Job ID = 2640715 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,291,353 reads read : 52,582,706 reads written : 26,291,353 reads 0-length : 26,291,353 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:47 26291353 reads; of these: 26291353 (100.00%) were unpaired; of these: 587942 (2.24%) aligned 0 times 20569878 (78.24%) aligned exactly 1 time 5133533 (19.53%) aligned >1 times 97.76% overall alignment rate Time searching: 00:19:50 Overall time: 00:19:50 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] 5032186 / 25703411 = 0.1958 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:58:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.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 18:58:47: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:58:47: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:58:56: 1000000 INFO @ Sat, 24 Aug 2019 18:59:05: 2000000 INFO @ Sat, 24 Aug 2019 18:59:13: 3000000 INFO @ Sat, 24 Aug 2019 18:59:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.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 18:59:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:59:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:59:21: 4000000 INFO @ Sat, 24 Aug 2019 18:59:26: 1000000 INFO @ Sat, 24 Aug 2019 18:59:29: 5000000 INFO @ Sat, 24 Aug 2019 18:59:37: 2000000 INFO @ Sat, 24 Aug 2019 18:59:37: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:59:45: 7000000 INFO @ Sat, 24 Aug 2019 18:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.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 18:59:45: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:59:45: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:59:47: 3000000 INFO @ Sat, 24 Aug 2019 18:59:53: 8000000 INFO @ Sat, 24 Aug 2019 18:59:56: 1000000 INFO @ Sat, 24 Aug 2019 18:59:58: 4000000 INFO @ Sat, 24 Aug 2019 19:00:01: 9000000 INFO @ Sat, 24 Aug 2019 19:00:06: 2000000 INFO @ Sat, 24 Aug 2019 19:00:08: 5000000 INFO @ Sat, 24 Aug 2019 19:00:10: 10000000 INFO @ Sat, 24 Aug 2019 19:00:15: 3000000 INFO @ Sat, 24 Aug 2019 19:00:18: 6000000 INFO @ Sat, 24 Aug 2019 19:00:18: 11000000 INFO @ Sat, 24 Aug 2019 19:00:25: 4000000 INFO @ Sat, 24 Aug 2019 19:00:26: 12000000 INFO @ Sat, 24 Aug 2019 19:00:28: 7000000 INFO @ Sat, 24 Aug 2019 19:00:34: 13000000 INFO @ Sat, 24 Aug 2019 19:00:35: 5000000 INFO @ Sat, 24 Aug 2019 19:00:39: 8000000 INFO @ Sat, 24 Aug 2019 19:00:43: 14000000 INFO @ Sat, 24 Aug 2019 19:00:45: 6000000 INFO @ Sat, 24 Aug 2019 19:00:50: 9000000 INFO @ Sat, 24 Aug 2019 19:00:51: 15000000 INFO @ Sat, 24 Aug 2019 19:00:55: 7000000 INFO @ Sat, 24 Aug 2019 19:00:59: 16000000 INFO @ Sat, 24 Aug 2019 19:01:00: 10000000 INFO @ Sat, 24 Aug 2019 19:01:05: 8000000 INFO @ Sat, 24 Aug 2019 19:01:07: 17000000 INFO @ Sat, 24 Aug 2019 19:01:10: 11000000 INFO @ Sat, 24 Aug 2019 19:01:15: 9000000 INFO @ Sat, 24 Aug 2019 19:01:16: 18000000 INFO @ Sat, 24 Aug 2019 19:01:21: 12000000 INFO @ Sat, 24 Aug 2019 19:01:25: 19000000 INFO @ Sat, 24 Aug 2019 19:01:25: 10000000 INFO @ Sat, 24 Aug 2019 19:01:31: 13000000 INFO @ Sat, 24 Aug 2019 19:01:34: 20000000 INFO @ Sat, 24 Aug 2019 19:01:35: 11000000 INFO @ Sat, 24 Aug 2019 19:01:40: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:01:40: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:01:40: #1 total tags in treatment: 20671225 INFO @ Sat, 24 Aug 2019 19:01:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:01:40: #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 19:01:41: #1 tags after filtering in treatment: 20671037 INFO @ Sat, 24 Aug 2019 19:01:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:01:41: #1 finished! INFO @ Sat, 24 Aug 2019 19:01:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:01:42: 14000000 INFO @ Sat, 24 Aug 2019 19:01:45: 12000000 INFO @ Sat, 24 Aug 2019 19:01:46: #2 number of paired peaks: 53630 INFO @ Sat, 24 Aug 2019 19:01:46: start model_add_line... INFO @ Sat, 24 Aug 2019 19:01:46: start X-correlation... INFO @ Sat, 24 Aug 2019 19:01:46: end of X-cor INFO @ Sat, 24 Aug 2019 19:01:46: #2 finished! INFO @ Sat, 24 Aug 2019 19:01:46: #2 predicted fragment length is 156 bps INFO @ Sat, 24 Aug 2019 19:01:46: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 24 Aug 2019 19:01:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.05_model.r INFO @ Sat, 24 Aug 2019 19:01:46: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:01:52: 15000000 INFO @ Sat, 24 Aug 2019 19:01:55: 13000000 INFO @ Sat, 24 Aug 2019 19:02:03: 16000000 INFO @ Sat, 24 Aug 2019 19:02:05: 14000000 INFO @ Sat, 24 Aug 2019 19:02:13: 17000000 INFO @ Sat, 24 Aug 2019 19:02:15: 15000000 INFO @ Sat, 24 Aug 2019 19:02:23: 18000000 INFO @ Sat, 24 Aug 2019 19:02:25: 16000000 INFO @ Sat, 24 Aug 2019 19:02:34: 19000000 INFO @ Sat, 24 Aug 2019 19:02:35: 17000000 INFO @ Sat, 24 Aug 2019 19:02:44: 20000000 INFO @ Sat, 24 Aug 2019 19:02:45: 18000000 INFO @ Sat, 24 Aug 2019 19:02:51: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:02:51: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:02:51: #1 total tags in treatment: 20671225 INFO @ Sat, 24 Aug 2019 19:02:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:02:51: #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 19:02:51: #1 tags after filtering in treatment: 20671037 INFO @ Sat, 24 Aug 2019 19:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:02:51: #1 finished! INFO @ Sat, 24 Aug 2019 19:02:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:02:54: 19000000 INFO @ Sat, 24 Aug 2019 19:02:56: #2 number of paired peaks: 53630 INFO @ Sat, 24 Aug 2019 19:02:56: start model_add_line... INFO @ Sat, 24 Aug 2019 19:02:57: start X-correlation... INFO @ Sat, 24 Aug 2019 19:02:57: end of X-cor INFO @ Sat, 24 Aug 2019 19:02:57: #2 finished! INFO @ Sat, 24 Aug 2019 19:02:57: #2 predicted fragment length is 156 bps INFO @ Sat, 24 Aug 2019 19:02:57: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 24 Aug 2019 19:02:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.10_model.r INFO @ Sat, 24 Aug 2019 19:02:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:02:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:03:02: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:03:04: 20000000 INFO @ Sat, 24 Aug 2019 19:03:10: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:03:10: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:03:10: #1 total tags in treatment: 20671225 INFO @ Sat, 24 Aug 2019 19:03:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:03:10: #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 19:03:11: #1 tags after filtering in treatment: 20671037 INFO @ Sat, 24 Aug 2019 19:03:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:03:11: #1 finished! INFO @ Sat, 24 Aug 2019 19:03:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:03:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:03:16: #2 number of paired peaks: 53630 INFO @ Sat, 24 Aug 2019 19:03:16: start model_add_line... INFO @ Sat, 24 Aug 2019 19:03:16: start X-correlation... INFO @ Sat, 24 Aug 2019 19:03:16: end of X-cor INFO @ Sat, 24 Aug 2019 19:03:16: #2 finished! INFO @ Sat, 24 Aug 2019 19:03:16: #2 predicted fragment length is 156 bps INFO @ Sat, 24 Aug 2019 19:03:16: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 24 Aug 2019 19:03:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.20_model.r INFO @ Sat, 24 Aug 2019 19:03:16: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:03:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.05_summits.bed INFO @ Sat, 24 Aug 2019 19:03:43: Done! pass1 - making usageList (108 chroms): 9 millis pass2 - checking and writing primary data (22576 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:04:09: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:04:26: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:04:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:04:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.10_summits.bed INFO @ Sat, 24 Aug 2019 19:04:50: Done! pass1 - making usageList (85 chroms): 7 millis pass2 - checking and writing primary data (17261 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:05:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:05:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:05:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375068/SRX5375068.20_summits.bed INFO @ Sat, 24 Aug 2019 19:05:03: Done! pass1 - making usageList (68 chroms): 4 millis pass2 - checking and writing primary data (11773 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。