RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MeZYQx/RM_1518912.FriApr112206212025 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: 1744434379 Database = /dev/shm/rModeler.MeZYQx/GCA_964374335.1_fAstCal68.1 - Sequences = 31 - Bases = 933429770 Storage Throughput = excellent ( 1598.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027708 bp ( 40027508 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:24 (hh:mm:ss) Elapsed Time Round Time: 00:10:26 (hh:mm:ss) Elapsed Time : 577 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9293 repeats masked totaling 2196685 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001043 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10001043 bp After Masking: 7452498 bp Masked: 25.48 % -- Input Database Coverage: 10001043 bp out of 933429770 bp ( 1.07 % ) Sampling Time: 00:00:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:46 (hh:mm:ss) Elapsed Time, 8896 HSPs Collected Number of families returned by RECON: 1134 Round Time: 00:03:22 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29973 repeats masked totaling 7576502 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026651 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30026451 bp After Masking: 21505456 bp Masked: 28.38 % -- Input Database Coverage: 40027694 bp out of 933429770 bp ( 4.29 % ) Sampling Time: 00:01:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:11:32 (hh:mm:ss) Elapsed Time, 41397 HSPs Collected Number of families returned by RECON: 3954 Round Time: 00:13:33 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 98929 repeats masked totaling 24062524 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035871 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90035571 bp After Masking: 63029644 bp Masked: 29.99 % -- Input Database Coverage: 130063565 bp out of 933429770 bp ( 13.93 % ) Sampling Time: 00:04:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:10:48 (hh:mm:ss) Elapsed Time, 254980 HSPs Collected Number of families returned by RECON: 13542 Round Time: 01:19:17 (hh:mm:ss) Elapsed Time : 392 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 354349 repeats masked totaling 86286653 bp(s). - TE Masking time 00:04:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021632 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 270020432 bp After Masking: 174660026 bp Masked: 35.32 % -- Input Database Coverage: 400085197 bp out of 933429770 bp ( 42.86 % ) Sampling Time: 00:17:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 08:12:23 (hh:mm:ss) Elapsed Time, 805258 HSPs Collected Number of families returned by RECON: 48976 Round Time: 08:54:13 (hh:mm:ss) Elapsed Time : 1083 families discovered. RepeatScout/RECON discovery complete: 2155 families found Classification Time: 01:05:59 (hh:mm:ss) Elapsed Time Program Time: 11:46:50 (hh:mm:ss) Elapsed Time