Job ID = 2640522 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,939,502 reads read : 37,879,004 reads written : 18,939,502 reads 0-length : 18,939,502 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: 00:15:08 18939502 reads; of these: 18939502 (100.00%) were unpaired; of these: 572551 (3.02%) aligned 0 times 13421280 (70.86%) aligned exactly 1 time 4945671 (26.11%) aligned >1 times 96.98% overall alignment rate Time searching: 00:15:11 Overall time: 00:15:11 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 8 files... [bam_rmdupse_core] 2808147 / 18366951 = 0.1529 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.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 17:50:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:50:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:51:06: 1000000 INFO @ Sat, 24 Aug 2019 17:51:15: 2000000 INFO @ Sat, 24 Aug 2019 17:51:23: 3000000 INFO @ Sat, 24 Aug 2019 17:51:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.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 17:51:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:51:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:51:31: 4000000 INFO @ Sat, 24 Aug 2019 17:51:36: 1000000 INFO @ Sat, 24 Aug 2019 17:51:40: 5000000 INFO @ Sat, 24 Aug 2019 17:51:45: 2000000 INFO @ Sat, 24 Aug 2019 17:51:47: 6000000 INFO @ Sat, 24 Aug 2019 17:51:54: 3000000 INFO @ Sat, 24 Aug 2019 17:51:54: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:51:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.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 17:51:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:51:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:52:01: 8000000 INFO @ Sat, 24 Aug 2019 17:52:02: 4000000 INFO @ Sat, 24 Aug 2019 17:52:06: 1000000 INFO @ Sat, 24 Aug 2019 17:52:08: 9000000 INFO @ Sat, 24 Aug 2019 17:52:11: 5000000 INFO @ Sat, 24 Aug 2019 17:52:14: 2000000 INFO @ Sat, 24 Aug 2019 17:52:15: 10000000 INFO @ Sat, 24 Aug 2019 17:52:20: 6000000 INFO @ Sat, 24 Aug 2019 17:52:22: 11000000 INFO @ Sat, 24 Aug 2019 17:52:22: 3000000 INFO @ Sat, 24 Aug 2019 17:52:28: 7000000 INFO @ Sat, 24 Aug 2019 17:52:29: 12000000 INFO @ Sat, 24 Aug 2019 17:52:30: 4000000 INFO @ Sat, 24 Aug 2019 17:52:36: 13000000 INFO @ Sat, 24 Aug 2019 17:52:37: 8000000 INFO @ Sat, 24 Aug 2019 17:52:38: 5000000 INFO @ Sat, 24 Aug 2019 17:52:43: 14000000 INFO @ Sat, 24 Aug 2019 17:52:45: 9000000 INFO @ Sat, 24 Aug 2019 17:52:46: 6000000 INFO @ Sat, 24 Aug 2019 17:52:50: 15000000 INFO @ Sat, 24 Aug 2019 17:52:54: 10000000 INFO @ Sat, 24 Aug 2019 17:52:54: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:52:54: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:52:54: #1 total tags in treatment: 15558804 INFO @ Sat, 24 Aug 2019 17:52:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:52:54: #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 17:52:54: 7000000 INFO @ Sat, 24 Aug 2019 17:52:54: #1 tags after filtering in treatment: 15558626 INFO @ Sat, 24 Aug 2019 17:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:52:54: #1 finished! INFO @ Sat, 24 Aug 2019 17:52:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:52:56: #2 number of paired peaks: 7866 INFO @ Sat, 24 Aug 2019 17:52:56: start model_add_line... INFO @ Sat, 24 Aug 2019 17:52:57: start X-correlation... INFO @ Sat, 24 Aug 2019 17:52:57: end of X-cor INFO @ Sat, 24 Aug 2019 17:52:57: #2 finished! INFO @ Sat, 24 Aug 2019 17:52:57: #2 predicted fragment length is 109 bps INFO @ Sat, 24 Aug 2019 17:52:57: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 24 Aug 2019 17:52:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.05_model.r INFO @ Sat, 24 Aug 2019 17:52:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:53:02: 8000000 INFO @ Sat, 24 Aug 2019 17:53:03: 11000000 INFO @ Sat, 24 Aug 2019 17:53:10: 9000000 INFO @ Sat, 24 Aug 2019 17:53:12: 12000000 INFO @ Sat, 24 Aug 2019 17:53:18: 10000000 INFO @ Sat, 24 Aug 2019 17:53:20: 13000000 INFO @ Sat, 24 Aug 2019 17:53:27: 11000000 INFO @ Sat, 24 Aug 2019 17:53:29: 14000000 INFO @ Sat, 24 Aug 2019 17:53:35: 12000000 INFO @ Sat, 24 Aug 2019 17:53:37: 15000000 INFO @ Sat, 24 Aug 2019 17:53:42: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:53:42: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:53:42: #1 total tags in treatment: 15558804 INFO @ Sat, 24 Aug 2019 17:53:42: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:53:42: #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 17:53:43: #1 tags after filtering in treatment: 15558626 INFO @ Sat, 24 Aug 2019 17:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:53:43: #1 finished! INFO @ Sat, 24 Aug 2019 17:53:43: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:53:43: 13000000 INFO @ Sat, 24 Aug 2019 17:53:45: #2 number of paired peaks: 7866 INFO @ Sat, 24 Aug 2019 17:53:45: start model_add_line... INFO @ Sat, 24 Aug 2019 17:53:45: start X-correlation... INFO @ Sat, 24 Aug 2019 17:53:45: end of X-cor INFO @ Sat, 24 Aug 2019 17:53:45: #2 finished! INFO @ Sat, 24 Aug 2019 17:53:45: #2 predicted fragment length is 109 bps INFO @ Sat, 24 Aug 2019 17:53:45: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 24 Aug 2019 17:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.10_model.r INFO @ Sat, 24 Aug 2019 17:53:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:53:46: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:53:51: 14000000 INFO @ Sat, 24 Aug 2019 17:53:59: 15000000 INFO @ Sat, 24 Aug 2019 17:54:03: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:54:03: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:54:03: #1 total tags in treatment: 15558804 INFO @ Sat, 24 Aug 2019 17:54:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:54:03: #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 17:54:04: #1 tags after filtering in treatment: 15558626 INFO @ Sat, 24 Aug 2019 17:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:54:04: #1 finished! INFO @ Sat, 24 Aug 2019 17:54:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:54:06: #2 number of paired peaks: 7866 INFO @ Sat, 24 Aug 2019 17:54:06: start model_add_line... INFO @ Sat, 24 Aug 2019 17:54:06: start X-correlation... INFO @ Sat, 24 Aug 2019 17:54:06: end of X-cor INFO @ Sat, 24 Aug 2019 17:54:06: #2 finished! INFO @ Sat, 24 Aug 2019 17:54:06: #2 predicted fragment length is 109 bps INFO @ Sat, 24 Aug 2019 17:54:06: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 24 Aug 2019 17:54:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.20_model.r INFO @ Sat, 24 Aug 2019 17:54:06: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:54:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.05_summits.bed INFO @ Sat, 24 Aug 2019 17:54:10: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (2134 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:54:34: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:54:56: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:54:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.10_summits.bed INFO @ Sat, 24 Aug 2019 17:54:58: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (1126 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:55:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375003/SRX5375003.20_summits.bed INFO @ Sat, 24 Aug 2019 17:55:19: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (493 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。