Job ID = 2640560 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,262,672 reads read : 16,525,344 reads written : 8,262,672 reads 0-length : 8,262,672 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: 00:00:00 Multiseed full-index search: 00:08:56 8262672 reads; of these: 8262672 (100.00%) were unpaired; of these: 862512 (10.44%) aligned 0 times 5663433 (68.54%) aligned exactly 1 time 1736727 (21.02%) aligned >1 times 89.56% overall alignment rate Time searching: 00:08:58 Overall time: 00:08:58 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] 535076 / 7400160 = 0.0723 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.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 17:49:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:49:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:49:38: 1000000 INFO @ Sat, 24 Aug 2019 17:49:44: 2000000 INFO @ Sat, 24 Aug 2019 17:49:51: 3000000 INFO @ Sat, 24 Aug 2019 17:49:57: 4000000 INFO @ Sat, 24 Aug 2019 17:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.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 17:50:00: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:50:00: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:50:03: 5000000 INFO @ Sat, 24 Aug 2019 17:50:09: 1000000 INFO @ Sat, 24 Aug 2019 17:50:10: 6000000 INFO @ Sat, 24 Aug 2019 17:50:15: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:50:15: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:50:15: #1 total tags in treatment: 6865084 INFO @ Sat, 24 Aug 2019 17:50:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:50:15: #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 17:50:16: #1 tags after filtering in treatment: 6864811 INFO @ Sat, 24 Aug 2019 17:50:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:50:16: #1 finished! INFO @ Sat, 24 Aug 2019 17:50:16: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:50:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:50:17: 2000000 INFO @ Sat, 24 Aug 2019 17:50:19: #2 number of paired peaks: 49356 INFO @ Sat, 24 Aug 2019 17:50:19: start model_add_line... INFO @ Sat, 24 Aug 2019 17:50:19: start X-correlation... INFO @ Sat, 24 Aug 2019 17:50:19: end of X-cor INFO @ Sat, 24 Aug 2019 17:50:19: #2 finished! INFO @ Sat, 24 Aug 2019 17:50:19: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 17:50:19: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 17:50:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.05_model.r INFO @ Sat, 24 Aug 2019 17:50:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:50:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:50:24: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.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 17:50:30: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:50:30: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:50:32: 4000000 INFO @ Sat, 24 Aug 2019 17:50:37: 1000000 INFO @ Sat, 24 Aug 2019 17:50:40: 5000000 INFO @ Sat, 24 Aug 2019 17:50:41: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:50:44: 2000000 INFO @ Sat, 24 Aug 2019 17:50:47: 6000000 INFO @ Sat, 24 Aug 2019 17:50:50: 3000000 INFO @ Sat, 24 Aug 2019 17:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.05_summits.bed INFO @ Sat, 24 Aug 2019 17:50:52: Done! pass1 - making usageList (73 chroms): 5 millis pass2 - checking and writing primary data (9990 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:50:54: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:50:54: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:50:54: #1 total tags in treatment: 6865084 INFO @ Sat, 24 Aug 2019 17:50:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:50:54: #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 17:50:54: #1 tags after filtering in treatment: 6864811 INFO @ Sat, 24 Aug 2019 17:50:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:50:54: #1 finished! INFO @ Sat, 24 Aug 2019 17:50:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:50:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:50:56: 4000000 INFO @ Sat, 24 Aug 2019 17:50:57: #2 number of paired peaks: 49356 INFO @ Sat, 24 Aug 2019 17:50:57: start model_add_line... INFO @ Sat, 24 Aug 2019 17:50:57: start X-correlation... INFO @ Sat, 24 Aug 2019 17:50:57: end of X-cor INFO @ Sat, 24 Aug 2019 17:50:57: #2 finished! INFO @ Sat, 24 Aug 2019 17:50:57: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 17:50:57: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 17:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.10_model.r INFO @ Sat, 24 Aug 2019 17:50:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:50:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:51:03: 5000000 INFO @ Sat, 24 Aug 2019 17:51:09: 6000000 INFO @ Sat, 24 Aug 2019 17:51:15: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:51:15: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:51:15: #1 total tags in treatment: 6865084 INFO @ Sat, 24 Aug 2019 17:51:15: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:51:15: #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 17:51:15: #1 tags after filtering in treatment: 6864811 INFO @ Sat, 24 Aug 2019 17:51:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:51:15: #1 finished! INFO @ Sat, 24 Aug 2019 17:51:15: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:51:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:51:18: #2 number of paired peaks: 49356 INFO @ Sat, 24 Aug 2019 17:51:18: start model_add_line... INFO @ Sat, 24 Aug 2019 17:51:18: start X-correlation... INFO @ Sat, 24 Aug 2019 17:51:18: end of X-cor INFO @ Sat, 24 Aug 2019 17:51:18: #2 finished! INFO @ Sat, 24 Aug 2019 17:51:18: #2 predicted fragment length is 164 bps INFO @ Sat, 24 Aug 2019 17:51:18: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 24 Aug 2019 17:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.20_model.r INFO @ Sat, 24 Aug 2019 17:51:18: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:51:19: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:51:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:51:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:51:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.10_summits.bed INFO @ Sat, 24 Aug 2019 17:51:30: Done! pass1 - making usageList (42 chroms): 3 millis pass2 - checking and writing primary data (3675 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:51:40: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:51:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375011/SRX5375011.20_summits.bed INFO @ Sat, 24 Aug 2019 17:51:51: Done! pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (547 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。