Job ID = 2589726 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,300,667 reads read : 9,300,667 reads written : 9,300,667 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947328.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: 00:01:22 9300667 reads; of these: 9300667 (100.00%) were unpaired; of these: 1480427 (15.92%) aligned 0 times 6713953 (72.19%) aligned exactly 1 time 1106287 (11.89%) aligned >1 times 84.08% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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] 1012731 / 7820240 = 0.1295 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 18:22:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.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 18:22:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:22:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.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 18:22:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:22:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:22:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.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 18:22:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:22:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:22:29: 1000000 INFO @ Mon, 12 Aug 2019 18:22:30: 1000000 INFO @ Mon, 12 Aug 2019 18:22:31: 1000000 INFO @ Mon, 12 Aug 2019 18:22:35: 2000000 INFO @ Mon, 12 Aug 2019 18:22:36: 2000000 INFO @ Mon, 12 Aug 2019 18:22:36: 2000000 INFO @ Mon, 12 Aug 2019 18:22:41: 3000000 INFO @ Mon, 12 Aug 2019 18:22:42: 3000000 INFO @ Mon, 12 Aug 2019 18:22:42: 3000000 INFO @ Mon, 12 Aug 2019 18:22:47: 4000000 INFO @ Mon, 12 Aug 2019 18:22:48: 4000000 INFO @ Mon, 12 Aug 2019 18:22:48: 4000000 INFO @ Mon, 12 Aug 2019 18:22:53: 5000000 INFO @ Mon, 12 Aug 2019 18:22:54: 5000000 INFO @ Mon, 12 Aug 2019 18:22:54: 5000000 INFO @ Mon, 12 Aug 2019 18:22:59: 6000000 INFO @ Mon, 12 Aug 2019 18:23:00: 6000000 INFO @ Mon, 12 Aug 2019 18:23:00: 6000000 INFO @ Mon, 12 Aug 2019 18:23:04: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:23:04: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:23:04: #1 total tags in treatment: 6807509 INFO @ Mon, 12 Aug 2019 18:23:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:23:04: #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 18:23:04: #1 tags after filtering in treatment: 6807509 INFO @ Mon, 12 Aug 2019 18:23:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:23:04: #1 finished! INFO @ Mon, 12 Aug 2019 18:23:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:23:04: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:23:04: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:23:04: #1 total tags in treatment: 6807509 INFO @ Mon, 12 Aug 2019 18:23:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:23:04: #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 18:23:04: #1 tags after filtering in treatment: 6807509 INFO @ Mon, 12 Aug 2019 18:23:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:23:04: #1 finished! INFO @ Mon, 12 Aug 2019 18:23:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:23:05: #2 number of paired peaks: 1195 INFO @ Mon, 12 Aug 2019 18:23:05: start model_add_line... INFO @ Mon, 12 Aug 2019 18:23:05: start X-correlation... INFO @ Mon, 12 Aug 2019 18:23:05: end of X-cor INFO @ Mon, 12 Aug 2019 18:23:05: #2 finished! INFO @ Mon, 12 Aug 2019 18:23:05: #2 predicted fragment length is 162 bps INFO @ Mon, 12 Aug 2019 18:23:05: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 12 Aug 2019 18:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.05_model.r INFO @ Mon, 12 Aug 2019 18:23:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:23:05: #2 number of paired peaks: 1195 INFO @ Mon, 12 Aug 2019 18:23:05: start model_add_line... INFO @ Mon, 12 Aug 2019 18:23:05: start X-correlation... INFO @ Mon, 12 Aug 2019 18:23:05: end of X-cor INFO @ Mon, 12 Aug 2019 18:23:05: #2 finished! INFO @ Mon, 12 Aug 2019 18:23:05: #2 predicted fragment length is 162 bps INFO @ Mon, 12 Aug 2019 18:23:05: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 12 Aug 2019 18:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.20_model.r INFO @ Mon, 12 Aug 2019 18:23:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:23:05: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:23:05: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:23:05: #1 total tags in treatment: 6807509 INFO @ Mon, 12 Aug 2019 18:23:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:23:05: #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 18:23:05: #1 tags after filtering in treatment: 6807509 INFO @ Mon, 12 Aug 2019 18:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:23:05: #1 finished! INFO @ Mon, 12 Aug 2019 18:23:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:23:06: #2 number of paired peaks: 1195 INFO @ Mon, 12 Aug 2019 18:23:06: start model_add_line... INFO @ Mon, 12 Aug 2019 18:23:06: start X-correlation... INFO @ Mon, 12 Aug 2019 18:23:06: end of X-cor INFO @ Mon, 12 Aug 2019 18:23:06: #2 finished! INFO @ Mon, 12 Aug 2019 18:23:06: #2 predicted fragment length is 162 bps INFO @ Mon, 12 Aug 2019 18:23:06: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 12 Aug 2019 18:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.10_model.r INFO @ Mon, 12 Aug 2019 18:23:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:23:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:23:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:23:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.05_summits.bed INFO @ Mon, 12 Aug 2019 18:23:36: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (6323 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:23:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:23:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:23:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.20_summits.bed INFO @ Mon, 12 Aug 2019 18:23:37: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2089 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:23:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:23:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:23:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331098/SRX331098.10_summits.bed INFO @ Mon, 12 Aug 2019 18:23:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4035 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。