RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.3tvqQn/RM_28453.WedDec40528162024 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: 1733318895 Database = /scratch/tmp/rModeler.3tvqQn/GCA_029215795.1_rAnnSte1.0.hap2 - Sequences = 91 - Bases = 1891076299 Storage Throughput = fair ( 656.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024531 bp ( 40024531 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:05:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:27 (hh:mm:ss) Elapsed Time Round Time: 00:35:33 (hh:mm:ss) Elapsed Time : 650 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21761 repeats masked totaling 3640875 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008887 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10008887 bp After Masking: 6085710 bp Masked: 39.20 % -- Input Database Coverage: 10008887 bp out of 1891076299 bp ( 0.53 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:05 (hh:mm:ss) Elapsed Time, 12177 HSPs Collected Number of families returned by RECON: 1566 Round Time: 00:08:47 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66857 repeats masked totaling 11473165 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015564 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 30015564 bp After Masking: 18009187 bp Masked: 40.00 % -- Input Database Coverage: 40024451 bp out of 1891076299 bp ( 2.12 % ) Sampling Time: 00:06:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:25:37 (hh:mm:ss) Elapsed Time, 69035 HSPs Collected Number of families returned by RECON: 4899 Round Time: 00:46:35 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:12:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 216250 repeats masked totaling 37782318 bp(s). - TE Masking time 00:02:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004845 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90004745 bp After Masking: 50205865 bp Masked: 44.22 % -- Input Database Coverage: 130029296 bp out of 1891076299 bp ( 6.88 % ) Sampling Time: 00:23:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:42:06 (hh:mm:ss) Elapsed Time, 197995 HSPs Collected Number of families returned by RECON: 13723 Round Time: 03:19:43 (hh:mm:ss) Elapsed Time : 459 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:37:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 727889 repeats masked totaling 127039793 bp(s). - TE Masking time 00:12:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012190 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 270011890 bp After Masking: 137510853 bp Masked: 49.07 % -- Input Database Coverage: 400041486 bp out of 1891076299 bp ( 21.15 % ) Sampling Time: 01:08:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 19:50:35 (hh:mm:ss) Elapsed Time, 590007 HSPs Collected Number of families returned by RECON: 42465 Round Time: 22:30:53 (hh:mm:ss) Elapsed Time : 1124 families discovered. RepeatScout/RECON discovery complete: 2425 families found Classification Time: 01:24:36 (hh:mm:ss) Elapsed Time Program Time: 28:46:07 (hh:mm:ss) Elapsed Time