Job ID = 2640415 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,341,204 reads read : 36,341,204 reads written : 36,341,204 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR399331.sra.cache’: 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:35 36341204 reads; of these: 36341204 (100.00%) were unpaired; of these: 1303793 (3.59%) aligned 0 times 26089620 (71.79%) aligned exactly 1 time 8947791 (24.62%) aligned >1 times 96.41% overall alignment rate Time searching: 00:11:38 Overall time: 00:11:38 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] 786728 / 35037411 = 0.0225 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 16:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.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 16:45:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:45:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:46:08: 1000000 INFO @ Sat, 24 Aug 2019 16:46:18: 2000000 INFO @ Sat, 24 Aug 2019 16:46:27: 3000000 INFO @ Sat, 24 Aug 2019 16:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.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 16:46:29: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:46:29: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:46:36: 4000000 INFO @ Sat, 24 Aug 2019 16:46:37: 1000000 INFO @ Sat, 24 Aug 2019 16:46:45: 2000000 INFO @ Sat, 24 Aug 2019 16:46:45: 5000000 INFO @ Sat, 24 Aug 2019 16:46:53: 3000000 INFO @ Sat, 24 Aug 2019 16:46:54: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 16:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.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 16:46:59: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:46:59: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:47:01: 4000000 INFO @ Sat, 24 Aug 2019 16:47:03: 7000000 INFO @ Sat, 24 Aug 2019 16:47:06: 1000000 INFO @ Sat, 24 Aug 2019 16:47:09: 5000000 INFO @ Sat, 24 Aug 2019 16:47:11: 8000000 INFO @ Sat, 24 Aug 2019 16:47:14: 2000000 INFO @ Sat, 24 Aug 2019 16:47:17: 6000000 INFO @ Sat, 24 Aug 2019 16:47:20: 9000000 INFO @ Sat, 24 Aug 2019 16:47:22: 3000000 INFO @ Sat, 24 Aug 2019 16:47:25: 7000000 INFO @ Sat, 24 Aug 2019 16:47:29: 10000000 INFO @ Sat, 24 Aug 2019 16:47:30: 4000000 INFO @ Sat, 24 Aug 2019 16:47:32: 8000000 INFO @ Sat, 24 Aug 2019 16:47:37: 5000000 INFO @ Sat, 24 Aug 2019 16:47:37: 11000000 INFO @ Sat, 24 Aug 2019 16:47:40: 9000000 INFO @ Sat, 24 Aug 2019 16:47:45: 6000000 INFO @ Sat, 24 Aug 2019 16:47:46: 12000000 INFO @ Sat, 24 Aug 2019 16:47:48: 10000000 INFO @ Sat, 24 Aug 2019 16:47:53: 7000000 INFO @ Sat, 24 Aug 2019 16:47:54: 13000000 INFO @ Sat, 24 Aug 2019 16:47:55: 11000000 INFO @ Sat, 24 Aug 2019 16:48:00: 8000000 INFO @ Sat, 24 Aug 2019 16:48:03: 12000000 INFO @ Sat, 24 Aug 2019 16:48:03: 14000000 INFO @ Sat, 24 Aug 2019 16:48:07: 9000000 INFO @ Sat, 24 Aug 2019 16:48:10: 13000000 INFO @ Sat, 24 Aug 2019 16:48:12: 15000000 INFO @ Sat, 24 Aug 2019 16:48:15: 10000000 INFO @ Sat, 24 Aug 2019 16:48:18: 14000000 INFO @ Sat, 24 Aug 2019 16:48:20: 16000000 INFO @ Sat, 24 Aug 2019 16:48:22: 11000000 INFO @ Sat, 24 Aug 2019 16:48:26: 15000000 INFO @ Sat, 24 Aug 2019 16:48:29: 17000000 INFO @ Sat, 24 Aug 2019 16:48:29: 12000000 INFO @ Sat, 24 Aug 2019 16:48:33: 16000000 INFO @ Sat, 24 Aug 2019 16:48:37: 13000000 INFO @ Sat, 24 Aug 2019 16:48:37: 18000000 INFO @ Sat, 24 Aug 2019 16:48:41: 17000000 INFO @ Sat, 24 Aug 2019 16:48:44: 14000000 INFO @ Sat, 24 Aug 2019 16:48:46: 19000000 INFO @ Sat, 24 Aug 2019 16:48:48: 18000000 INFO @ Sat, 24 Aug 2019 16:48:51: 15000000 INFO @ Sat, 24 Aug 2019 16:48:54: 20000000 INFO @ Sat, 24 Aug 2019 16:48:56: 19000000 INFO @ Sat, 24 Aug 2019 16:48:59: 16000000 INFO @ Sat, 24 Aug 2019 16:49:03: 21000000 INFO @ Sat, 24 Aug 2019 16:49:03: 20000000 INFO @ Sat, 24 Aug 2019 16:49:06: 17000000 INFO @ Sat, 24 Aug 2019 16:49:11: 21000000 INFO @ Sat, 24 Aug 2019 16:49:11: 22000000 INFO @ Sat, 24 Aug 2019 16:49:13: 18000000 INFO @ Sat, 24 Aug 2019 16:49:18: 22000000 INFO @ Sat, 24 Aug 2019 16:49:19: 23000000 INFO @ Sat, 24 Aug 2019 16:49:21: 19000000 INFO @ Sat, 24 Aug 2019 16:49:25: 23000000 INFO @ Sat, 24 Aug 2019 16:49:28: 24000000 INFO @ Sat, 24 Aug 2019 16:49:28: 20000000 INFO @ Sat, 24 Aug 2019 16:49:32: 24000000 INFO @ Sat, 24 Aug 2019 16:49:35: 21000000 INFO @ Sat, 24 Aug 2019 16:49:36: 25000000 INFO @ Sat, 24 Aug 2019 16:49:39: 25000000 INFO @ Sat, 24 Aug 2019 16:49:42: 22000000 INFO @ Sat, 24 Aug 2019 16:49:44: 26000000 INFO @ Sat, 24 Aug 2019 16:49:47: 26000000 INFO @ Sat, 24 Aug 2019 16:49:50: 23000000 INFO @ Sat, 24 Aug 2019 16:49:53: 27000000 INFO @ Sat, 24 Aug 2019 16:49:54: 27000000 INFO @ Sat, 24 Aug 2019 16:49:57: 24000000 INFO @ Sat, 24 Aug 2019 16:50:01: 28000000 INFO @ Sat, 24 Aug 2019 16:50:01: 28000000 INFO @ Sat, 24 Aug 2019 16:50:04: 25000000 INFO @ Sat, 24 Aug 2019 16:50:08: 29000000 INFO @ Sat, 24 Aug 2019 16:50:10: 29000000 INFO @ Sat, 24 Aug 2019 16:50:11: 26000000 INFO @ Sat, 24 Aug 2019 16:50:15: 30000000 INFO @ Sat, 24 Aug 2019 16:50:18: 30000000 INFO @ Sat, 24 Aug 2019 16:50:19: 27000000 INFO @ Sat, 24 Aug 2019 16:50:23: 31000000 INFO @ Sat, 24 Aug 2019 16:50:26: 28000000 INFO @ Sat, 24 Aug 2019 16:50:27: 31000000 INFO @ Sat, 24 Aug 2019 16:50:30: 32000000 INFO @ Sat, 24 Aug 2019 16:50:33: 29000000 INFO @ Sat, 24 Aug 2019 16:50:35: 32000000 INFO @ Sat, 24 Aug 2019 16:50:37: 33000000 INFO @ Sat, 24 Aug 2019 16:50:41: 30000000 INFO @ Sat, 24 Aug 2019 16:50:44: 33000000 INFO @ Sat, 24 Aug 2019 16:50:44: 34000000 INFO @ Sat, 24 Aug 2019 16:50:46: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 16:50:46: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 16:50:46: #1 total tags in treatment: 34250683 INFO @ Sat, 24 Aug 2019 16:50:46: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:50:46: #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 16:50:47: #1 tags after filtering in treatment: 34250608 INFO @ Sat, 24 Aug 2019 16:50:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:50:47: #1 finished! INFO @ Sat, 24 Aug 2019 16:50:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:50:48: 31000000 INFO @ Sat, 24 Aug 2019 16:50:51: #2 number of paired peaks: 4078 INFO @ Sat, 24 Aug 2019 16:50:51: start model_add_line... INFO @ Sat, 24 Aug 2019 16:50:51: start X-correlation... INFO @ Sat, 24 Aug 2019 16:50:51: end of X-cor INFO @ Sat, 24 Aug 2019 16:50:51: #2 finished! INFO @ Sat, 24 Aug 2019 16:50:51: #2 predicted fragment length is 35 bps INFO @ Sat, 24 Aug 2019 16:50:51: #2 alternative fragment length(s) may be 35,591 bps INFO @ Sat, 24 Aug 2019 16:50:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.10_model.r WARNING @ Sat, 24 Aug 2019 16:50:51: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:50:51: #2 You may need to consider one of the other alternative d(s): 35,591 WARNING @ Sat, 24 Aug 2019 16:50:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 16:50:51: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:50:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:50:52: 34000000 INFO @ Sat, 24 Aug 2019 16:50:54: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 16:50:54: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 16:50:54: #1 total tags in treatment: 34250683 INFO @ Sat, 24 Aug 2019 16:50:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:50:54: #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 16:50:55: #1 tags after filtering in treatment: 34250608 INFO @ Sat, 24 Aug 2019 16:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:50:55: #1 finished! INFO @ Sat, 24 Aug 2019 16:50:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:50:55: 32000000 INFO @ Sat, 24 Aug 2019 16:50:59: #2 number of paired peaks: 4078 INFO @ Sat, 24 Aug 2019 16:50:59: start model_add_line... INFO @ Sat, 24 Aug 2019 16:50:59: start X-correlation... INFO @ Sat, 24 Aug 2019 16:50:59: end of X-cor INFO @ Sat, 24 Aug 2019 16:50:59: #2 finished! INFO @ Sat, 24 Aug 2019 16:50:59: #2 predicted fragment length is 35 bps INFO @ Sat, 24 Aug 2019 16:50:59: #2 alternative fragment length(s) may be 35,591 bps INFO @ Sat, 24 Aug 2019 16:50:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.05_model.r WARNING @ Sat, 24 Aug 2019 16:50:59: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:50:59: #2 You may need to consider one of the other alternative d(s): 35,591 WARNING @ Sat, 24 Aug 2019 16:50:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 16:50:59: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:50:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:51:02: 33000000 INFO @ Sat, 24 Aug 2019 16:51:10: 34000000 INFO @ Sat, 24 Aug 2019 16:51:12: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 16:51:12: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 16:51:12: #1 total tags in treatment: 34250683 INFO @ Sat, 24 Aug 2019 16:51:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:51:12: #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 16:51:13: #1 tags after filtering in treatment: 34250608 INFO @ Sat, 24 Aug 2019 16:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:51:13: #1 finished! INFO @ Sat, 24 Aug 2019 16:51:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:51:16: #2 number of paired peaks: 4078 INFO @ Sat, 24 Aug 2019 16:51:16: start model_add_line... INFO @ Sat, 24 Aug 2019 16:51:17: start X-correlation... INFO @ Sat, 24 Aug 2019 16:51:17: end of X-cor INFO @ Sat, 24 Aug 2019 16:51:17: #2 finished! INFO @ Sat, 24 Aug 2019 16:51:17: #2 predicted fragment length is 35 bps INFO @ Sat, 24 Aug 2019 16:51:17: #2 alternative fragment length(s) may be 35,591 bps INFO @ Sat, 24 Aug 2019 16:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.20_model.r WARNING @ Sat, 24 Aug 2019 16:51:17: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:51:17: #2 You may need to consider one of the other alternative d(s): 35,591 WARNING @ Sat, 24 Aug 2019 16:51:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 16:51:17: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:52:38: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:52:45: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:53:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.10_peaks.xls INFO @ Sat, 24 Aug 2019 16:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.10_summits.bed INFO @ Sat, 24 Aug 2019 16:53:34: Done! pass1 - making usageList (36 chroms): 2 millis pass2 - checking and writing primary data (1085 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.05_peaks.xls INFO @ Sat, 24 Aug 2019 16:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.05_summits.bed INFO @ Sat, 24 Aug 2019 16:53:40: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (1901 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:54:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.20_peaks.xls INFO @ Sat, 24 Aug 2019 16:54:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:54:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116053/SRX116053.20_summits.bed INFO @ Sat, 24 Aug 2019 16:54:00: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。