RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ufKGWR/RM_4160415.MonJul81256562024 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: 1720468616 Database = /dev/shm/rModeler.ufKGWR/GCF_030273125.1_C.striata_1.0 - Sequences = 92 - Bases = 926021963 Storage Throughput = excellent ( 1448.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021248 bp ( 40019048 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:17 (hh:mm:ss) Elapsed Time Round Time: 00:20:44 (hh:mm:ss) Elapsed Time : 754 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13926 repeats masked totaling 2364302 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020025 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10019525 bp After Masking: 7013728 bp Masked: 30.00 % -- Input Database Coverage: 10020025 bp out of 926021963 bp ( 1.08 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:48 (hh:mm:ss) Elapsed Time, 27038 HSPs Collected Number of families returned by RECON: 1612 Round Time: 00:07:41 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43412 repeats masked totaling 7322194 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041158 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30039458 bp After Masking: 21054452 bp Masked: 29.91 % -- Input Database Coverage: 40061183 bp out of 926021963 bp ( 4.33 % ) Sampling Time: 00:04:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:27:47 (hh:mm:ss) Elapsed Time, 57902 HSPs Collected Number of families returned by RECON: 5723 Round Time: 00:33:38 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142745 repeats masked totaling 23526792 bp(s). - TE Masking time 00:02:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011227 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 90008004 bp After Masking: 61560909 bp Masked: 31.61 % -- Input Database Coverage: 130072410 bp out of 926021963 bp ( 14.05 % ) Sampling Time: 00:12:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:00:54 (hh:mm:ss) Elapsed Time, 348847 HSPs Collected Number of families returned by RECON: 18458 Round Time: 03:26:38 (hh:mm:ss) Elapsed Time : 636 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 511499 repeats masked totaling 86421600 bp(s). - TE Masking time 00:12:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039243 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 270030274 bp After Masking: 168498398 bp Masked: 37.60 % -- Input Database Coverage: 400111653 bp out of 926021963 bp ( 43.21 % ) Sampling Time: 00:44:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22865703 Comparison Time: 20:50:37 (hh:mm:ss) Elapsed Time, 943270 HSPs Collected Number of families returned by RECON: 58302 Round Time: 22:59:23 (hh:mm:ss) Elapsed Time : 1464 families discovered. RepeatScout/RECON discovery complete: 3001 families found Classification Time: 01:43:27 (hh:mm:ss) Elapsed Time Program Time: 29:11:31 (hh:mm:ss) Elapsed Time