RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Y8h1hV/RM_15419.WedJan111438542023 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: 1673476734 Database = /dev/shm/rModeler.Y8h1hV/GCA_905319855.2_mCanLor1.2 - Sequences = 82 - Bases = 2447463909 Storage Throughput = excellent ( 1026.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036801 bp ( 40036201 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:13 (hh:mm:ss) Elapsed Time Round Time: 00:29:38 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12764 repeats masked totaling 2401195 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005790 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10005690 bp After Masking: 7516284 bp Masked: 24.88 % -- Input Database Coverage: 10005790 bp out of 2447463909 bp ( 0.41 % ) Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:07:13 (hh:mm:ss) Elapsed Time, 8385 HSPs Collected Number of families returned by RECON: 1021 Round Time: 00:08:45 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42066 repeats masked totaling 7809849 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030931 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30030431 bp After Masking: 21805500 bp Masked: 27.39 % -- Input Database Coverage: 40036721 bp out of 2447463909 bp ( 1.64 % ) Sampling Time: 00:02:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:37:52 (hh:mm:ss) Elapsed Time, 124866 HSPs Collected Number of families returned by RECON: 2378 Round Time: 00:41:56 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138103 repeats masked totaling 26792399 bp(s). - TE Masking time 00:01:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90019911 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90019211 bp After Masking: 61838757 bp Masked: 31.30 % -- Input Database Coverage: 130056632 bp out of 2447463909 bp ( 5.31 % ) Sampling Time: 00:09:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 04:34:27 (hh:mm:ss) Elapsed Time, 3057844 HSPs Collected Number of families returned by RECON: 8124 Round Time: 04:48:20 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 442941 repeats masked totaling 85669914 bp(s). - TE Masking time 00:06:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270016337 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 270006581 bp After Masking: 180293696 bp Masked: 33.23 % -- Input Database Coverage: 400072969 bp out of 2447463909 bp ( 16.35 % ) Sampling Time: 00:28:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 32:46:46 (hh:mm:ss) Elapsed Time, 17406037 HSPs Collected Number of families returned by RECON: 37527 Round Time: 33:57:12 (hh:mm:ss) Elapsed Time : 342 families discovered. RepeatScout/RECON discovery complete: 742 families found Classification Time: 00:30:24 (hh:mm:ss) Elapsed Time Program Time: 40:36:15 (hh:mm:ss) Elapsed Time