Job ID = 2589290 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,582,326 reads read : 4,582,326 reads written : 4,582,326 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217363.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: 00:00:39 4582326 reads; of these: 4582326 (100.00%) were unpaired; of these: 2525680 (55.12%) aligned 0 times 1815083 (39.61%) aligned exactly 1 time 241563 (5.27%) aligned >1 times 44.88% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 340328 / 2056646 = 0.1655 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 17:20:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.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 17:20:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:20:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.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 17:20:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:20:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:20:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.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 17:20:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:20:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:20:45: 1000000 INFO @ Mon, 12 Aug 2019 17:20:46: 1000000 INFO @ Mon, 12 Aug 2019 17:20:46: 1000000 INFO @ Mon, 12 Aug 2019 17:20:51: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:20:51: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:20:51: #1 total tags in treatment: 1716318 INFO @ Mon, 12 Aug 2019 17:20:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:20:51: #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 17:20:52: #1 tags after filtering in treatment: 1716318 INFO @ Mon, 12 Aug 2019 17:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:20:52: #1 finished! INFO @ Mon, 12 Aug 2019 17:20:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:20:52: #2 number of paired peaks: 3056 INFO @ Mon, 12 Aug 2019 17:20:52: start model_add_line... INFO @ Mon, 12 Aug 2019 17:20:52: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:20:52: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:20:52: #1 total tags in treatment: 1716318 INFO @ Mon, 12 Aug 2019 17:20:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:20:52: #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 17:20:52: start X-correlation... INFO @ Mon, 12 Aug 2019 17:20:52: end of X-cor INFO @ Mon, 12 Aug 2019 17:20:52: #2 finished! INFO @ Mon, 12 Aug 2019 17:20:52: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 17:20:52: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 17:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.20_model.r INFO @ Mon, 12 Aug 2019 17:20:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:20:52: #1 tags after filtering in treatment: 1716318 INFO @ Mon, 12 Aug 2019 17:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:20:52: #1 finished! INFO @ Mon, 12 Aug 2019 17:20:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:20:52: #2 number of paired peaks: 3056 INFO @ Mon, 12 Aug 2019 17:20:52: start model_add_line... INFO @ Mon, 12 Aug 2019 17:20:52: start X-correlation... INFO @ Mon, 12 Aug 2019 17:20:52: end of X-cor INFO @ Mon, 12 Aug 2019 17:20:52: #2 finished! INFO @ Mon, 12 Aug 2019 17:20:52: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 17:20:52: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 17:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.05_model.r INFO @ Mon, 12 Aug 2019 17:20:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:20:53: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:20:53: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:20:53: #1 total tags in treatment: 1716318 INFO @ Mon, 12 Aug 2019 17:20:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:20:53: #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 17:20:53: #1 tags after filtering in treatment: 1716318 INFO @ Mon, 12 Aug 2019 17:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:20:53: #1 finished! INFO @ Mon, 12 Aug 2019 17:20:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:20:53: #2 number of paired peaks: 3056 INFO @ Mon, 12 Aug 2019 17:20:53: start model_add_line... INFO @ Mon, 12 Aug 2019 17:20:53: start X-correlation... INFO @ Mon, 12 Aug 2019 17:20:53: end of X-cor INFO @ Mon, 12 Aug 2019 17:20:53: #2 finished! INFO @ Mon, 12 Aug 2019 17:20:53: #2 predicted fragment length is 156 bps INFO @ Mon, 12 Aug 2019 17:20:53: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 12 Aug 2019 17:20:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.10_model.r INFO @ Mon, 12 Aug 2019 17:20:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:20:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:20:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:20:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:21:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:21:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:21:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.20_summits.bed INFO @ Mon, 12 Aug 2019 17:21:01: Done! INFO @ Mon, 12 Aug 2019 17:21:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:21:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.05_peaks.narrowPeak pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1142 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:21:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.05_summits.bed INFO @ Mon, 12 Aug 2019 17:21:01: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5450 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065657/SRX065657.10_summits.bed INFO @ Mon, 12 Aug 2019 17:21:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2893 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。