Job ID = 2640416 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,579,628 reads read : 29,579,628 reads written : 29,579,628 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR399332.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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:02:58 29579628 reads; of these: 29579628 (100.00%) were unpaired; of these: 23655249 (79.97%) aligned 0 times 4449577 (15.04%) aligned exactly 1 time 1474802 (4.99%) aligned >1 times 20.03% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 704821 / 5924379 = 0.1190 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 16:32:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:32:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:32:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:32:08: 1000000 INFO @ Sat, 24 Aug 2019 16:32:15: 2000000 INFO @ Sat, 24 Aug 2019 16:32:22: 3000000 INFO @ Sat, 24 Aug 2019 16:32:29: 4000000 INFO @ Sat, 24 Aug 2019 16:32:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:32:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:32:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:32:36: 5000000 INFO @ Sat, 24 Aug 2019 16:32:37: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 16:32:37: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 16:32:37: #1 total tags in treatment: 5219558 INFO @ Sat, 24 Aug 2019 16:32:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:32:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:32:37: #1 tags after filtering in treatment: 5219308 INFO @ Sat, 24 Aug 2019 16:32:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:32:37: #1 finished! INFO @ Sat, 24 Aug 2019 16:32:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:32:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:32:38: 1000000 INFO @ Sat, 24 Aug 2019 16:32:39: #2 number of paired peaks: 15781 INFO @ Sat, 24 Aug 2019 16:32:39: start model_add_line... INFO @ Sat, 24 Aug 2019 16:32:39: start X-correlation... INFO @ Sat, 24 Aug 2019 16:32:39: end of X-cor INFO @ Sat, 24 Aug 2019 16:32:39: #2 finished! INFO @ Sat, 24 Aug 2019 16:32:39: #2 predicted fragment length is 87 bps INFO @ Sat, 24 Aug 2019 16:32:39: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 24 Aug 2019 16:32:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.05_model.r INFO @ Sat, 24 Aug 2019 16:32:39: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:32:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:32:44: 2000000 INFO @ Sat, 24 Aug 2019 16:32:51: 3000000 INFO @ Sat, 24 Aug 2019 16:32:56: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:32:58: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 16:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:33:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:33:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:33:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.05_peaks.xls INFO @ Sat, 24 Aug 2019 16:33:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:33:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.05_summits.bed INFO @ Sat, 24 Aug 2019 16:33:04: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (1176 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:33:05: 5000000 INFO @ Sat, 24 Aug 2019 16:33:07: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 16:33:07: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 16:33:07: #1 total tags in treatment: 5219558 INFO @ Sat, 24 Aug 2019 16:33:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:33:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:33:07: 1000000 INFO @ Sat, 24 Aug 2019 16:33:07: #1 tags after filtering in treatment: 5219308 INFO @ Sat, 24 Aug 2019 16:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:33:07: #1 finished! INFO @ Sat, 24 Aug 2019 16:33:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:33:09: #2 number of paired peaks: 15781 INFO @ Sat, 24 Aug 2019 16:33:09: start model_add_line... INFO @ Sat, 24 Aug 2019 16:33:09: start X-correlation... INFO @ Sat, 24 Aug 2019 16:33:09: end of X-cor INFO @ Sat, 24 Aug 2019 16:33:09: #2 finished! INFO @ Sat, 24 Aug 2019 16:33:09: #2 predicted fragment length is 87 bps INFO @ Sat, 24 Aug 2019 16:33:09: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 24 Aug 2019 16:33:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.10_model.r INFO @ Sat, 24 Aug 2019 16:33:09: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:33:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:33:13: 2000000 INFO @ Sat, 24 Aug 2019 16:33:20: 3000000 INFO @ Sat, 24 Aug 2019 16:33:26: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:33:26: 4000000 INFO @ Sat, 24 Aug 2019 16:33:32: 5000000 INFO @ Sat, 24 Aug 2019 16:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.10_peaks.xls INFO @ Sat, 24 Aug 2019 16:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.10_summits.bed INFO @ Sat, 24 Aug 2019 16:33:34: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (323 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:33:34: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 16:33:34: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 16:33:34: #1 total tags in treatment: 5219558 INFO @ Sat, 24 Aug 2019 16:33:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:33:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:33:34: #1 tags after filtering in treatment: 5219308 INFO @ Sat, 24 Aug 2019 16:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:33:34: #1 finished! INFO @ Sat, 24 Aug 2019 16:33:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:33:36: #2 number of paired peaks: 15781 INFO @ Sat, 24 Aug 2019 16:33:36: start model_add_line... INFO @ Sat, 24 Aug 2019 16:33:36: start X-correlation... INFO @ Sat, 24 Aug 2019 16:33:36: end of X-cor INFO @ Sat, 24 Aug 2019 16:33:36: #2 finished! INFO @ Sat, 24 Aug 2019 16:33:36: #2 predicted fragment length is 87 bps INFO @ Sat, 24 Aug 2019 16:33:36: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 24 Aug 2019 16:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.20_model.r INFO @ Sat, 24 Aug 2019 16:33:36: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:33:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:33:53: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:34:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.20_peaks.xls INFO @ Sat, 24 Aug 2019 16:34:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:34:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116054/SRX116054.20_summits.bed INFO @ Sat, 24 Aug 2019 16:34:01: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。