Job ID = 2589264 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,717,141 reads read : 5,717,141 reads written : 5,717,141 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217339.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: 00:00:52 5717141 reads; of these: 5717141 (100.00%) were unpaired; of these: 1269079 (22.20%) aligned 0 times 3805205 (66.56%) aligned exactly 1 time 642857 (11.24%) aligned >1 times 77.80% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 1254838 / 4448062 = 0.2821 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 17:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.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 17:17:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:17:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.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 17:17:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:17:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:17:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.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 17:17:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:17:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:18:00: 1000000 INFO @ Mon, 12 Aug 2019 17:18:00: 1000000 INFO @ Mon, 12 Aug 2019 17:18:00: 1000000 INFO @ Mon, 12 Aug 2019 17:18:08: 2000000 INFO @ Mon, 12 Aug 2019 17:18:08: 2000000 INFO @ Mon, 12 Aug 2019 17:18:08: 2000000 INFO @ Mon, 12 Aug 2019 17:18:15: 3000000 INFO @ Mon, 12 Aug 2019 17:18:16: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:18:16: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:18:16: #1 total tags in treatment: 3193224 INFO @ Mon, 12 Aug 2019 17:18:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:18:16: #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 17:18:16: #1 tags after filtering in treatment: 3193224 INFO @ Mon, 12 Aug 2019 17:18:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:18:16: #1 finished! INFO @ Mon, 12 Aug 2019 17:18:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:18:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:18:16: 3000000 INFO @ Mon, 12 Aug 2019 17:18:16: #2 number of paired peaks: 636 WARNING @ Mon, 12 Aug 2019 17:18:16: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Mon, 12 Aug 2019 17:18:16: start model_add_line... INFO @ Mon, 12 Aug 2019 17:18:16: start X-correlation... INFO @ Mon, 12 Aug 2019 17:18:16: 3000000 INFO @ Mon, 12 Aug 2019 17:18:16: end of X-cor INFO @ Mon, 12 Aug 2019 17:18:16: #2 finished! INFO @ Mon, 12 Aug 2019 17:18:16: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 17:18:16: #2 alternative fragment length(s) may be 128,597 bps INFO @ Mon, 12 Aug 2019 17:18:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.20_model.r INFO @ Mon, 12 Aug 2019 17:18:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:18:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:18:18: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:18:18: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:18:18: #1 total tags in treatment: 3193224 INFO @ Mon, 12 Aug 2019 17:18:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:18:18: #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 17:18:18: #1 tags after filtering in treatment: 3193224 INFO @ Mon, 12 Aug 2019 17:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:18:18: #1 finished! INFO @ Mon, 12 Aug 2019 17:18:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:18:18: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:18:18: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:18:18: #1 total tags in treatment: 3193224 INFO @ Mon, 12 Aug 2019 17:18:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:18:18: #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 17:18:18: #1 tags after filtering in treatment: 3193224 INFO @ Mon, 12 Aug 2019 17:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:18:18: #1 finished! INFO @ Mon, 12 Aug 2019 17:18:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:18:18: #2 number of paired peaks: 636 WARNING @ Mon, 12 Aug 2019 17:18:18: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Mon, 12 Aug 2019 17:18:18: start model_add_line... INFO @ Mon, 12 Aug 2019 17:18:18: start X-correlation... INFO @ Mon, 12 Aug 2019 17:18:18: end of X-cor INFO @ Mon, 12 Aug 2019 17:18:18: #2 finished! INFO @ Mon, 12 Aug 2019 17:18:18: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 17:18:18: #2 alternative fragment length(s) may be 128,597 bps INFO @ Mon, 12 Aug 2019 17:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.05_model.r INFO @ Mon, 12 Aug 2019 17:18:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:18:18: #2 number of paired peaks: 636 WARNING @ Mon, 12 Aug 2019 17:18:18: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Mon, 12 Aug 2019 17:18:18: start model_add_line... INFO @ Mon, 12 Aug 2019 17:18:18: start X-correlation... INFO @ Mon, 12 Aug 2019 17:18:18: end of X-cor INFO @ Mon, 12 Aug 2019 17:18:18: #2 finished! INFO @ Mon, 12 Aug 2019 17:18:18: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 17:18:18: #2 alternative fragment length(s) may be 128,597 bps INFO @ Mon, 12 Aug 2019 17:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.10_model.r INFO @ Mon, 12 Aug 2019 17:18:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:18:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:18:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:18:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.20_summits.bed INFO @ Mon, 12 Aug 2019 17:18:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:18:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:18:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:18:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:18:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.10_summits.bed INFO @ Mon, 12 Aug 2019 17:18:33: Done! INFO @ Mon, 12 Aug 2019 17:18:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:18:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065633/SRX065633.05_summits.bed INFO @ Mon, 12 Aug 2019 17:18:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (946 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2380 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。