Job ID = 2640707 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,526,489 reads read : 53,052,978 reads written : 26,526,489 reads 0-length : 26,526,489 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: 00:19:08 26526489 reads; of these: 26526489 (100.00%) were unpaired; of these: 713202 (2.69%) aligned 0 times 20319609 (76.60%) aligned exactly 1 time 5493678 (20.71%) aligned >1 times 97.31% overall alignment rate Time searching: 00:19:11 Overall time: 00:19:11 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] 4754022 / 25813287 = 0.1842 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:53:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.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 18:53:54: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:53:54: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:54:01: 1000000 INFO @ Sat, 24 Aug 2019 18:54:08: 2000000 INFO @ Sat, 24 Aug 2019 18:54:19: 3000000 INFO @ Sat, 24 Aug 2019 18:54:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.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 18:54:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:54:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:54:34: 4000000 INFO @ Sat, 24 Aug 2019 18:54:47: 1000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:54:53: 5000000 INFO @ Sat, 24 Aug 2019 18:54:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.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 18:54:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:54:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:55:02: 2000000 INFO @ Sat, 24 Aug 2019 18:55:07: 6000000 INFO @ Sat, 24 Aug 2019 18:55:08: 1000000 INFO @ Sat, 24 Aug 2019 18:55:13: 3000000 INFO @ Sat, 24 Aug 2019 18:55:14: 7000000 INFO @ Sat, 24 Aug 2019 18:55:16: 2000000 INFO @ Sat, 24 Aug 2019 18:55:21: 4000000 INFO @ Sat, 24 Aug 2019 18:55:21: 8000000 INFO @ Sat, 24 Aug 2019 18:55:23: 3000000 INFO @ Sat, 24 Aug 2019 18:55:28: 9000000 INFO @ Sat, 24 Aug 2019 18:55:28: 5000000 INFO @ Sat, 24 Aug 2019 18:55:31: 4000000 INFO @ Sat, 24 Aug 2019 18:55:35: 10000000 INFO @ Sat, 24 Aug 2019 18:55:36: 6000000 INFO @ Sat, 24 Aug 2019 18:55:39: 5000000 INFO @ Sat, 24 Aug 2019 18:55:42: 11000000 INFO @ Sat, 24 Aug 2019 18:55:46: 7000000 INFO @ Sat, 24 Aug 2019 18:55:47: 6000000 INFO @ Sat, 24 Aug 2019 18:55:49: 12000000 INFO @ Sat, 24 Aug 2019 18:55:55: 8000000 INFO @ Sat, 24 Aug 2019 18:55:55: 7000000 INFO @ Sat, 24 Aug 2019 18:55:56: 13000000 INFO @ Sat, 24 Aug 2019 18:56:03: 14000000 INFO @ Sat, 24 Aug 2019 18:56:04: 9000000 INFO @ Sat, 24 Aug 2019 18:56:04: 8000000 INFO @ Sat, 24 Aug 2019 18:56:10: 15000000 INFO @ Sat, 24 Aug 2019 18:56:12: 9000000 INFO @ Sat, 24 Aug 2019 18:56:13: 10000000 INFO @ Sat, 24 Aug 2019 18:56:17: 16000000 INFO @ Sat, 24 Aug 2019 18:56:20: 10000000 INFO @ Sat, 24 Aug 2019 18:56:21: 11000000 INFO @ Sat, 24 Aug 2019 18:56:23: 17000000 INFO @ Sat, 24 Aug 2019 18:56:29: 11000000 INFO @ Sat, 24 Aug 2019 18:56:29: 12000000 INFO @ Sat, 24 Aug 2019 18:56:31: 18000000 INFO @ Sat, 24 Aug 2019 18:56:37: 12000000 INFO @ Sat, 24 Aug 2019 18:56:37: 13000000 INFO @ Sat, 24 Aug 2019 18:56:38: 19000000 INFO @ Sat, 24 Aug 2019 18:56:45: 13000000 INFO @ Sat, 24 Aug 2019 18:56:45: 20000000 INFO @ Sat, 24 Aug 2019 18:56:46: 14000000 INFO @ Sat, 24 Aug 2019 18:56:52: 21000000 INFO @ Sat, 24 Aug 2019 18:56:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:56:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:56:53: #1 total tags in treatment: 21059265 INFO @ Sat, 24 Aug 2019 18:56:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:56:53: #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 18:56:53: 14000000 INFO @ Sat, 24 Aug 2019 18:56:54: #1 tags after filtering in treatment: 21059093 INFO @ Sat, 24 Aug 2019 18:56:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:56:54: #1 finished! INFO @ Sat, 24 Aug 2019 18:56:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:56:54: 15000000 INFO @ Sat, 24 Aug 2019 18:56:58: #2 number of paired peaks: 48512 INFO @ Sat, 24 Aug 2019 18:56:58: start model_add_line... INFO @ Sat, 24 Aug 2019 18:56:58: start X-correlation... INFO @ Sat, 24 Aug 2019 18:56:58: end of X-cor INFO @ Sat, 24 Aug 2019 18:56:58: #2 finished! INFO @ Sat, 24 Aug 2019 18:56:58: #2 predicted fragment length is 156 bps INFO @ Sat, 24 Aug 2019 18:56:58: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 24 Aug 2019 18:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.05_model.r INFO @ Sat, 24 Aug 2019 18:56:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:57:01: 15000000 INFO @ Sat, 24 Aug 2019 18:57:02: 16000000 INFO @ Sat, 24 Aug 2019 18:57:09: 16000000 INFO @ Sat, 24 Aug 2019 18:57:11: 17000000 INFO @ Sat, 24 Aug 2019 18:57:18: 17000000 INFO @ Sat, 24 Aug 2019 18:57:20: 18000000 INFO @ Sat, 24 Aug 2019 18:57:26: 18000000 INFO @ Sat, 24 Aug 2019 18:57:29: 19000000 INFO @ Sat, 24 Aug 2019 18:57:35: 19000000 INFO @ Sat, 24 Aug 2019 18:57:37: 20000000 INFO @ Sat, 24 Aug 2019 18:57:44: 20000000 INFO @ Sat, 24 Aug 2019 18:57:44: 21000000 INFO @ Sat, 24 Aug 2019 18:57:45: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:57:45: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:57:45: #1 total tags in treatment: 21059265 INFO @ Sat, 24 Aug 2019 18:57:45: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:57:45: #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 18:57:46: #1 tags after filtering in treatment: 21059093 INFO @ Sat, 24 Aug 2019 18:57:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:57:46: #1 finished! INFO @ Sat, 24 Aug 2019 18:57:46: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:57:50: #2 number of paired peaks: 48512 INFO @ Sat, 24 Aug 2019 18:57:50: start model_add_line... INFO @ Sat, 24 Aug 2019 18:57:50: start X-correlation... INFO @ Sat, 24 Aug 2019 18:57:50: end of X-cor INFO @ Sat, 24 Aug 2019 18:57:50: #2 finished! INFO @ Sat, 24 Aug 2019 18:57:50: #2 predicted fragment length is 156 bps INFO @ Sat, 24 Aug 2019 18:57:50: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 24 Aug 2019 18:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.10_model.r INFO @ Sat, 24 Aug 2019 18:57:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:57:53: 21000000 INFO @ Sat, 24 Aug 2019 18:57:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:57:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:57:53: #1 total tags in treatment: 21059265 INFO @ Sat, 24 Aug 2019 18:57:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:57:53: #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 18:57:54: #1 tags after filtering in treatment: 21059093 INFO @ Sat, 24 Aug 2019 18:57:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:57:54: #1 finished! INFO @ Sat, 24 Aug 2019 18:57:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:57:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:57:58: #2 number of paired peaks: 48512 INFO @ Sat, 24 Aug 2019 18:57:58: start model_add_line... INFO @ Sat, 24 Aug 2019 18:57:59: start X-correlation... INFO @ Sat, 24 Aug 2019 18:57:59: end of X-cor INFO @ Sat, 24 Aug 2019 18:57:59: #2 finished! INFO @ Sat, 24 Aug 2019 18:57:59: #2 predicted fragment length is 156 bps INFO @ Sat, 24 Aug 2019 18:57:59: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 24 Aug 2019 18:57:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.20_model.r INFO @ Sat, 24 Aug 2019 18:57:59: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:57:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:58:08: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.05_summits.bed INFO @ Sat, 24 Aug 2019 18:58:43: Done! pass1 - making usageList (103 chroms): 8 millis pass2 - checking and writing primary data (20301 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:58:59: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:59:07: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:59:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:59:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:59:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.10_summits.bed INFO @ Sat, 24 Aug 2019 18:59:33: Done! pass1 - making usageList (77 chroms): 8 millis pass2 - checking and writing primary data (14070 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:59:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:59:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:59:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375064/SRX5375064.20_summits.bed INFO @ Sat, 24 Aug 2019 18:59:42: Done! pass1 - making usageList (52 chroms): 5 millis pass2 - checking and writing primary data (8185 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。