Job ID = 2589888 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,231,801 reads read : 2,231,801 reads written : 2,231,801 spots read : 3,988,589 reads read : 3,988,589 reads written : 3,988,589 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947524.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947525.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 6220390 reads; of these: 6220390 (100.00%) were unpaired; of these: 4016893 (64.58%) aligned 0 times 1875271 (30.15%) aligned exactly 1 time 328226 (5.28%) aligned >1 times 35.42% 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] 356248 / 2203497 = 0.1617 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 18:43:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.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 18:43:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.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 18:43:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.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 18:43:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:43:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:43:28: 1000000 INFO @ Mon, 12 Aug 2019 18:43:29: 1000000 INFO @ Mon, 12 Aug 2019 18:43:32: 1000000 INFO @ Mon, 12 Aug 2019 18:43:34: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:43:34: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:43:34: #1 total tags in treatment: 1847249 INFO @ Mon, 12 Aug 2019 18:43:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:43:34: #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 18:43:34: #1 tags after filtering in treatment: 1847249 INFO @ Mon, 12 Aug 2019 18:43:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:43:34: #1 finished! INFO @ Mon, 12 Aug 2019 18:43:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:43:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:43:35: #2 number of paired peaks: 729 WARNING @ Mon, 12 Aug 2019 18:43:35: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Mon, 12 Aug 2019 18:43:35: start model_add_line... INFO @ Mon, 12 Aug 2019 18:43:35: start X-correlation... INFO @ Mon, 12 Aug 2019 18:43:35: end of X-cor INFO @ Mon, 12 Aug 2019 18:43:35: #2 finished! INFO @ Mon, 12 Aug 2019 18:43:35: #2 predicted fragment length is 132 bps INFO @ Mon, 12 Aug 2019 18:43:35: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 12 Aug 2019 18:43:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.05_model.r INFO @ Mon, 12 Aug 2019 18:43:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:43:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:43:36: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:43:36: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:43:36: #1 total tags in treatment: 1847249 INFO @ Mon, 12 Aug 2019 18:43:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:43:36: #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 18:43:36: #1 tags after filtering in treatment: 1847249 INFO @ Mon, 12 Aug 2019 18:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:43:36: #1 finished! INFO @ Mon, 12 Aug 2019 18:43:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:43:36: #2 number of paired peaks: 729 WARNING @ Mon, 12 Aug 2019 18:43:36: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Mon, 12 Aug 2019 18:43:36: start model_add_line... INFO @ Mon, 12 Aug 2019 18:43:36: start X-correlation... INFO @ Mon, 12 Aug 2019 18:43:36: end of X-cor INFO @ Mon, 12 Aug 2019 18:43:36: #2 finished! INFO @ Mon, 12 Aug 2019 18:43:36: #2 predicted fragment length is 132 bps INFO @ Mon, 12 Aug 2019 18:43:36: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 12 Aug 2019 18:43:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.10_model.r INFO @ Mon, 12 Aug 2019 18:43:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:43:38: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:43:38: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:43:38: #1 total tags in treatment: 1847249 INFO @ Mon, 12 Aug 2019 18:43:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:43:38: #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 18:43:38: #1 tags after filtering in treatment: 1847249 INFO @ Mon, 12 Aug 2019 18:43:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:43:38: #1 finished! INFO @ Mon, 12 Aug 2019 18:43:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:43:38: #2 number of paired peaks: 729 WARNING @ Mon, 12 Aug 2019 18:43:38: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Mon, 12 Aug 2019 18:43:38: start model_add_line... INFO @ Mon, 12 Aug 2019 18:43:38: start X-correlation... INFO @ Mon, 12 Aug 2019 18:43:38: end of X-cor INFO @ Mon, 12 Aug 2019 18:43:38: #2 finished! INFO @ Mon, 12 Aug 2019 18:43:38: #2 predicted fragment length is 132 bps INFO @ Mon, 12 Aug 2019 18:43:38: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 12 Aug 2019 18:43:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.20_model.r INFO @ Mon, 12 Aug 2019 18:43:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:43:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:43:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:43:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:43:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:43:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:43:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.05_summits.bed INFO @ Mon, 12 Aug 2019 18:43:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1473 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:43:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:43:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.10_summits.bed INFO @ Mon, 12 Aug 2019 18:43:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331288/SRX331288.20_summits.bed INFO @ Mon, 12 Aug 2019 18:43:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。