RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.FGgise/RM_3530164.SatNov161829472024 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: 1731810587 Database = /scratch/tmp/rModeler.FGgise/GCA_039655065.1_mGloMut1.hap1 - Sequences = 82 - Bases = 2159908085 Storage Throughput = excellent ( 1515.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030818 bp ( 40030618 non ambiguous ) - Num Contigs Represented = 18 - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:31 (hh:mm:ss) Elapsed Time Round Time: 00:14:14 (hh:mm:ss) Elapsed Time : 201 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7759 repeats masked totaling 2550530 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000434 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 10000234 bp After Masking: 7409918 bp Masked: 25.90 % -- Input Database Coverage: 10000434 bp out of 2159908085 bp ( 0.46 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:55 (hh:mm:ss) Elapsed Time, 4771 HSPs Collected Number of families returned by RECON: 804 Round Time: 00:03:38 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:08 (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... 26677 repeats masked totaling 7978023 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030382 bp Num Contigs Represented = 18 Non ambiguous bp: Initial: 30030382 bp After Masking: 21941466 bp Masked: 26.94 % -- Input Database Coverage: 40030816 bp out of 2159908085 bp ( 1.85 % ) Sampling Time: 00:01:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:12:59 (hh:mm:ss) Elapsed Time, 24728 HSPs Collected Number of families returned by RECON: 2507 Round Time: 00:15:10 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 91545 repeats masked totaling 26887420 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037612 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 90036912 bp After Masking: 62819559 bp Masked: 30.23 % -- Input Database Coverage: 130068428 bp out of 2159908085 bp ( 6.02 % ) Sampling Time: 00:05:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 01:15:01 (hh:mm:ss) Elapsed Time, 99552 HSPs Collected Number of families returned by RECON: 8549 Round Time: 01:21:53 (hh:mm:ss) Elapsed Time : 166 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 306249 repeats masked totaling 88274408 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270024095 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270023195 bp After Masking: 180796466 bp Masked: 33.04 % -- Input Database Coverage: 400092523 bp out of 2159908085 bp ( 18.52 % ) Sampling Time: 00:15:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 08:39:46 (hh:mm:ss) Elapsed Time, 219725 HSPs Collected Number of families returned by RECON: 37437 Round Time: 09:07:23 (hh:mm:ss) Elapsed Time : 392 families discovered. RepeatScout/RECON discovery complete: 839 families found Classification Time: 00:19:34 (hh:mm:ss) Elapsed Time Program Time: 11:21:52 (hh:mm:ss) Elapsed Time