RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EpVnKA/RM_2418448.FriJul181029072025 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: 1752859747 Database = /dev/shm/rModeler.EpVnKA/GCA_048129025.1_fCaeTer1.1_haplotype_2 - Sequences = 250 - Bases = 1033416279 - N50 = 42727780 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 60977376-65331744 | [ 1 ] 56623008-60977375 | [ ] 52268640-56623007 | [ ] 47914272-52268639 | [ 4 ] 43559904-47914271 | [ 4 ] 39205536-43559903 |* [ 7 ] 34851168-39205535 | [ 4 ] 30496800-34851167 | [ 2 ] 26142432-30496799 | [ 1 ] 21788064-26142431 | [ ] 17433696-21788063 | [ ] 13079328-17433695 | [ ] 8724960-13079327 | [ ] 4370592-8724959 | [ ] 16225-4370592 |************************************************** [ 227 ] Storage Throughput = excellent ( 1085.68 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036280 bp ( 40036280 non ambiguous ) - Num Contigs Represented = 64 - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:54 (hh:mm:ss) Elapsed Time Round Time: 00:30:37 (hh:mm:ss) Elapsed Time : 820 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 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18045 repeats masked totaling 2279371 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023614 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10023614 bp After Masking: 7464157 bp Masked: 25.53 % -- Input Database Coverage: 10023614 bp out of 1033416279 bp ( 0.97 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:09 (hh:mm:ss) Elapsed Time, 16393 HSPs Collected Number of families returned by RECON: 2396 Round Time: 00:06:42 (hh:mm:ss) Elapsed Time : 36 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56465 repeats masked totaling 7184054 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012586 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 30012586 bp After Masking: 22109276 bp Masked: 26.33 % -- Input Database Coverage: 40036200 bp out of 1033416279 bp ( 3.87 % ) Sampling Time: 00:02:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:29:44 (hh:mm:ss) Elapsed Time, 121815 HSPs Collected Number of families returned by RECON: 7473 Round Time: 00:36:19 (hh:mm:ss) Elapsed Time : 271 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 197504 repeats masked totaling 26528026 bp(s). - TE Masking time 00:02:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016222 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 90016022 bp After Masking: 60796677 bp Masked: 32.46 % -- Input Database Coverage: 130052422 bp out of 1033416279 bp ( 12.58 % ) Sampling Time: 00:08:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:23:53 (hh:mm:ss) Elapsed Time, 401781 HSPs Collected Number of families returned by RECON: 20570 Round Time: 03:55:53 (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 : 00:04:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 680297 repeats masked totaling 97727409 bp(s). - TE Masking time 00:15:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012846 bp Num Contigs Represented = 178 Non ambiguous bp: Initial: 270011646 bp After Masking: 165215061 bp Masked: 38.81 % -- Input Database Coverage: 400065268 bp out of 1033416279 bp ( 38.71 % ) Sampling Time: 00:32:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22994371 Comparison Time: 24:57:39 (hh:mm:ss) Elapsed Time, 1028040 HSPs Collected Number of families returned by RECON: 61967 Round Time: 27:55:21 (hh:mm:ss) Elapsed Time : 1585 families discovered. RepeatScout/RECON discovery complete: 3348 families found Classification Time: 02:09:56 (hh:mm:ss) Elapsed Time Program Time: 35:14:48 (hh:mm:ss) Elapsed Time