Job ID = 2589427 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,099,942 reads read : 3,099,942 reads written : 3,099,942 spots read : 1,978,701 reads read : 1,978,701 reads written : 1,978,701 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR494666.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: 00:00:34 5078643 reads; of these: 5078643 (100.00%) were unpaired; of these: 4251328 (83.71%) aligned 0 times 730646 (14.39%) aligned exactly 1 time 96669 (1.90%) aligned >1 times 16.29% overall alignment rate Time searching: 00:00:34 Overall time: 00:00:34 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] 55279 / 827315 = 0.0668 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 17:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.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 17:40:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:40:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:40:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.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 17:40:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:40:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:40:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.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 17:40:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:40:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:40:39: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:40:39: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:40:39: #1 total tags in treatment: 772036 INFO @ Mon, 12 Aug 2019 17:40:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:40:39: #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 17:40:39: #1 tags after filtering in treatment: 772036 INFO @ Mon, 12 Aug 2019 17:40:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:40:39: #1 finished! INFO @ Mon, 12 Aug 2019 17:40:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:40:39: #2 number of paired peaks: 2009 INFO @ Mon, 12 Aug 2019 17:40:39: start model_add_line... INFO @ Mon, 12 Aug 2019 17:40:39: start X-correlation... INFO @ Mon, 12 Aug 2019 17:40:39: end of X-cor INFO @ Mon, 12 Aug 2019 17:40:39: #2 finished! INFO @ Mon, 12 Aug 2019 17:40:39: #2 predicted fragment length is 189 bps INFO @ Mon, 12 Aug 2019 17:40:39: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 12 Aug 2019 17:40:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.05_model.r INFO @ Mon, 12 Aug 2019 17:40:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:40:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:40:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:40:42: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:40:42: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:40:42: #1 total tags in treatment: 772036 INFO @ Mon, 12 Aug 2019 17:40:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:40:42: #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 17:40:42: #1 tags after filtering in treatment: 772036 INFO @ Mon, 12 Aug 2019 17:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:40:42: #1 finished! INFO @ Mon, 12 Aug 2019 17:40:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:40:42: #2 number of paired peaks: 2009 INFO @ Mon, 12 Aug 2019 17:40:42: start model_add_line... INFO @ Mon, 12 Aug 2019 17:40:42: start X-correlation... INFO @ Mon, 12 Aug 2019 17:40:42: end of X-cor INFO @ Mon, 12 Aug 2019 17:40:42: #2 finished! INFO @ Mon, 12 Aug 2019 17:40:42: #2 predicted fragment length is 189 bps INFO @ Mon, 12 Aug 2019 17:40:42: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 12 Aug 2019 17:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.20_model.r INFO @ Mon, 12 Aug 2019 17:40:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:40:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:40:43: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:40:43: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:40:43: #1 total tags in treatment: 772036 INFO @ Mon, 12 Aug 2019 17:40:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:40:43: #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 17:40:43: #1 tags after filtering in treatment: 772036 INFO @ Mon, 12 Aug 2019 17:40:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:40:43: #1 finished! INFO @ Mon, 12 Aug 2019 17:40:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:40:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:40:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:40:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:40:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.05_summits.bed INFO @ Mon, 12 Aug 2019 17:40:43: Done! INFO @ Mon, 12 Aug 2019 17:40:43: #2 number of paired peaks: 2009 INFO @ Mon, 12 Aug 2019 17:40:43: start model_add_line... INFO @ Mon, 12 Aug 2019 17:40:43: start X-correlation... INFO @ Mon, 12 Aug 2019 17:40:43: end of X-cor INFO @ Mon, 12 Aug 2019 17:40:43: #2 finished! INFO @ Mon, 12 Aug 2019 17:40:43: #2 predicted fragment length is 189 bps INFO @ Mon, 12 Aug 2019 17:40:43: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 12 Aug 2019 17:40:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.10_model.r INFO @ Mon, 12 Aug 2019 17:40:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:40:43: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1453 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:40:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:40:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:40:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:40:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:40:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.20_summits.bed INFO @ Mon, 12 Aug 2019 17:40:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:40:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:40:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:40:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX146500/SRX146500.10_summits.bed INFO @ Mon, 12 Aug 2019 17:40:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (555 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。