Job ID = 2589848 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,641,929 reads read : 7,641,929 reads written : 7,641,929 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947481.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: 00:01:19 7641929 reads; of these: 7641929 (100.00%) were unpaired; of these: 1611982 (21.09%) aligned 0 times 5020451 (65.70%) aligned exactly 1 time 1009496 (13.21%) aligned >1 times 78.91% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 497667 / 6029947 = 0.0825 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 18:38:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.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 18:38:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:38:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:38:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.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 18:38:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:38:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:38:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.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 18:38:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:38:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:38:39: 1000000 INFO @ Mon, 12 Aug 2019 18:38:43: 1000000 INFO @ Mon, 12 Aug 2019 18:38:44: 1000000 INFO @ Mon, 12 Aug 2019 18:38:46: 2000000 INFO @ Mon, 12 Aug 2019 18:38:52: 2000000 INFO @ Mon, 12 Aug 2019 18:38:53: 2000000 INFO @ Mon, 12 Aug 2019 18:38:53: 3000000 INFO @ Mon, 12 Aug 2019 18:39:01: 4000000 INFO @ Mon, 12 Aug 2019 18:39:02: 3000000 INFO @ Mon, 12 Aug 2019 18:39:02: 3000000 INFO @ Mon, 12 Aug 2019 18:39:08: 5000000 INFO @ Mon, 12 Aug 2019 18:39:12: 4000000 INFO @ Mon, 12 Aug 2019 18:39:12: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:39:12: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:39:12: #1 total tags in treatment: 5532280 INFO @ Mon, 12 Aug 2019 18:39:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:39:12: #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 18:39:12: #1 tags after filtering in treatment: 5532280 INFO @ Mon, 12 Aug 2019 18:39:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:39:12: #1 finished! INFO @ Mon, 12 Aug 2019 18:39:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:39:12: 4000000 INFO @ Mon, 12 Aug 2019 18:39:12: #2 number of paired peaks: 556 WARNING @ Mon, 12 Aug 2019 18:39:12: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Mon, 12 Aug 2019 18:39:12: start model_add_line... INFO @ Mon, 12 Aug 2019 18:39:12: start X-correlation... INFO @ Mon, 12 Aug 2019 18:39:12: end of X-cor INFO @ Mon, 12 Aug 2019 18:39:12: #2 finished! INFO @ Mon, 12 Aug 2019 18:39:12: #2 predicted fragment length is 86 bps INFO @ Mon, 12 Aug 2019 18:39:12: #2 alternative fragment length(s) may be 4,81,86,575,589,597 bps INFO @ Mon, 12 Aug 2019 18:39:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.05_model.r INFO @ Mon, 12 Aug 2019 18:39:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:39:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:39:21: 5000000 INFO @ Mon, 12 Aug 2019 18:39:22: 5000000 INFO @ Mon, 12 Aug 2019 18:39:26: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:39:26: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:39:26: #1 total tags in treatment: 5532280 INFO @ Mon, 12 Aug 2019 18:39:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:39:26: #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 18:39:26: #1 tags after filtering in treatment: 5532280 INFO @ Mon, 12 Aug 2019 18:39:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:39:26: #1 finished! INFO @ Mon, 12 Aug 2019 18:39:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:39:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:39:26: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:39:26: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:39:26: #1 total tags in treatment: 5532280 INFO @ Mon, 12 Aug 2019 18:39:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:39:26: #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 18:39:27: #1 tags after filtering in treatment: 5532280 INFO @ Mon, 12 Aug 2019 18:39:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:39:27: #1 finished! INFO @ Mon, 12 Aug 2019 18:39:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:39:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:39:27: #2 number of paired peaks: 556 WARNING @ Mon, 12 Aug 2019 18:39:27: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Mon, 12 Aug 2019 18:39:27: start model_add_line... INFO @ Mon, 12 Aug 2019 18:39:27: start X-correlation... INFO @ Mon, 12 Aug 2019 18:39:27: end of X-cor INFO @ Mon, 12 Aug 2019 18:39:27: #2 finished! INFO @ Mon, 12 Aug 2019 18:39:27: #2 predicted fragment length is 86 bps INFO @ Mon, 12 Aug 2019 18:39:27: #2 alternative fragment length(s) may be 4,81,86,575,589,597 bps INFO @ Mon, 12 Aug 2019 18:39:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.10_model.r INFO @ Mon, 12 Aug 2019 18:39:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:39:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:39:27: #2 number of paired peaks: 556 WARNING @ Mon, 12 Aug 2019 18:39:27: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Mon, 12 Aug 2019 18:39:27: start model_add_line... INFO @ Mon, 12 Aug 2019 18:39:27: start X-correlation... INFO @ Mon, 12 Aug 2019 18:39:27: end of X-cor INFO @ Mon, 12 Aug 2019 18:39:27: #2 finished! INFO @ Mon, 12 Aug 2019 18:39:27: #2 predicted fragment length is 86 bps INFO @ Mon, 12 Aug 2019 18:39:27: #2 alternative fragment length(s) may be 4,81,86,575,589,597 bps INFO @ Mon, 12 Aug 2019 18:39:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.20_model.r INFO @ Mon, 12 Aug 2019 18:39:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:39:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:39:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.05_summits.bed INFO @ Mon, 12 Aug 2019 18:39:37: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1444 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:39:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:39:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:39:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:39:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:39:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.10_summits.bed INFO @ Mon, 12 Aug 2019 18:39:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331249/SRX331249.20_summits.bed INFO @ Mon, 12 Aug 2019 18:39:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。