RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.lqv2E1/RM_319026.ThuApr171001402025 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: 1744909299 Database = /dev/shm/rModeler.lqv2E1/GCF_029281585.2_NHGRI_mGorGor1-v2.1_pri - Sequences = 26 - Bases = 3545850636 Storage Throughput = excellent ( 1784.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001695 bp ( 40001695 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:18 (hh:mm:ss) Elapsed Time Round Time: 00:15:06 (hh:mm:ss) Elapsed Time : 229 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10328 repeats masked totaling 2696841 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000451 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000451 bp After Masking: 5682940 bp Masked: 43.17 % -- Input Database Coverage: 10000451 bp out of 3545850636 bp ( 0.28 % ) Sampling Time: 00:02:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:51 (hh:mm:ss) Elapsed Time, 6494 HSPs Collected Number of families returned by RECON: 779 Round Time: 00:06:13 (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 : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35541 repeats masked totaling 8661302 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001240 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30001240 bp After Masking: 16344450 bp Masked: 45.52 % -- Input Database Coverage: 40001691 bp out of 3545850636 bp ( 1.13 % ) Sampling Time: 00:09:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:11:12 (hh:mm:ss) Elapsed Time, 21836 HSPs Collected Number of families returned by RECON: 2054 Round Time: 00:21:19 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113989 repeats masked totaling 27525147 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90083769 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90003762 bp After Masking: 46252110 bp Masked: 48.61 % -- Input Database Coverage: 130085460 bp out of 3545850636 bp ( 3.67 % ) Sampling Time: 00:32:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 00:58:52 (hh:mm:ss) Elapsed Time, 83045 HSPs Collected Number of families returned by RECON: 6378 Round Time: 01:32:15 (hh:mm:ss) Elapsed Time : 178 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:25:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 380924 repeats masked totaling 91470738 bp(s). - TE Masking time 00:02:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270248445 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270008424 bp After Masking: 131980979 bp Masked: 51.12 % -- Input Database Coverage: 400333905 bp out of 3545850636 bp ( 11.29 % ) Sampling Time: 01:31:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 06:26:29 (hh:mm:ss) Elapsed Time, 254573 HSPs Collected Number of families returned by RECON: 25827 Round Time: 08:04:38 (hh:mm:ss) Elapsed Time : 363 families discovered. RepeatScout/RECON discovery complete: 847 families found Classification Time: 00:17:02 (hh:mm:ss) Elapsed Time Program Time: 10:36:33 (hh:mm:ss) Elapsed Time