Job ID = 2589484 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,410,115 reads read : 6,410,115 reads written : 6,410,115 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR496322.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: 00:00:48 6410115 reads; of these: 6410115 (100.00%) were unpaired; of these: 3221452 (50.26%) aligned 0 times 2649937 (41.34%) aligned exactly 1 time 538726 (8.40%) aligned >1 times 49.74% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 183494 / 3188663 = 0.0575 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 17:47:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.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 17:47:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:47:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:47:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.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 17:47:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:47:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.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 17:47:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:47:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:47:56: 1000000 INFO @ Mon, 12 Aug 2019 17:47:57: 1000000 INFO @ Mon, 12 Aug 2019 17:47:58: 1000000 INFO @ Mon, 12 Aug 2019 17:48:05: 2000000 INFO @ Mon, 12 Aug 2019 17:48:05: 2000000 INFO @ Mon, 12 Aug 2019 17:48:07: 2000000 INFO @ Mon, 12 Aug 2019 17:48:14: 3000000 INFO @ Mon, 12 Aug 2019 17:48:14: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:48:14: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:48:14: #1 total tags in treatment: 3005169 INFO @ Mon, 12 Aug 2019 17:48:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:48:14: #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 17:48:14: #1 tags after filtering in treatment: 3005169 INFO @ Mon, 12 Aug 2019 17:48:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:48:14: #1 finished! INFO @ Mon, 12 Aug 2019 17:48:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:48:14: 3000000 INFO @ Mon, 12 Aug 2019 17:48:14: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:48:14: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:48:14: #1 total tags in treatment: 3005169 INFO @ Mon, 12 Aug 2019 17:48:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:48:14: #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 17:48:15: #1 tags after filtering in treatment: 3005169 INFO @ Mon, 12 Aug 2019 17:48:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:48:15: #1 finished! INFO @ Mon, 12 Aug 2019 17:48:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:48:15: #2 number of paired peaks: 1208 INFO @ Mon, 12 Aug 2019 17:48:15: start model_add_line... INFO @ Mon, 12 Aug 2019 17:48:15: start X-correlation... INFO @ Mon, 12 Aug 2019 17:48:15: end of X-cor INFO @ Mon, 12 Aug 2019 17:48:15: #2 finished! INFO @ Mon, 12 Aug 2019 17:48:15: #2 predicted fragment length is 108 bps INFO @ Mon, 12 Aug 2019 17:48:15: #2 alternative fragment length(s) may be 108 bps INFO @ Mon, 12 Aug 2019 17:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.10_model.r INFO @ Mon, 12 Aug 2019 17:48:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:48:15: #2 number of paired peaks: 1208 INFO @ Mon, 12 Aug 2019 17:48:15: start model_add_line... INFO @ Mon, 12 Aug 2019 17:48:15: start X-correlation... INFO @ Mon, 12 Aug 2019 17:48:15: end of X-cor INFO @ Mon, 12 Aug 2019 17:48:15: #2 finished! INFO @ Mon, 12 Aug 2019 17:48:15: #2 predicted fragment length is 108 bps INFO @ Mon, 12 Aug 2019 17:48:15: #2 alternative fragment length(s) may be 108 bps INFO @ Mon, 12 Aug 2019 17:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.05_model.r INFO @ Mon, 12 Aug 2019 17:48:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:48:16: 3000000 INFO @ Mon, 12 Aug 2019 17:48:16: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:48:16: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:48:16: #1 total tags in treatment: 3005169 INFO @ Mon, 12 Aug 2019 17:48:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:48:16: #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 17:48:16: #1 tags after filtering in treatment: 3005169 INFO @ Mon, 12 Aug 2019 17:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:48:16: #1 finished! INFO @ Mon, 12 Aug 2019 17:48:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:48:16: #2 number of paired peaks: 1208 INFO @ Mon, 12 Aug 2019 17:48:16: start model_add_line... INFO @ Mon, 12 Aug 2019 17:48:16: start X-correlation... INFO @ Mon, 12 Aug 2019 17:48:16: end of X-cor INFO @ Mon, 12 Aug 2019 17:48:16: #2 finished! INFO @ Mon, 12 Aug 2019 17:48:16: #2 predicted fragment length is 108 bps INFO @ Mon, 12 Aug 2019 17:48:16: #2 alternative fragment length(s) may be 108 bps INFO @ Mon, 12 Aug 2019 17:48:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.20_model.r INFO @ Mon, 12 Aug 2019 17:48:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:48:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:48:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:48:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:48:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:48:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:48:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.10_summits.bed INFO @ Mon, 12 Aug 2019 17:48:29: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2488 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:48:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:48:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.05_summits.bed INFO @ Mon, 12 Aug 2019 17:48:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3897 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX147645/SRX147645.20_summits.bed INFO @ Mon, 12 Aug 2019 17:48:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1186 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。