Job ID = 2589135 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,157,862 reads read : 4,157,862 reads written : 4,157,862 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107325.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: 00:00:45 4157862 reads; of these: 4157862 (100.00%) were unpaired; of these: 913053 (21.96%) aligned 0 times 2831192 (68.09%) aligned exactly 1 time 413617 (9.95%) aligned >1 times 78.04% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 255523 / 3244809 = 0.0787 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 16:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.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 16:59:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:59:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.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 16:59:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:59:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.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 16:59:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:59:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:00:01: 1000000 INFO @ Mon, 12 Aug 2019 17:00:01: 1000000 INFO @ Mon, 12 Aug 2019 17:00:02: 1000000 INFO @ Mon, 12 Aug 2019 17:00:08: 2000000 INFO @ Mon, 12 Aug 2019 17:00:09: 2000000 INFO @ Mon, 12 Aug 2019 17:00:10: 2000000 INFO @ Mon, 12 Aug 2019 17:00:15: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:00:15: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:00:15: #1 total tags in treatment: 2989286 INFO @ Mon, 12 Aug 2019 17:00:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:00:15: #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 17:00:15: #1 tags after filtering in treatment: 2989286 INFO @ Mon, 12 Aug 2019 17:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:00:15: #1 finished! INFO @ Mon, 12 Aug 2019 17:00:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:00:15: #2 number of paired peaks: 766 WARNING @ Mon, 12 Aug 2019 17:00:15: Fewer paired peaks (766) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 766 pairs to build model! INFO @ Mon, 12 Aug 2019 17:00:15: start model_add_line... INFO @ Mon, 12 Aug 2019 17:00:16: start X-correlation... INFO @ Mon, 12 Aug 2019 17:00:16: end of X-cor INFO @ Mon, 12 Aug 2019 17:00:16: #2 finished! INFO @ Mon, 12 Aug 2019 17:00:16: #2 predicted fragment length is 157 bps INFO @ Mon, 12 Aug 2019 17:00:16: #2 alternative fragment length(s) may be 157 bps INFO @ Mon, 12 Aug 2019 17:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.10_model.r INFO @ Mon, 12 Aug 2019 17:00:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:00:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:00:17: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:00:17: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:00:17: #1 total tags in treatment: 2989286 INFO @ Mon, 12 Aug 2019 17:00:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:00:17: #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 17:00:17: #1 tags after filtering in treatment: 2989286 INFO @ Mon, 12 Aug 2019 17:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:00:17: #1 finished! INFO @ Mon, 12 Aug 2019 17:00:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:00:18: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:00:18: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:00:18: #1 total tags in treatment: 2989286 INFO @ Mon, 12 Aug 2019 17:00:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:00:18: #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 17:00:18: #1 tags after filtering in treatment: 2989286 INFO @ Mon, 12 Aug 2019 17:00:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:00:18: #1 finished! INFO @ Mon, 12 Aug 2019 17:00:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:00:18: #2 number of paired peaks: 766 WARNING @ Mon, 12 Aug 2019 17:00:18: Fewer paired peaks (766) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 766 pairs to build model! INFO @ Mon, 12 Aug 2019 17:00:18: start model_add_line... INFO @ Mon, 12 Aug 2019 17:00:18: start X-correlation... INFO @ Mon, 12 Aug 2019 17:00:18: end of X-cor INFO @ Mon, 12 Aug 2019 17:00:18: #2 finished! INFO @ Mon, 12 Aug 2019 17:00:18: #2 predicted fragment length is 157 bps INFO @ Mon, 12 Aug 2019 17:00:18: #2 alternative fragment length(s) may be 157 bps INFO @ Mon, 12 Aug 2019 17:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.05_model.r INFO @ Mon, 12 Aug 2019 17:00:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:00:18: #2 number of paired peaks: 766 WARNING @ Mon, 12 Aug 2019 17:00:18: Fewer paired peaks (766) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 766 pairs to build model! INFO @ Mon, 12 Aug 2019 17:00:18: start model_add_line... INFO @ Mon, 12 Aug 2019 17:00:18: start X-correlation... INFO @ Mon, 12 Aug 2019 17:00:18: end of X-cor INFO @ Mon, 12 Aug 2019 17:00:18: #2 finished! INFO @ Mon, 12 Aug 2019 17:00:18: #2 predicted fragment length is 157 bps INFO @ Mon, 12 Aug 2019 17:00:18: #2 alternative fragment length(s) may be 157 bps INFO @ Mon, 12 Aug 2019 17:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.20_model.r INFO @ Mon, 12 Aug 2019 17:00:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:00:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:00:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:00:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:00:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:00:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.10_summits.bed INFO @ Mon, 12 Aug 2019 17:00:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (244 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.05_summits.bed INFO @ Mon, 12 Aug 2019 17:00:32: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (610 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043864/SRX043864.20_summits.bed INFO @ Mon, 12 Aug 2019 17:00:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (77 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。