING @ Mon, 12 Aug 2019 16:55:54: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Mon, 12 Aug 2019 16:55:54: start model_add_line... INFO @ Mon, 12 Aug 2019 16:55:54: start X-correlation... INFO @ Mon, 12 Aug 2019 16:55:55: end of X-cor INFO @ Mon, 12 Aug 2019 16:55:55: #2 finished! INFO @ Mon, 12 Aug 2019 16:55:55: #2 predicted fragment length is 99 bps INFO @ Mon, 12 Aug 2019 16:55:55: #2 alternative fragment length(s) may be 99 bps INFO @ Mon, 12 Aug 2019 16:55:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.10_model.r INFO @ Mon, 12 Aug 2019 16:55:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 16:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 16:55:55: #1 tag size is determined as 27 bps INFO @ Mon, 12 Aug 2019 16:55:55: #1 tag size = 27 INFO @ Mon, 12 Aug 2019 16:55:55: #1 total tags in treatment: 965886 INFO @ Mon, 12 Aug 2019 16:55:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 16:55:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 16:55:55: #1 tag size is determined as 27 bps INFO @ Mon, 12 Aug 2019 16:55:55: #1 tag size = 27 INFO @ Mon, 12 Aug 2019 16:55:55: #1 total tags in treatment: 965886 INFO @ Mon, 12 Aug 2019 16:55:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 16:55:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 16:55:55: #1 tags after filtering in treatment: 965886 INFO @ Mon, 12 Aug 2019 16:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 16:55:55: #1 finished! INFO @ Mon, 12 Aug 2019 16:55:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 16:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 16:55:55: #1 tags after filtering in treatment: 965886 INFO @ Mon, 12 Aug 2019 16:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 16:55:55: #1 finished! INFO @ Mon, 12 Aug 2019 16:55:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 16:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 16:55:55: #2 number of paired peaks: 371 WARNING @ Mon, 12 Aug 2019 16:55:55: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Mon, 12 Aug 2019 16:55:55: start model_add_line... INFO @ Mon, 12 Aug 2019 16:55:55: #2 number of paired peaks: 371 WARNING @ Mon, 12 Aug 2019 16:55:55: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Mon, 12 Aug 2019 16:55:55: start model_add_line... INFO @ Mon, 12 Aug 2019 16:55:55: start X-correlation... INFO @ Mon, 12 Aug 2019 16:55:55: start X-correlation... INFO @ Mon, 12 Aug 2019 16:55:55: end of X-cor INFO @ Mon, 12 Aug 2019 16:55:55: #2 finished! INFO @ Mon, 12 Aug 2019 16:55:55: #2 predicted fragment length is 99 bps INFO @ Mon, 12 Aug 2019 16:55:55: #2 alternative fragment length(s) may be 99 bps INFO @ Mon, 12 Aug 2019 16:55:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.05_model.r INFO @ Mon, 12 Aug 2019 16:55:55: end of X-cor INFO @ Mon, 12 Aug 2019 16:55:55: #2 finished! INFO @ Mon, 12 Aug 2019 16:55:55: #2 predicted fragment length is 99 bps INFO @ Mon, 12 Aug 2019 16:55:55: #2 alternative fragment length(s) may be 99 bps INFO @ Mon, 12 Aug 2019 16:55:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.20_model.r INFO @ Mon, 12 Aug 2019 16:55:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 16:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 16:55:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 16:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 16:55:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 16:55:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 16:55:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 16:55:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.10_peaks.xls INFO @ Mon, 12 Aug 2019 16:55:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 16:55:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.10_summits.bed INFO @ Mon, 12 Aug 2019 16:55:59: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (84 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 16:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.20_peaks.xls INFO @ Mon, 12 Aug 2019 16:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 16:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.20_summits.bed INFO @ Mon, 12 Aug 2019 16:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.05_peaks.xls INFO @ Mon, 12 Aug 2019 16:56:00: Done! INFO @ Mon, 12 Aug 2019 16:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 16:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043843/SRX043843.05_summits.bed INFO @ Mon, 12 Aug 2019 16:56:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。