Job ID = 2590270 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,291,912 reads read : 6,291,912 reads written : 6,291,912 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR504792.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: 00:01:47 6291912 reads; of these: 6291912 (100.00%) were unpaired; of these: 284886 (4.53%) aligned 0 times 4506358 (71.62%) aligned exactly 1 time 1500668 (23.85%) aligned >1 times 95.47% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 501191 / 6007026 = 0.0834 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 20:23:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.bam'] # control file = None # effective genome size = 1.20e+08 # 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 20:23:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:23:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:23:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.bam'] # control file = None # effective genome size = 1.20e+08 # 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 20:23:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:23:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:23:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.bam'] # control file = None # effective genome size = 1.20e+08 # 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 20:23:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:23:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:23:19: 1000000 INFO @ Mon, 12 Aug 2019 20:23:20: 1000000 INFO @ Mon, 12 Aug 2019 20:23:21: 1000000 INFO @ Mon, 12 Aug 2019 20:23:26: 2000000 INFO @ Mon, 12 Aug 2019 20:23:27: 2000000 INFO @ Mon, 12 Aug 2019 20:23:28: 2000000 INFO @ Mon, 12 Aug 2019 20:23:34: 3000000 INFO @ Mon, 12 Aug 2019 20:23:35: 3000000 INFO @ Mon, 12 Aug 2019 20:23:36: 3000000 INFO @ Mon, 12 Aug 2019 20:23:41: 4000000 INFO @ Mon, 12 Aug 2019 20:23:42: 4000000 INFO @ Mon, 12 Aug 2019 20:23:43: 4000000 INFO @ Mon, 12 Aug 2019 20:23:48: 5000000 INFO @ Mon, 12 Aug 2019 20:23:49: 5000000 INFO @ Mon, 12 Aug 2019 20:23:50: 5000000 INFO @ Mon, 12 Aug 2019 20:23:52: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:23:52: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:23:52: #1 total tags in treatment: 5505835 INFO @ Mon, 12 Aug 2019 20:23:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:23:52: #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 20:23:52: #1 tags after filtering in treatment: 5505835 INFO @ Mon, 12 Aug 2019 20:23:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:23:52: #1 finished! INFO @ Mon, 12 Aug 2019 20:23:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:23:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:23:53: #2 number of paired peaks: 1238 INFO @ Mon, 12 Aug 2019 20:23:53: start model_add_line... INFO @ Mon, 12 Aug 2019 20:23:53: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:23:53: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:23:53: #1 total tags in treatment: 5505835 INFO @ Mon, 12 Aug 2019 20:23:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:23:53: #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 20:23:53: start X-correlation... INFO @ Mon, 12 Aug 2019 20:23:53: end of X-cor INFO @ Mon, 12 Aug 2019 20:23:53: #2 finished! INFO @ Mon, 12 Aug 2019 20:23:53: #2 predicted fragment length is 101 bps INFO @ Mon, 12 Aug 2019 20:23:53: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 12 Aug 2019 20:23:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.05_model.r INFO @ Mon, 12 Aug 2019 20:23:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:23:53: #1 tags after filtering in treatment: 5505835 INFO @ Mon, 12 Aug 2019 20:23:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:23:53: #1 finished! INFO @ Mon, 12 Aug 2019 20:23:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:23:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:23:53: #2 number of paired peaks: 1238 INFO @ Mon, 12 Aug 2019 20:23:53: start model_add_line... INFO @ Mon, 12 Aug 2019 20:23:54: start X-correlation... INFO @ Mon, 12 Aug 2019 20:23:54: end of X-cor INFO @ Mon, 12 Aug 2019 20:23:54: #2 finished! INFO @ Mon, 12 Aug 2019 20:23:54: #2 predicted fragment length is 101 bps INFO @ Mon, 12 Aug 2019 20:23:54: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 12 Aug 2019 20:23:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.10_model.r INFO @ Mon, 12 Aug 2019 20:23:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:23:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:23:54: #1 tag size is determined as 30 bps INFO @ Mon, 12 Aug 2019 20:23:54: #1 tag size = 30 INFO @ Mon, 12 Aug 2019 20:23:54: #1 total tags in treatment: 5505835 INFO @ Mon, 12 Aug 2019 20:23:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:23:54: #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 20:23:54: #1 tags after filtering in treatment: 5505835 INFO @ Mon, 12 Aug 2019 20:23:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:23:54: #1 finished! INFO @ Mon, 12 Aug 2019 20:23:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:23:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:23:54: #2 number of paired peaks: 1238 INFO @ Mon, 12 Aug 2019 20:23:54: start model_add_line... INFO @ Mon, 12 Aug 2019 20:23:54: start X-correlation... INFO @ Mon, 12 Aug 2019 20:23:54: end of X-cor INFO @ Mon, 12 Aug 2019 20:23:54: #2 finished! INFO @ Mon, 12 Aug 2019 20:23:54: #2 predicted fragment length is 101 bps INFO @ Mon, 12 Aug 2019 20:23:54: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 12 Aug 2019 20:23:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.20_model.r INFO @ Mon, 12 Aug 2019 20:23:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:23:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:24:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:24:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:24:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:24:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:24:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:24:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.05_summits.bed INFO @ Mon, 12 Aug 2019 20:24:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6722 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:24:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:24:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:24:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.10_summits.bed INFO @ Mon, 12 Aug 2019 20:24:18: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3543 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:24:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:24:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:24:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151958/SRX151958.20_summits.bed INFO @ Mon, 12 Aug 2019 20:24:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1188 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。