Job ID = 2640696 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,891,519 reads read : 41,783,038 reads written : 20,891,519 reads 0-length : 20,891,519 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:16:32 20891519 reads; of these: 20891519 (100.00%) were unpaired; of these: 1165595 (5.58%) aligned 0 times 14726607 (70.49%) aligned exactly 1 time 4999317 (23.93%) aligned >1 times 94.42% overall alignment rate Time searching: 00:16:34 Overall time: 00:16:34 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] 1125799 / 19725924 = 0.0571 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.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 18:42:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:42:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:42:50: 1000000 INFO @ Sat, 24 Aug 2019 18:42:57: 2000000 INFO @ Sat, 24 Aug 2019 18:43:03: 3000000 INFO @ Sat, 24 Aug 2019 18:43:10: 4000000 INFO @ Sat, 24 Aug 2019 18:43:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.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 18:43:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:43:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:43:17: 5000000 INFO @ Sat, 24 Aug 2019 18:43:20: 1000000 INFO @ Sat, 24 Aug 2019 18:43:24: 6000000 INFO @ Sat, 24 Aug 2019 18:43:27: 2000000 INFO @ Sat, 24 Aug 2019 18:43:30: 7000000 INFO @ Sat, 24 Aug 2019 18:43:34: 3000000 INFO @ Sat, 24 Aug 2019 18:43:37: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:43:42: 4000000 INFO @ Sat, 24 Aug 2019 18:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.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 18:43:42: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:43:42: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:43:44: 9000000 INFO @ Sat, 24 Aug 2019 18:43:49: 5000000 INFO @ Sat, 24 Aug 2019 18:43:51: 10000000 INFO @ Sat, 24 Aug 2019 18:43:51: 1000000 INFO @ Sat, 24 Aug 2019 18:43:56: 6000000 INFO @ Sat, 24 Aug 2019 18:43:58: 11000000 INFO @ Sat, 24 Aug 2019 18:44:00: 2000000 INFO @ Sat, 24 Aug 2019 18:44:04: 7000000 INFO @ Sat, 24 Aug 2019 18:44:04: 12000000 INFO @ Sat, 24 Aug 2019 18:44:08: 3000000 INFO @ Sat, 24 Aug 2019 18:44:11: 8000000 INFO @ Sat, 24 Aug 2019 18:44:11: 13000000 INFO @ Sat, 24 Aug 2019 18:44:17: 4000000 INFO @ Sat, 24 Aug 2019 18:44:18: 14000000 INFO @ Sat, 24 Aug 2019 18:44:18: 9000000 INFO @ Sat, 24 Aug 2019 18:44:24: 15000000 INFO @ Sat, 24 Aug 2019 18:44:25: 10000000 INFO @ Sat, 24 Aug 2019 18:44:25: 5000000 INFO @ Sat, 24 Aug 2019 18:44:31: 16000000 INFO @ Sat, 24 Aug 2019 18:44:32: 11000000 INFO @ Sat, 24 Aug 2019 18:44:34: 6000000 INFO @ Sat, 24 Aug 2019 18:44:38: 17000000 INFO @ Sat, 24 Aug 2019 18:44:39: 12000000 INFO @ Sat, 24 Aug 2019 18:44:42: 7000000 INFO @ Sat, 24 Aug 2019 18:44:45: 18000000 INFO @ Sat, 24 Aug 2019 18:44:47: 13000000 INFO @ Sat, 24 Aug 2019 18:44:49: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:44:49: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:44:49: #1 total tags in treatment: 18600125 INFO @ Sat, 24 Aug 2019 18:44:49: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:44:49: #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 18:44:50: #1 tags after filtering in treatment: 18599932 INFO @ Sat, 24 Aug 2019 18:44:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:44:50: #1 finished! INFO @ Sat, 24 Aug 2019 18:44:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:44:50: 8000000 INFO @ Sat, 24 Aug 2019 18:44:53: #2 number of paired peaks: 21968 INFO @ Sat, 24 Aug 2019 18:44:53: start model_add_line... INFO @ Sat, 24 Aug 2019 18:44:53: start X-correlation... INFO @ Sat, 24 Aug 2019 18:44:53: end of X-cor INFO @ Sat, 24 Aug 2019 18:44:53: #2 finished! INFO @ Sat, 24 Aug 2019 18:44:53: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:44:53: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:44:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.05_model.r INFO @ Sat, 24 Aug 2019 18:44:53: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:44:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:44:54: 14000000 INFO @ Sat, 24 Aug 2019 18:44:58: 9000000 INFO @ Sat, 24 Aug 2019 18:45:01: 15000000 INFO @ Sat, 24 Aug 2019 18:45:07: 10000000 INFO @ Sat, 24 Aug 2019 18:45:08: 16000000 INFO @ Sat, 24 Aug 2019 18:45:15: 11000000 INFO @ Sat, 24 Aug 2019 18:45:15: 17000000 INFO @ Sat, 24 Aug 2019 18:45:22: 18000000 INFO @ Sat, 24 Aug 2019 18:45:23: 12000000 INFO @ Sat, 24 Aug 2019 18:45:27: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:45:27: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:45:27: #1 total tags in treatment: 18600125 INFO @ Sat, 24 Aug 2019 18:45:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:45:27: #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 18:45:27: #1 tags after filtering in treatment: 18599932 INFO @ Sat, 24 Aug 2019 18:45:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:45:27: #1 finished! INFO @ Sat, 24 Aug 2019 18:45:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:45:30: #2 number of paired peaks: 21968 INFO @ Sat, 24 Aug 2019 18:45:30: start model_add_line... INFO @ Sat, 24 Aug 2019 18:45:30: start X-correlation... INFO @ Sat, 24 Aug 2019 18:45:30: end of X-cor INFO @ Sat, 24 Aug 2019 18:45:30: #2 finished! INFO @ Sat, 24 Aug 2019 18:45:30: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:45:30: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:45:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.10_model.r INFO @ Sat, 24 Aug 2019 18:45:30: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:45:31: 13000000 INFO @ Sat, 24 Aug 2019 18:45:39: 14000000 INFO @ Sat, 24 Aug 2019 18:45:47: 15000000 INFO @ Sat, 24 Aug 2019 18:45:52: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:45:55: 16000000 INFO @ Sat, 24 Aug 2019 18:46:03: 17000000 INFO @ Sat, 24 Aug 2019 18:46:11: 18000000 INFO @ Sat, 24 Aug 2019 18:46:16: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:46:16: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:46:16: #1 total tags in treatment: 18600125 INFO @ Sat, 24 Aug 2019 18:46:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:46:16: #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 18:46:16: #1 tags after filtering in treatment: 18599932 INFO @ Sat, 24 Aug 2019 18:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:46:16: #1 finished! INFO @ Sat, 24 Aug 2019 18:46:16: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:46:19: #2 number of paired peaks: 21968 INFO @ Sat, 24 Aug 2019 18:46:19: start model_add_line... INFO @ Sat, 24 Aug 2019 18:46:19: start X-correlation... INFO @ Sat, 24 Aug 2019 18:46:19: end of X-cor INFO @ Sat, 24 Aug 2019 18:46:19: #2 finished! INFO @ Sat, 24 Aug 2019 18:46:19: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:46:19: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:46:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.20_model.r INFO @ Sat, 24 Aug 2019 18:46:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:46:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:46:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:46:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:46:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.05_summits.bed INFO @ Sat, 24 Aug 2019 18:46:24: Done! pass1 - making usageList (74 chroms): 5 millis pass2 - checking and writing primary data (11296 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:46:29: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:47:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:47:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:47:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.10_summits.bed INFO @ Sat, 24 Aug 2019 18:47:01: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (6629 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:47:18: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375053/SRX5375053.20_summits.bed INFO @ Sat, 24 Aug 2019 18:47:50: Done! pass1 - making usageList (39 chroms): 3 millis pass2 - checking and writing primary data (3448 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。