RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.Ri6nnW/RM_1116782.MonApr211629272025 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: 1745278166 Database = /data/tmp/rModeler.Ri6nnW/GCA_040954625.2_keBalMisa1.hap1 - Sequences = 100 - Bases = 329694088 Storage Throughput = excellent ( 1015.15 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010894 bp ( 40007394 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:17 (hh:mm:ss) Elapsed Time Round Time: 00:29:32 (hh:mm:ss) Elapsed Time : 401 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6293 repeats masked totaling 1772284 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021307 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10020307 bp After Masking: 7172543 bp Masked: 28.42 % -- Input Database Coverage: 10021307 bp out of 329694088 bp ( 3.04 % ) Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:34 (hh:mm:ss) Elapsed Time, 3190 HSPs Collected Number of families returned by RECON: 676 Round Time: 00:06:38 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19462 repeats masked totaling 5426215 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029533 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30027033 bp After Masking: 21497891 bp Masked: 28.40 % -- Input Database Coverage: 40050840 bp out of 329694088 bp ( 12.15 % ) Sampling Time: 00:04:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:24:27 (hh:mm:ss) Elapsed Time, 24746 HSPs Collected Number of families returned by RECON: 2735 Round Time: 00:31:31 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61696 repeats masked totaling 16625350 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021352 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90015352 bp After Masking: 63921217 bp Masked: 28.99 % -- Input Database Coverage: 130072192 bp out of 329694088 bp ( 39.45 % ) Sampling Time: 00:17:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 02:38:40 (hh:mm:ss) Elapsed Time, 338413 HSPs Collected Number of families returned by RECON: 10409 Round Time: 03:16:52 (hh:mm:ss) Elapsed Time : 282 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 156886 repeats masked totaling 44210437 bp(s). - TE Masking time 00:08:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 199621604 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 199609004 bp After Masking: 134847663 bp Masked: 32.44 % -- Input Database Coverage: 329693796 bp out of 329694088 bp ( 100.00 % ) Sampling Time: 00:35:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 12602710 Comparison Time: 11:11:11 (hh:mm:ss) Elapsed Time, 905180 HSPs Collected Number of families returned by RECON: 26419 Round Time: 12:59:20 (hh:mm:ss) Elapsed Time : 584 families discovered. RepeatScout/RECON discovery complete: 1304 families found Classification Time: 01:53:09 (hh:mm:ss) Elapsed Time Program Time: 19:17:02 (hh:mm:ss) Elapsed Time