RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mil7Yn/RM_3628695.WedDec181103292024 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: 1734548607 Database = /dev/shm/rModeler.mil7Yn/GCA_039877575.1_fChaTrf1.hap2 - Sequences = 71 - Bases = 664933391 Storage Throughput = fair ( 456.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001365 bp ( 40000765 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:01:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:36:09 (hh:mm:ss) Elapsed Time Round Time: 00:47:09 (hh:mm:ss) Elapsed Time : 346 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5661 repeats masked totaling 943472 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031492 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10031492 bp After Masking: 8670768 bp Masked: 13.56 % -- Input Database Coverage: 10031492 bp out of 664933391 bp ( 1.51 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:12:23 (hh:mm:ss) Elapsed Time, 9857 HSPs Collected Number of families returned by RECON: 1526 Round Time: 00:14:18 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19702 repeats masked totaling 3040443 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009793 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30009193 bp After Masking: 25735307 bp Masked: 14.24 % -- Input Database Coverage: 40041285 bp out of 664933391 bp ( 6.02 % ) Sampling Time: 00:05:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 01:20:23 (hh:mm:ss) Elapsed Time, 49161 HSPs Collected Number of families returned by RECON: 5611 Round Time: 01:27:42 (hh:mm:ss) Elapsed Time : 102 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 70815 repeats masked totaling 11381735 bp(s). - TE Masking time 00:04:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90002678 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 90001478 bp After Masking: 75742210 bp Masked: 15.84 % -- Input Database Coverage: 130043963 bp out of 664933391 bp ( 19.56 % ) Sampling Time: 00:14:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 09:50:50 (hh:mm:ss) Elapsed Time, 264726 HSPs Collected Number of families returned by RECON: 21563 Round Time: 10:28:45 (hh:mm:ss) Elapsed Time : 446 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 278636 repeats masked totaling 46364499 bp(s). - TE Masking time 00:25:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032665 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 270029165 bp After Masking: 214404876 bp Masked: 20.60 % -- Input Database Coverage: 400076628 bp out of 664933391 bp ( 60.17 % ) Sampling Time: 01:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22865703 Comparison Time: 82:17:08 (hh:mm:ss) Elapsed Time, 875734 HSPs Collected Number of families returned by RECON: 81857 Round Time: 86:59:55 (hh:mm:ss) Elapsed Time : 1126 families discovered. RepeatScout/RECON discovery complete: 2041 families found Classification Time: 03:05:45 (hh:mm:ss) Elapsed Time Program Time: 103:03:34 (hh:mm:ss) Elapsed Time