Job ID = 2003708 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,992,557 reads read : 12,992,557 reads written : 12,992,557 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1267403.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:13 12992557 reads; of these: 12992557 (100.00%) were unpaired; of these: 947837 (7.30%) aligned 0 times 8540007 (65.73%) aligned exactly 1 time 3504713 (26.97%) aligned >1 times 92.70% overall alignment rate Time searching: 00:10:14 Overall time: 00:10:14 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10878448 / 12044720 = 0.9032 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 @ Fri, 05 Jul 2019 13:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.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 @ Fri, 05 Jul 2019 13:48:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:48:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:48:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.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 @ Fri, 05 Jul 2019 13:48:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:48:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.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 @ Fri, 05 Jul 2019 13:48:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:48:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:48:47: 1000000 INFO @ Fri, 05 Jul 2019 13:48:48: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:48:48: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:48:48: #1 total tags in treatment: 1166272 INFO @ Fri, 05 Jul 2019 13:48:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:48:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:48:48: #1 tags after filtering in treatment: 1165944 INFO @ Fri, 05 Jul 2019 13:48:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:48:48: #1 finished! INFO @ Fri, 05 Jul 2019 13:48:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:48:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:48:49: 1000000 INFO @ Fri, 05 Jul 2019 13:48:50: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:48:50: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:48:50: #1 total tags in treatment: 1166272 INFO @ Fri, 05 Jul 2019 13:48:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:48:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:48:50: #1 tags after filtering in treatment: 1165944 INFO @ Fri, 05 Jul 2019 13:48:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:48:50: #1 finished! INFO @ Fri, 05 Jul 2019 13:48:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:48:52: #2 number of paired peaks: 53453 INFO @ Fri, 05 Jul 2019 13:48:52: start model_add_line... INFO @ Fri, 05 Jul 2019 13:48:52: start X-correlation... INFO @ Fri, 05 Jul 2019 13:48:52: end of X-cor INFO @ Fri, 05 Jul 2019 13:48:52: #2 finished! INFO @ Fri, 05 Jul 2019 13:48:52: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 13:48:52: #2 alternative fragment length(s) may be 294 bps INFO @ Fri, 05 Jul 2019 13:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.05_model.r INFO @ Fri, 05 Jul 2019 13:48:52: 1000000 INFO @ Fri, 05 Jul 2019 13:48:54: #2 number of paired peaks: 53453 INFO @ Fri, 05 Jul 2019 13:48:54: start model_add_line... INFO @ Fri, 05 Jul 2019 13:48:54: start X-correlation... INFO @ Fri, 05 Jul 2019 13:48:54: end of X-cor INFO @ Fri, 05 Jul 2019 13:48:54: #2 finished! INFO @ Fri, 05 Jul 2019 13:48:54: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 13:48:54: #2 alternative fragment length(s) may be 294 bps INFO @ Fri, 05 Jul 2019 13:48:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.10_model.r INFO @ Fri, 05 Jul 2019 13:48:54: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:48:54: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:48:54: #1 total tags in treatment: 1166272 INFO @ Fri, 05 Jul 2019 13:48:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:48:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:48:54: #1 tags after filtering in treatment: 1165944 INFO @ Fri, 05 Jul 2019 13:48:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:48:54: #1 finished! INFO @ Fri, 05 Jul 2019 13:48:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:48:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:48:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:48:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:48:58: #2 number of paired peaks: 53453 INFO @ Fri, 05 Jul 2019 13:48:59: start model_add_line... INFO @ Fri, 05 Jul 2019 13:48:59: start X-correlation... INFO @ Fri, 05 Jul 2019 13:48:59: end of X-cor INFO @ Fri, 05 Jul 2019 13:48:59: #2 finished! INFO @ Fri, 05 Jul 2019 13:48:59: #2 predicted fragment length is 294 bps INFO @ Fri, 05 Jul 2019 13:48:59: #2 alternative fragment length(s) may be 294 bps INFO @ Fri, 05 Jul 2019 13:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.20_model.r INFO @ Fri, 05 Jul 2019 13:48:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:49:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:49:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.05_summits.bed INFO @ Fri, 05 Jul 2019 13:49:02: Done! INFO @ Fri, 05 Jul 2019 13:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.10_summits.bed INFO @ Fri, 05 Jul 2019 13:49:02: Done! pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (225 records, 4 fields): 3 millis pass1 - making usageList (23 chroms): 2 millis pass2 - checking and writing primary data (129 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 13:49:03: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:49:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX530449/SRX530449.20_summits.bed INFO @ Fri, 05 Jul 2019 13:49:05: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling