RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.5GjI2q/RM_12023.ThuNov142211112024 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: 1731651070 Database = /scratch/tmp/rModeler.5GjI2q/GCA_030440675.1_ASM3044067v1 - Sequences = 11 - Bases = 1609777135 Storage Throughput = fair ( 586.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000538 bp ( 40000538 non ambiguous ) - Num Contigs Represented = 11 - Sequence extraction : 00:03:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:14 (hh:mm:ss) Elapsed Time Round Time: 00:29:19 (hh:mm:ss) Elapsed Time : 669 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:59 (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... 21575 repeats masked totaling 3781367 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000188 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 10000188 bp After Masking: 6092352 bp Masked: 39.08 % -- Input Database Coverage: 10000188 bp out of 1609777135 bp ( 0.62 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:05 (hh:mm:ss) Elapsed Time, 5285 HSPs Collected Number of families returned by RECON: 1094 Round Time: 00:06:57 (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 : 00:02:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67263 repeats masked totaling 11813154 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000348 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 30000348 bp After Masking: 17783951 bp Masked: 40.72 % -- Input Database Coverage: 40000536 bp out of 1609777135 bp ( 2.48 % ) Sampling Time: 00:04:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:25:56 (hh:mm:ss) Elapsed Time, 40838 HSPs Collected Number of families returned by RECON: 3700 Round Time: 00:32:31 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 215947 repeats masked totaling 37697646 bp(s). - TE Masking time 00:02:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90001320 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 90001320 bp After Masking: 51075642 bp Masked: 43.25 % -- Input Database Coverage: 130001856 bp out of 1609777135 bp ( 8.08 % ) Sampling Time: 00:14:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 02:53:00 (hh:mm:ss) Elapsed Time, 195629 HSPs Collected Number of families returned by RECON: 10987 Round Time: 03:18:14 (hh:mm:ss) Elapsed Time : 405 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:25:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 717232 repeats masked totaling 124860681 bp(s). - TE Masking time 00:11:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270003962 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 270000939 bp After Masking: 141450155 bp Masked: 47.61 % -- Input Database Coverage: 400005818 bp out of 1609777135 bp ( 24.85 % ) Sampling Time: 00:46:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22777875 Comparison Time: 21:33:22 (hh:mm:ss) Elapsed Time, 431337 HSPs Collected Number of families returned by RECON: 34879 Round Time: 23:25:38 (hh:mm:ss) Elapsed Time : 856 families discovered. RepeatScout/RECON discovery complete: 2045 families found Classification Time: 01:10:06 (hh:mm:ss) Elapsed Time Program Time: 29:02:45 (hh:mm:ss) Elapsed Time