RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.v7lmb2/RM_2207473.ThuApr241046352025 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: 1745516793 Database = /data/tmp/rModeler.v7lmb2/GCA_048338725.1_T2T_pig1.0 - Sequences = 20 - Bases = 2633166191 Storage Throughput = excellent ( 1250.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001075 bp ( 40001075 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:26 (hh:mm:ss) Elapsed Time Round Time: 00:16:16 (hh:mm:ss) Elapsed Time : 182 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 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13861 repeats masked totaling 2657350 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000186 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10000186 bp After Masking: 7118930 bp Masked: 28.81 % -- Input Database Coverage: 10000186 bp out of 2633166191 bp ( 0.38 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:19 (hh:mm:ss) Elapsed Time, 18099 HSPs Collected Number of families returned by RECON: 763 Round Time: 00:04:11 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45495 repeats masked totaling 8838577 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000809 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30000809 bp After Masking: 20146953 bp Masked: 32.85 % -- Input Database Coverage: 40000995 bp out of 2633166191 bp ( 1.52 % ) Sampling Time: 00:01:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:14:50 (hh:mm:ss) Elapsed Time, 31573 HSPs Collected Number of families returned by RECON: 2269 Round Time: 00:17:11 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143024 repeats masked totaling 28043771 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90002583 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 90002583 bp After Masking: 58013159 bp Masked: 35.54 % -- Input Database Coverage: 130003578 bp out of 2633166191 bp ( 4.94 % ) Sampling Time: 00:07:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 01:56:19 (hh:mm:ss) Elapsed Time, 499757 HSPs Collected Number of families returned by RECON: 8221 Round Time: 02:05:38 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:04 (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... 473930 repeats masked totaling 93722535 bp(s). - TE Masking time 00:03:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028262 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 270028262 bp After Masking: 165023396 bp Masked: 38.89 % -- Input Database Coverage: 400031840 bp out of 2633166191 bp ( 15.19 % ) Sampling Time: 00:24:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22784625 Comparison Time: 15:15:19 (hh:mm:ss) Elapsed Time, 4947085 HSPs Collected Number of families returned by RECON: 32049 Round Time: 15:56:23 (hh:mm:ss) Elapsed Time : 302 families discovered. RepeatScout/RECON discovery complete: 729 families found Classification Time: 00:19:00 (hh:mm:ss) Elapsed Time Program Time: 18:58:39 (hh:mm:ss) Elapsed Time