RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WEm8nO/RM_19408.SatJul271436532024 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: 1722116209 Database = /dev/shm/rModeler.WEm8nO/GCF_021018895.1_ASM2101889v1 - Sequences = 31 - Bases = 647095223 Storage Throughput = excellent ( 1048.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40044346 bp ( 40037457 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:22 (hh:mm:ss) Elapsed Time Round Time: 00:26:15 (hh:mm:ss) Elapsed Time : 342 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 00:01:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5962 repeats masked totaling 702603 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041673 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10039673 bp After Masking: 8876050 bp Masked: 11.59 % -- Input Database Coverage: 10041673 bp out of 647095223 bp ( 1.55 % ) Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:12 (hh:mm:ss) Elapsed Time, 7198 HSPs Collected Number of families returned by RECON: 1607 Round Time: 00:09:11 (hh:mm:ss) Elapsed Time : 11 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 00:03:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19170 repeats masked totaling 2260072 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042676 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30037787 bp After Masking: 26319808 bp Masked: 12.38 % -- Input Database Coverage: 40084349 bp out of 647095223 bp ( 6.19 % ) Sampling Time: 00:04:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:36:40 (hh:mm:ss) Elapsed Time, 50240 HSPs Collected Number of families returned by RECON: 6130 Round Time: 00:43:19 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71245 repeats masked totaling 9161577 bp(s). - TE Masking time 00:01:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033323 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 90024323 bp After Masking: 76598699 bp Masked: 14.91 % -- Input Database Coverage: 130117672 bp out of 647095223 bp ( 20.11 % ) Sampling Time: 00:13:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 04:49:54 (hh:mm:ss) Elapsed Time, 256302 HSPs Collected Number of families returned by RECON: 22082 Round Time: 05:20:31 (hh:mm:ss) Elapsed Time : 417 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 275800 repeats masked totaling 38741373 bp(s). - TE Masking time 00:08:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270060524 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270030913 bp After Masking: 218833193 bp Masked: 18.96 % -- Input Database Coverage: 400178196 bp out of 647095223 bp ( 61.84 % ) Sampling Time: 00:43:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 36:01:09 (hh:mm:ss) Elapsed Time, 783362 HSPs Collected Number of families returned by RECON: 86023 Round Time: 39:39:23 (hh:mm:ss) Elapsed Time : 1099 families discovered. RepeatScout/RECON discovery complete: 1997 families found Classification Time: 01:14:20 (hh:mm:ss) Elapsed Time Program Time: 47:32:59 (hh:mm:ss) Elapsed Time