Job ID = 2589222 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,182,021 reads read : 2,182,021 reads written : 2,182,021 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR163976.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: 00:00:13 2182021 reads; of these: 2182021 (100.00%) were unpaired; of these: 1584961 (72.64%) aligned 0 times 529924 (24.29%) aligned exactly 1 time 67136 (3.08%) aligned >1 times 27.36% overall alignment rate Time searching: 00:00:13 Overall time: 00:00:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 33895 / 597060 = 0.0568 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 17:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.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 17:10:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:10:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.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 17:10:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:10:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.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 17:10:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:10:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:10:26: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:10:26: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:10:26: #1 total tags in treatment: 563165 INFO @ Mon, 12 Aug 2019 17:10:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:10:26: #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 17:10:26: #1 tags after filtering in treatment: 563165 INFO @ Mon, 12 Aug 2019 17:10:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:10:26: #1 finished! INFO @ Mon, 12 Aug 2019 17:10:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:10:26: #2 number of paired peaks: 775 WARNING @ Mon, 12 Aug 2019 17:10:26: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Mon, 12 Aug 2019 17:10:26: start model_add_line... INFO @ Mon, 12 Aug 2019 17:10:26: start X-correlation... INFO @ Mon, 12 Aug 2019 17:10:26: end of X-cor INFO @ Mon, 12 Aug 2019 17:10:26: #2 finished! INFO @ Mon, 12 Aug 2019 17:10:26: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 17:10:26: #2 alternative fragment length(s) may be 149,569 bps INFO @ Mon, 12 Aug 2019 17:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.05_model.r INFO @ Mon, 12 Aug 2019 17:10:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:28: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:10:28: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:10:28: #1 total tags in treatment: 563165 INFO @ Mon, 12 Aug 2019 17:10:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:10:28: #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 17:10:28: #1 tags after filtering in treatment: 563165 INFO @ Mon, 12 Aug 2019 17:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:10:28: #1 finished! INFO @ Mon, 12 Aug 2019 17:10:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:10:28: #2 number of paired peaks: 775 WARNING @ Mon, 12 Aug 2019 17:10:28: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Mon, 12 Aug 2019 17:10:28: start model_add_line... INFO @ Mon, 12 Aug 2019 17:10:28: start X-correlation... INFO @ Mon, 12 Aug 2019 17:10:28: end of X-cor INFO @ Mon, 12 Aug 2019 17:10:28: #2 finished! INFO @ Mon, 12 Aug 2019 17:10:28: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 17:10:28: #2 alternative fragment length(s) may be 149,569 bps INFO @ Mon, 12 Aug 2019 17:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.10_model.r INFO @ Mon, 12 Aug 2019 17:10:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:28: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:10:28: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:10:28: #1 total tags in treatment: 563165 INFO @ Mon, 12 Aug 2019 17:10:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:10:28: #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 17:10:28: #1 tags after filtering in treatment: 563165 INFO @ Mon, 12 Aug 2019 17:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:10:28: #1 finished! INFO @ Mon, 12 Aug 2019 17:10:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:10:28: #2 number of paired peaks: 775 WARNING @ Mon, 12 Aug 2019 17:10:28: Fewer paired peaks (775) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 775 pairs to build model! INFO @ Mon, 12 Aug 2019 17:10:28: start model_add_line... INFO @ Mon, 12 Aug 2019 17:10:28: start X-correlation... INFO @ Mon, 12 Aug 2019 17:10:28: end of X-cor INFO @ Mon, 12 Aug 2019 17:10:28: #2 finished! INFO @ Mon, 12 Aug 2019 17:10:28: #2 predicted fragment length is 149 bps INFO @ Mon, 12 Aug 2019 17:10:28: #2 alternative fragment length(s) may be 149,569 bps INFO @ Mon, 12 Aug 2019 17:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.20_model.r INFO @ Mon, 12 Aug 2019 17:10:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.05_summits.bed INFO @ Mon, 12 Aug 2019 17:10:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:10:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.10_summits.bed INFO @ Mon, 12 Aug 2019 17:10:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054210/SRX054210.20_summits.bed INFO @ Mon, 12 Aug 2019 17:10:31: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。