Job ID = 2003180 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 48,669,667 reads read : 48,669,667 reads written : 48,669,667 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR498447.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:57 48669667 reads; of these: 48669667 (100.00%) were unpaired; of these: 8548598 (17.56%) aligned 0 times 31182425 (64.07%) aligned exactly 1 time 8938644 (18.37%) aligned >1 times 82.44% overall alignment rate Time searching: 00:17:58 Overall time: 00:17:58 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] 12688221 / 40121069 = 0.3162 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 12:41:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.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 @ Fri, 05 Jul 2019 12:41:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:41:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:41:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.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 @ Fri, 05 Jul 2019 12:41:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:41:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:41:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.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 @ Fri, 05 Jul 2019 12:41:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:41:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:41:18: 1000000 INFO @ Fri, 05 Jul 2019 12:41:19: 1000000 INFO @ Fri, 05 Jul 2019 12:41:21: 1000000 INFO @ Fri, 05 Jul 2019 12:41:25: 2000000 INFO @ Fri, 05 Jul 2019 12:41:26: 2000000 INFO @ Fri, 05 Jul 2019 12:41:29: 2000000 INFO @ Fri, 05 Jul 2019 12:41:32: 3000000 INFO @ Fri, 05 Jul 2019 12:41:33: 3000000 INFO @ Fri, 05 Jul 2019 12:41:38: 3000000 INFO @ Fri, 05 Jul 2019 12:41:39: 4000000 INFO @ Fri, 05 Jul 2019 12:41:40: 4000000 INFO @ Fri, 05 Jul 2019 12:41:46: 4000000 INFO @ Fri, 05 Jul 2019 12:41:46: 5000000 INFO @ Fri, 05 Jul 2019 12:41:47: 5000000 INFO @ Fri, 05 Jul 2019 12:41:53: 6000000 INFO @ Fri, 05 Jul 2019 12:41:54: 5000000 INFO @ Fri, 05 Jul 2019 12:41:55: 6000000 INFO @ Fri, 05 Jul 2019 12:42:00: 7000000 INFO @ Fri, 05 Jul 2019 12:42:02: 7000000 INFO @ Fri, 05 Jul 2019 12:42:02: 6000000 INFO @ Fri, 05 Jul 2019 12:42:07: 8000000 INFO @ Fri, 05 Jul 2019 12:42:09: 8000000 INFO @ Fri, 05 Jul 2019 12:42:11: 7000000 INFO @ Fri, 05 Jul 2019 12:42:14: 9000000 INFO @ Fri, 05 Jul 2019 12:42:16: 9000000 INFO @ Fri, 05 Jul 2019 12:42:19: 8000000 INFO @ Fri, 05 Jul 2019 12:42:21: 10000000 INFO @ Fri, 05 Jul 2019 12:42:23: 10000000 INFO @ Fri, 05 Jul 2019 12:42:27: 9000000 INFO @ Fri, 05 Jul 2019 12:42:28: 11000000 INFO @ Fri, 05 Jul 2019 12:42:30: 11000000 INFO @ Fri, 05 Jul 2019 12:42:35: 10000000 INFO @ Fri, 05 Jul 2019 12:42:35: 12000000 INFO @ Fri, 05 Jul 2019 12:42:37: 12000000 INFO @ Fri, 05 Jul 2019 12:42:42: 13000000 INFO @ Fri, 05 Jul 2019 12:42:43: 11000000 INFO @ Fri, 05 Jul 2019 12:42:45: 13000000 INFO @ Fri, 05 Jul 2019 12:42:49: 14000000 INFO @ Fri, 05 Jul 2019 12:42:51: 12000000 INFO @ Fri, 05 Jul 2019 12:42:52: 14000000 INFO @ Fri, 05 Jul 2019 12:42:57: 15000000 INFO @ Fri, 05 Jul 2019 12:42:59: 15000000 INFO @ Fri, 05 Jul 2019 12:42:59: 13000000 INFO @ Fri, 05 Jul 2019 12:43:04: 16000000 INFO @ Fri, 05 Jul 2019 12:43:06: 16000000 INFO @ Fri, 05 Jul 2019 12:43:07: 14000000 INFO @ Fri, 05 Jul 2019 12:43:12: 17000000 INFO @ Fri, 05 Jul 2019 12:43:13: 17000000 INFO @ Fri, 05 Jul 2019 12:43:15: 15000000 INFO @ Fri, 05 Jul 2019 12:43:19: 18000000 INFO @ Fri, 05 Jul 2019 12:43:20: 18000000 INFO @ Fri, 05 Jul 2019 12:43:23: 16000000 INFO @ Fri, 05 Jul 2019 12:43:27: 19000000 INFO @ Fri, 05 Jul 2019 12:43:27: 19000000 INFO @ Fri, 05 Jul 2019 12:43:31: 17000000 INFO @ Fri, 05 Jul 2019 12:43:34: 20000000 INFO @ Fri, 05 Jul 2019 12:43:34: 20000000 INFO @ Fri, 05 Jul 2019 12:43:39: 18000000 INFO @ Fri, 05 Jul 2019 12:43:41: 21000000 INFO @ Fri, 05 Jul 2019 12:43:42: 21000000 INFO @ Fri, 05 Jul 2019 12:43:47: 19000000 INFO @ Fri, 05 Jul 2019 12:43:48: 22000000 INFO @ Fri, 05 Jul 2019 12:43:49: 22000000 INFO @ Fri, 05 Jul 2019 12:43:55: 20000000 INFO @ Fri, 05 Jul 2019 12:43:56: 23000000 INFO @ Fri, 05 Jul 2019 12:43:56: 23000000 INFO @ Fri, 05 Jul 2019 12:44:03: 24000000 INFO @ Fri, 05 Jul 2019 12:44:03: 21000000 INFO @ Fri, 05 Jul 2019 12:44:04: 24000000 INFO @ Fri, 05 Jul 2019 12:44:10: 25000000 INFO @ Fri, 05 Jul 2019 12:44:11: 25000000 INFO @ Fri, 05 Jul 2019 12:44:11: 22000000 INFO @ Fri, 05 Jul 2019 12:44:17: 26000000 INFO @ Fri, 05 Jul 2019 12:44:18: 26000000 INFO @ Fri, 05 Jul 2019 12:44:19: 23000000 INFO @ Fri, 05 Jul 2019 12:44:24: 27000000 INFO @ Fri, 05 Jul 2019 12:44:26: 27000000 INFO @ Fri, 05 Jul 2019 12:44:27: 24000000 INFO @ Fri, 05 Jul 2019 12:44:28: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:44:28: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:44:28: #1 total tags in treatment: 27432848 INFO @ Fri, 05 Jul 2019 12:44:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:44:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:44:28: #1 tags after filtering in treatment: 27432739 INFO @ Fri, 05 Jul 2019 12:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:44:28: #1 finished! INFO @ Fri, 05 Jul 2019 12:44:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:44:29: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:44:29: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:44:29: #1 total tags in treatment: 27432848 INFO @ Fri, 05 Jul 2019 12:44:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:44:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:44:30: #1 tags after filtering in treatment: 27432739 INFO @ Fri, 05 Jul 2019 12:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:44:30: #1 finished! INFO @ Fri, 05 Jul 2019 12:44:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:44:32: #2 number of paired peaks: 5904 INFO @ Fri, 05 Jul 2019 12:44:32: start model_add_line... INFO @ Fri, 05 Jul 2019 12:44:32: start X-correlation... INFO @ Fri, 05 Jul 2019 12:44:32: end of X-cor INFO @ Fri, 05 Jul 2019 12:44:32: #2 finished! INFO @ Fri, 05 Jul 2019 12:44:32: #2 predicted fragment length is 164 bps INFO @ Fri, 05 Jul 2019 12:44:32: #2 alternative fragment length(s) may be 46,164 bps INFO @ Fri, 05 Jul 2019 12:44:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.05_model.r INFO @ Fri, 05 Jul 2019 12:44:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:44:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:44:33: #2 number of paired peaks: 5904 INFO @ Fri, 05 Jul 2019 12:44:33: start model_add_line... INFO @ Fri, 05 Jul 2019 12:44:33: start X-correlation... INFO @ Fri, 05 Jul 2019 12:44:33: end of X-cor INFO @ Fri, 05 Jul 2019 12:44:33: #2 finished! INFO @ Fri, 05 Jul 2019 12:44:33: #2 predicted fragment length is 164 bps INFO @ Fri, 05 Jul 2019 12:44:33: #2 alternative fragment length(s) may be 46,164 bps INFO @ Fri, 05 Jul 2019 12:44:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.10_model.r INFO @ Fri, 05 Jul 2019 12:44:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:44:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:44:35: 25000000 INFO @ Fri, 05 Jul 2019 12:44:43: 26000000 INFO @ Fri, 05 Jul 2019 12:44:51: 27000000 INFO @ Fri, 05 Jul 2019 12:44:54: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:44:54: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:44:54: #1 total tags in treatment: 27432848 INFO @ Fri, 05 Jul 2019 12:44:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:44:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:44:55: #1 tags after filtering in treatment: 27432739 INFO @ Fri, 05 Jul 2019 12:44:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:44:55: #1 finished! INFO @ Fri, 05 Jul 2019 12:44:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:44:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:44:58: #2 number of paired peaks: 5904 INFO @ Fri, 05 Jul 2019 12:44:58: start model_add_line... INFO @ Fri, 05 Jul 2019 12:44:59: start X-correlation... INFO @ Fri, 05 Jul 2019 12:44:59: end of X-cor INFO @ Fri, 05 Jul 2019 12:44:59: #2 finished! INFO @ Fri, 05 Jul 2019 12:44:59: #2 predicted fragment length is 164 bps INFO @ Fri, 05 Jul 2019 12:44:59: #2 alternative fragment length(s) may be 46,164 bps INFO @ Fri, 05 Jul 2019 12:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.20_model.r INFO @ Fri, 05 Jul 2019 12:44:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:44:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:45:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:46:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:46:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:46:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:46:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.05_summits.bed INFO @ Fri, 05 Jul 2019 12:46:41: Done! pass1 - making usageList (48 chroms): 3 millis pass2 - checking and writing primary data (3157 records, 4 fields): 12 millis INFO @ Fri, 05 Jul 2019 12:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.10_summits.bed INFO @ Fri, 05 Jul 2019 12:46:43: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (927 records, 4 fields): 14 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:47:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:47:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:47:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148693/SRX148693.20_summits.bed INFO @ Fri, 05 Jul 2019 12:47:07: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。