Job ID = 2640519 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,142,408 reads read : 44,284,816 reads written : 22,142,408 reads 0-length : 22,142,408 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: 00:17:36 22142408 reads; of these: 22142408 (100.00%) were unpaired; of these: 887608 (4.01%) aligned 0 times 15781488 (71.27%) aligned exactly 1 time 5473312 (24.72%) aligned >1 times 95.99% overall alignment rate Time searching: 00:17:39 Overall time: 00:17:39 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 12 files... [bam_rmdupse_core] 4291821 / 21254800 = 0.2019 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:52:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.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 17:52:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:52:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:52:45: 1000000 INFO @ Sat, 24 Aug 2019 17:52:52: 2000000 INFO @ Sat, 24 Aug 2019 17:52:59: 3000000 INFO @ Sat, 24 Aug 2019 17:53:05: 4000000 INFO @ Sat, 24 Aug 2019 17:53:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.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 17:53:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:53:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:53:12: 5000000 INFO @ Sat, 24 Aug 2019 17:53:15: 1000000 INFO @ Sat, 24 Aug 2019 17:53:20: 6000000 INFO @ Sat, 24 Aug 2019 17:53:22: 2000000 INFO @ Sat, 24 Aug 2019 17:53:27: 7000000 INFO @ Sat, 24 Aug 2019 17:53:30: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:53:34: 8000000 INFO @ Sat, 24 Aug 2019 17:53:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.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 17:53:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:53:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:53:37: 4000000 INFO @ Sat, 24 Aug 2019 17:53:42: 9000000 INFO @ Sat, 24 Aug 2019 17:53:45: 5000000 INFO @ Sat, 24 Aug 2019 17:53:45: 1000000 INFO @ Sat, 24 Aug 2019 17:53:49: 10000000 INFO @ Sat, 24 Aug 2019 17:53:52: 6000000 INFO @ Sat, 24 Aug 2019 17:53:54: 2000000 INFO @ Sat, 24 Aug 2019 17:53:56: 11000000 INFO @ Sat, 24 Aug 2019 17:54:00: 7000000 INFO @ Sat, 24 Aug 2019 17:54:02: 3000000 INFO @ Sat, 24 Aug 2019 17:54:04: 12000000 INFO @ Sat, 24 Aug 2019 17:54:08: 8000000 INFO @ Sat, 24 Aug 2019 17:54:10: 4000000 INFO @ Sat, 24 Aug 2019 17:54:12: 13000000 INFO @ Sat, 24 Aug 2019 17:54:15: 9000000 INFO @ Sat, 24 Aug 2019 17:54:19: 5000000 INFO @ Sat, 24 Aug 2019 17:54:19: 14000000 INFO @ Sat, 24 Aug 2019 17:54:23: 10000000 INFO @ Sat, 24 Aug 2019 17:54:27: 15000000 INFO @ Sat, 24 Aug 2019 17:54:27: 6000000 INFO @ Sat, 24 Aug 2019 17:54:30: 11000000 INFO @ Sat, 24 Aug 2019 17:54:34: 16000000 INFO @ Sat, 24 Aug 2019 17:54:36: 7000000 INFO @ Sat, 24 Aug 2019 17:54:38: 12000000 INFO @ Sat, 24 Aug 2019 17:54:42: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:54:42: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:54:42: #1 total tags in treatment: 16962979 INFO @ Sat, 24 Aug 2019 17:54:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:54:42: #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 17:54:42: #1 tags after filtering in treatment: 16962841 INFO @ Sat, 24 Aug 2019 17:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:54:42: #1 finished! INFO @ Sat, 24 Aug 2019 17:54:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:54:44: 8000000 INFO @ Sat, 24 Aug 2019 17:54:45: #2 number of paired peaks: 13726 INFO @ Sat, 24 Aug 2019 17:54:45: start model_add_line... INFO @ Sat, 24 Aug 2019 17:54:45: start X-correlation... INFO @ Sat, 24 Aug 2019 17:54:45: end of X-cor INFO @ Sat, 24 Aug 2019 17:54:45: #2 finished! INFO @ Sat, 24 Aug 2019 17:54:45: #2 predicted fragment length is 135 bps INFO @ Sat, 24 Aug 2019 17:54:45: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 24 Aug 2019 17:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.05_model.r INFO @ Sat, 24 Aug 2019 17:54:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:54:46: 13000000 INFO @ Sat, 24 Aug 2019 17:54:52: 9000000 INFO @ Sat, 24 Aug 2019 17:54:54: 14000000 INFO @ Sat, 24 Aug 2019 17:55:01: 10000000 INFO @ Sat, 24 Aug 2019 17:55:02: 15000000 INFO @ Sat, 24 Aug 2019 17:55:09: 11000000 INFO @ Sat, 24 Aug 2019 17:55:10: 16000000 INFO @ Sat, 24 Aug 2019 17:55:17: 12000000 INFO @ Sat, 24 Aug 2019 17:55:18: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:55:18: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:55:18: #1 total tags in treatment: 16962979 INFO @ Sat, 24 Aug 2019 17:55:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:55:18: #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 17:55:19: #1 tags after filtering in treatment: 16962841 INFO @ Sat, 24 Aug 2019 17:55:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:55:19: #1 finished! INFO @ Sat, 24 Aug 2019 17:55:19: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:55:21: #2 number of paired peaks: 13726 INFO @ Sat, 24 Aug 2019 17:55:21: start model_add_line... INFO @ Sat, 24 Aug 2019 17:55:21: start X-correlation... INFO @ Sat, 24 Aug 2019 17:55:21: end of X-cor INFO @ Sat, 24 Aug 2019 17:55:21: #2 finished! INFO @ Sat, 24 Aug 2019 17:55:21: #2 predicted fragment length is 135 bps INFO @ Sat, 24 Aug 2019 17:55:21: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 24 Aug 2019 17:55:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.10_model.r INFO @ Sat, 24 Aug 2019 17:55:21: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:55:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:55:24: 13000000 INFO @ Sat, 24 Aug 2019 17:55:33: 14000000 INFO @ Sat, 24 Aug 2019 17:55:41: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:55:41: 15000000 INFO @ Sat, 24 Aug 2019 17:55:50: 16000000 INFO @ Sat, 24 Aug 2019 17:55:59: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:55:59: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:55:59: #1 total tags in treatment: 16962979 INFO @ Sat, 24 Aug 2019 17:55:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:55:59: #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 17:55:59: #1 tags after filtering in treatment: 16962841 INFO @ Sat, 24 Aug 2019 17:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:55:59: #1 finished! INFO @ Sat, 24 Aug 2019 17:55:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:56:02: #2 number of paired peaks: 13726 INFO @ Sat, 24 Aug 2019 17:56:02: start model_add_line... INFO @ Sat, 24 Aug 2019 17:56:02: start X-correlation... INFO @ Sat, 24 Aug 2019 17:56:02: end of X-cor INFO @ Sat, 24 Aug 2019 17:56:02: #2 finished! INFO @ Sat, 24 Aug 2019 17:56:02: #2 predicted fragment length is 135 bps INFO @ Sat, 24 Aug 2019 17:56:02: #2 alternative fragment length(s) may be 135 bps INFO @ Sat, 24 Aug 2019 17:56:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.20_model.r INFO @ Sat, 24 Aug 2019 17:56:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:56:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:56:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:56:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:56:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.05_summits.bed INFO @ Sat, 24 Aug 2019 17:56:10: Done! pass1 - making usageList (62 chroms): 4 millis pass2 - checking and writing primary data (6090 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:56:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:56:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:56:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:56:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.10_summits.bed INFO @ Sat, 24 Aug 2019 17:56:46: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (3629 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:56:58: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:57:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:57:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:57:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375000/SRX5375000.20_summits.bed INFO @ Sat, 24 Aug 2019 17:57:26: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (1921 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。