RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.G07Zqy/RM_28255.WedDec282258322022 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1672297110 Database = /dev/shm/rModeler.G07Zqy/GCF_900700375.1_fDenClu1.1 - Sequences = 460 - Bases = 567401054 - N50 = 23378448 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 39360639-42171479 | [ 1 ] 36549799-39360638 | [ 2 ] 33738959-36549798 | [ 2 ] 30928119-33738958 | [ ] 28117280-30928119 | [ ] 25306440-28117279 | [ 2 ] 22495600-25306439 | [ 5 ] 19684760-22495599 | [ 7 ] 16873920-19684759 | [ 1 ] 14063081-16873920 | [ ] 11252241-14063080 | [ ] 8441401-11252240 | [ ] 5630561-8441400 | [ ] 2819721-5630560 | [ ] 8882-2819721 |************************************************* [ 440 ] Storage Throughput = good ( 901.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40417974 bp ( 40009841 non ambiguous ) - Num Contigs Represented = 99 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:51 (hh:mm:ss) Elapsed Time Round Time: 00:24:30 (hh:mm:ss) Elapsed Time : 500 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11517 repeats masked totaling 1852185 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10139381 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10010224 bp After Masking: 7887559 bp Masked: 21.20 % -- Input Database Coverage: 10139381 bp out of 567401054 bp ( 1.79 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:06:26 (hh:mm:ss) Elapsed Time, 8070 HSPs Collected Number of families returned by RECON: 1342 Round Time: 00:07:38 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34619 repeats masked totaling 5502716 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30318593 bp Num Contigs Represented = 87 Non ambiguous bp: Initial: 30039617 bp After Masking: 23717005 bp Masked: 21.05 % -- Input Database Coverage: 40457974 bp out of 567401054 bp ( 7.13 % ) Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 296835 Comparison Time: 00:35:03 (hh:mm:ss) Elapsed Time, 70155 HSPs Collected Number of families returned by RECON: 4400 Round Time: 00:38:46 (hh:mm:ss) Elapsed Time : 92 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113229 repeats masked totaling 17472354 bp(s). - TE Masking time 00:01:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90704940 bp Num Contigs Represented = 173 Non ambiguous bp: Initial: 90038991 bp After Masking: 70162881 bp Masked: 22.08 % -- Input Database Coverage: 131162914 bp out of 567401054 bp ( 23.12 % ) Sampling Time: 00:07:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2634660 Comparison Time: 04:05:47 (hh:mm:ss) Elapsed Time, 545365 HSPs Collected Number of families returned by RECON: 16830 Round Time: 04:25:21 (hh:mm:ss) Elapsed Time : 355 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 402046 repeats masked totaling 62732964 bp(s). - TE Masking time 00:10:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272316093 bp Num Contigs Represented = 349 Non ambiguous bp: Initial: 270011665 bp After Masking: 199471419 bp Masked: 26.12 % -- Input Database Coverage: 403479007 bp out of 567401054 bp ( 71.11 % ) Sampling Time: 00:27:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23891328 Comparison Time: 31:00:00 (hh:mm:ss) Elapsed Time, 1414579 HSPs Collected Number of families returned by RECON: 63350 Round Time: 33:12:05 (hh:mm:ss) Elapsed Time : 760 families discovered. RepeatScout/RECON discovery complete: 1724 families found Classification Time: 01:34:56 (hh:mm:ss) Elapsed Time Program Time: 40:23:16 (hh:mm:ss) Elapsed Time