Job ID = 2640676 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,396,691 reads read : 14,793,382 reads written : 7,396,691 reads 0-length : 7,396,691 rm: cannot remove ‘[DSE]RR*’: 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: 00:06:00 7396691 reads; of these: 7396691 (100.00%) were unpaired; of these: 614866 (8.31%) aligned 0 times 4971229 (67.21%) aligned exactly 1 time 1810596 (24.48%) aligned >1 times 91.69% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 293136 / 6781825 = 0.0432 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.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 18:15:50: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:15:50: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:15:56: 1000000 INFO @ Sat, 24 Aug 2019 18:16:03: 2000000 INFO @ Sat, 24 Aug 2019 18:16:09: 3000000 INFO @ Sat, 24 Aug 2019 18:16:16: 4000000 INFO @ Sat, 24 Aug 2019 18:16:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.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 18:16:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:16:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:16:22: 5000000 INFO @ Sat, 24 Aug 2019 18:16:27: 1000000 INFO @ Sat, 24 Aug 2019 18:16:28: 6000000 INFO @ Sat, 24 Aug 2019 18:16:32: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:16:32: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:16:32: #1 total tags in treatment: 6488689 INFO @ Sat, 24 Aug 2019 18:16:32: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:16:32: #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 18:16:32: #1 tags after filtering in treatment: 6488448 INFO @ Sat, 24 Aug 2019 18:16:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:16:32: #1 finished! INFO @ Sat, 24 Aug 2019 18:16:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:16:34: #2 number of paired peaks: 14398 INFO @ Sat, 24 Aug 2019 18:16:34: start model_add_line... INFO @ Sat, 24 Aug 2019 18:16:34: start X-correlation... INFO @ Sat, 24 Aug 2019 18:16:34: end of X-cor INFO @ Sat, 24 Aug 2019 18:16:34: #2 finished! INFO @ Sat, 24 Aug 2019 18:16:34: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:16:34: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:16:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.05_model.r INFO @ Sat, 24 Aug 2019 18:16:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:16:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:16:34: 2000000 INFO @ Sat, 24 Aug 2019 18:16:41: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:16:48: 4000000 INFO @ Sat, 24 Aug 2019 18:16:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.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 18:16:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:16:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:16:54: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:16:55: 5000000 INFO @ Sat, 24 Aug 2019 18:16:58: 1000000 INFO @ Sat, 24 Aug 2019 18:17:02: 6000000 INFO @ Sat, 24 Aug 2019 18:17:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:17:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:17:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.05_summits.bed INFO @ Sat, 24 Aug 2019 18:17:05: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (2927 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:17:06: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:17:06: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:17:06: #1 total tags in treatment: 6488689 INFO @ Sat, 24 Aug 2019 18:17:06: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:17:06: #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 18:17:06: #1 tags after filtering in treatment: 6488448 INFO @ Sat, 24 Aug 2019 18:17:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:17:06: #1 finished! INFO @ Sat, 24 Aug 2019 18:17:06: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:17:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:17:07: 2000000 INFO @ Sat, 24 Aug 2019 18:17:07: #2 number of paired peaks: 14398 INFO @ Sat, 24 Aug 2019 18:17:07: start model_add_line... INFO @ Sat, 24 Aug 2019 18:17:07: start X-correlation... INFO @ Sat, 24 Aug 2019 18:17:07: end of X-cor INFO @ Sat, 24 Aug 2019 18:17:07: #2 finished! INFO @ Sat, 24 Aug 2019 18:17:07: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:17:07: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:17:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.10_model.r INFO @ Sat, 24 Aug 2019 18:17:07: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:17:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:17:15: 3000000 INFO @ Sat, 24 Aug 2019 18:17:23: 4000000 INFO @ Sat, 24 Aug 2019 18:17:28: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:17:31: 5000000 INFO @ Sat, 24 Aug 2019 18:17:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:17:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:17:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.10_summits.bed INFO @ Sat, 24 Aug 2019 18:17:39: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (1459 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:17:39: 6000000 INFO @ Sat, 24 Aug 2019 18:17:43: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:17:43: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:17:43: #1 total tags in treatment: 6488689 INFO @ Sat, 24 Aug 2019 18:17:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:17:43: #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 18:17:44: #1 tags after filtering in treatment: 6488448 INFO @ Sat, 24 Aug 2019 18:17:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:17:44: #1 finished! INFO @ Sat, 24 Aug 2019 18:17:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:17:45: #2 number of paired peaks: 14398 INFO @ Sat, 24 Aug 2019 18:17:45: start model_add_line... INFO @ Sat, 24 Aug 2019 18:17:45: start X-correlation... INFO @ Sat, 24 Aug 2019 18:17:45: end of X-cor INFO @ Sat, 24 Aug 2019 18:17:45: #2 finished! INFO @ Sat, 24 Aug 2019 18:17:45: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:17:45: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:17:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.20_model.r INFO @ Sat, 24 Aug 2019 18:17:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:17:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:18:06: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:18:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:18:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:18:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375043/SRX5375043.20_summits.bed INFO @ Sat, 24 Aug 2019 18:18:16: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (593 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。