RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MS6jnB/RM_10352.SatDec20244062023 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: 1701513845 Database = /dev/shm/rModeler.MS6jnB/GCA_030035675.1_rRhiFlo1.hap2 - Sequences = 77 - Bases = 2307436586 Storage Throughput = excellent ( 1213.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40189142 bp ( 40028147 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:03:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:30 (hh:mm:ss) Elapsed Time Round Time: 00:31:07 (hh:mm:ss) Elapsed Time : 579 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:54 (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... 19015 repeats masked totaling 4566199 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10120504 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10015577 bp After Masking: 5325824 bp Masked: 46.82 % -- Input Database Coverage: 10120504 bp out of 2307436586 bp ( 0.44 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:57 (hh:mm:ss) Elapsed Time, 9358 HSPs Collected Number of families returned by RECON: 1297 Round Time: 00:06:50 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57859 repeats masked totaling 14406847 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30068558 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30012490 bp After Masking: 14968509 bp Masked: 50.13 % -- Input Database Coverage: 40189062 bp out of 2307436586 bp ( 1.74 % ) Sampling Time: 00:04:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:22:37 (hh:mm:ss) Elapsed Time, 47498 HSPs Collected Number of families returned by RECON: 3867 Round Time: 00:29:08 (hh:mm:ss) Elapsed Time : 110 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 185757 repeats masked totaling 44812609 bp(s). - TE Masking time 00:02:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90139252 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90008555 bp After Masking: 43719216 bp Masked: 51.43 % -- Input Database Coverage: 130328314 bp out of 2307436586 bp ( 5.65 % ) Sampling Time: 00:14:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 02:22:06 (hh:mm:ss) Elapsed Time, 199618 HSPs Collected Number of families returned by RECON: 11833 Round Time: 02:50:14 (hh:mm:ss) Elapsed Time : 437 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:25:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 626106 repeats masked totaling 146694020 bp(s). - TE Masking time 00:13:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270534663 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 270013323 bp After Masking: 119206385 bp Masked: 55.85 % -- Input Database Coverage: 400862977 bp out of 2307436586 bp ( 17.37 % ) Sampling Time: 00:49:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22906296 Comparison Time: 17:18:25 (hh:mm:ss) Elapsed Time, 611515 HSPs Collected Number of families returned by RECON: 35815 Round Time: 19:05:20 (hh:mm:ss) Elapsed Time : 1065 families discovered. RepeatScout/RECON discovery complete: 2220 families found Classification Time: 01:31:43 (hh:mm:ss) Elapsed Time Program Time: 24:34:22 (hh:mm:ss) Elapsed Time