RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KKaPWU/RM_14216.SatMay251149572024 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: 1716662996 Database = /dev/shm/rModeler.KKaPWU/GCA_963969265.1_fRhaChi2.1 - Sequences = 82 - Bases = 921184210 Storage Throughput = excellent ( 1124.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027999 bp ( 40022799 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:54 (hh:mm:ss) Elapsed Time Round Time: 00:28:15 (hh:mm:ss) Elapsed Time : 619 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9567 repeats masked totaling 2392979 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012887 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10011687 bp After Masking: 7328358 bp Masked: 26.80 % -- Input Database Coverage: 10012887 bp out of 921184210 bp ( 1.09 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 9447 HSPs Collected Number of families returned by RECON: 1183 Round Time: 00:06:56 (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 : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31050 repeats masked totaling 7864662 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015032 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30011032 bp After Masking: 21398670 bp Masked: 28.70 % -- Input Database Coverage: 40027919 bp out of 921184210 bp ( 4.35 % ) Sampling Time: 00:03:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:55 (hh:mm:ss) Elapsed Time, 62049 HSPs Collected Number of families returned by RECON: 4257 Round Time: 00:33:39 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100025 repeats masked totaling 23869863 bp(s). - TE Masking time 00:02:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008698 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90001664 bp After Masking: 63040756 bp Masked: 29.96 % -- Input Database Coverage: 130036617 bp out of 921184210 bp ( 14.12 % ) Sampling Time: 00:10:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:28:30 (hh:mm:ss) Elapsed Time, 938866 HSPs Collected Number of families returned by RECON: 13468 Round Time: 03:51:28 (hh:mm:ss) Elapsed Time : 396 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:48:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 357398 repeats masked totaling 85626626 bp(s). - TE Masking time 00:14:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270057164 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 270030764 bp After Masking: 176149644 bp Masked: 34.77 % -- Input Database Coverage: 400093781 bp out of 921184210 bp ( 43.43 % ) Sampling Time: 01:09:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 26:32:29 (hh:mm:ss) Elapsed Time, 3920174 HSPs Collected Number of families returned by RECON: 48359 Round Time: 29:08:12 (hh:mm:ss) Elapsed Time : 1078 families discovered. RepeatScout/RECON discovery complete: 2209 families found Classification Time: 02:12:25 (hh:mm:ss) Elapsed Time Program Time: 36:20:55 (hh:mm:ss) Elapsed Time