Job ID = 2589869 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,605,958 reads read : 2,605,958 reads written : 2,605,958 spots read : 935,443 reads read : 935,443 reads written : 935,443 spots read : 2,732,049 reads read : 2,732,049 reads written : 2,732,049 spots read : 886,188 reads read : 886,188 reads written : 886,188 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947502.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947503.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947504.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947505.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: 00:00:50 7159638 reads; of these: 7159638 (100.00%) were unpaired; of these: 4854883 (67.81%) aligned 0 times 1628912 (22.75%) aligned exactly 1 time 675843 (9.44%) aligned >1 times 32.19% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 921270 / 2304755 = 0.3997 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 18:42:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.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 18:42:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:42:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.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 18:42:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:42:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:42:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.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 18:42:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:42:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:42:43: 1000000 INFO @ Mon, 12 Aug 2019 18:42:44: 1000000 INFO @ Mon, 12 Aug 2019 18:42:44: 1000000 INFO @ Mon, 12 Aug 2019 18:42:46: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:42:46: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:42:46: #1 total tags in treatment: 1383485 INFO @ Mon, 12 Aug 2019 18:42:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:42:46: #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 18:42:46: #1 tags after filtering in treatment: 1383485 INFO @ Mon, 12 Aug 2019 18:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:42:46: #1 finished! INFO @ Mon, 12 Aug 2019 18:42:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:42:46: #2 number of paired peaks: 1852 INFO @ Mon, 12 Aug 2019 18:42:46: start model_add_line... INFO @ Mon, 12 Aug 2019 18:42:46: start X-correlation... INFO @ Mon, 12 Aug 2019 18:42:46: end of X-cor INFO @ Mon, 12 Aug 2019 18:42:46: #2 finished! INFO @ Mon, 12 Aug 2019 18:42:46: #2 predicted fragment length is 157 bps INFO @ Mon, 12 Aug 2019 18:42:46: #2 alternative fragment length(s) may be 157 bps INFO @ Mon, 12 Aug 2019 18:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.05_model.r INFO @ Mon, 12 Aug 2019 18:42:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:42:47: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:42:47: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:42:47: #1 total tags in treatment: 1383485 INFO @ Mon, 12 Aug 2019 18:42:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:42:47: #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 18:42:47: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:42:47: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:42:47: #1 total tags in treatment: 1383485 INFO @ Mon, 12 Aug 2019 18:42:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:42:47: #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 18:42:47: #1 tags after filtering in treatment: 1383485 INFO @ Mon, 12 Aug 2019 18:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:42:47: #1 finished! INFO @ Mon, 12 Aug 2019 18:42:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:42:47: #1 tags after filtering in treatment: 1383485 INFO @ Mon, 12 Aug 2019 18:42:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:42:47: #1 finished! INFO @ Mon, 12 Aug 2019 18:42:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:42:47: #2 number of paired peaks: 1852 INFO @ Mon, 12 Aug 2019 18:42:47: start model_add_line... INFO @ Mon, 12 Aug 2019 18:42:47: #2 number of paired peaks: 1852 INFO @ Mon, 12 Aug 2019 18:42:47: start model_add_line... INFO @ Mon, 12 Aug 2019 18:42:47: start X-correlation... INFO @ Mon, 12 Aug 2019 18:42:47: start X-correlation... INFO @ Mon, 12 Aug 2019 18:42:47: end of X-cor INFO @ Mon, 12 Aug 2019 18:42:47: #2 finished! INFO @ Mon, 12 Aug 2019 18:42:47: #2 predicted fragment length is 157 bps INFO @ Mon, 12 Aug 2019 18:42:47: #2 alternative fragment length(s) may be 157 bps INFO @ Mon, 12 Aug 2019 18:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.10_model.r INFO @ Mon, 12 Aug 2019 18:42:47: end of X-cor INFO @ Mon, 12 Aug 2019 18:42:47: #2 finished! INFO @ Mon, 12 Aug 2019 18:42:47: #2 predicted fragment length is 157 bps INFO @ Mon, 12 Aug 2019 18:42:47: #2 alternative fragment length(s) may be 157 bps INFO @ Mon, 12 Aug 2019 18:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.20_model.r INFO @ Mon, 12 Aug 2019 18:42:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:42:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:42:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:42:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:42:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:42:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.05_summits.bed INFO @ Mon, 12 Aug 2019 18:42:53: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1826 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.20_summits.bed INFO @ Mon, 12 Aug 2019 18:42:54: Done! INFO @ Mon, 12 Aug 2019 18:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331270/SRX331270.10_summits.bed INFO @ Mon, 12 Aug 2019 18:42:54: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1234 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1515 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。