RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.rbTdMR/RM_107005.TueMar210940122023 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: 1679416811 Database = /dev/shm/rModeler.rbTdMR/hs1 - Sequences = 25 - Bases = 3117292070 Storage Throughput = excellent ( 1554.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001818 bp ( 40001818 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:16 (hh:mm:ss) Elapsed Time Round Time: 00:18:20 (hh:mm:ss) Elapsed Time : 265 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 00:01:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15305 repeats masked totaling 3261403 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000475 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000475 bp After Masking: 6077032 bp Masked: 39.23 % -- Input Database Coverage: 10000475 bp out of 3117292070 bp ( 0.32 % ) Sampling Time: 00:01:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:08:08 (hh:mm:ss) Elapsed Time, 7012 HSPs Collected Number of families returned by RECON: 758 Round Time: 00:10:15 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45629 repeats masked totaling 9660911 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001342 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30001342 bp After Masking: 18277035 bp Masked: 39.08 % -- Input Database Coverage: 40001817 bp out of 3117292070 bp ( 1.28 % ) Sampling Time: 00:06:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:25:08 (hh:mm:ss) Elapsed Time, 32188 HSPs Collected Number of families returned by RECON: 2305 Round Time: 00:41:35 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 144603 repeats masked totaling 31563693 bp(s). - TE Masking time 00:01:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004132 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90004132 bp After Masking: 51374461 bp Masked: 42.92 % -- Input Database Coverage: 130005949 bp out of 3117292070 bp ( 4.17 % ) Sampling Time: 00:23:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 02:01:01 (hh:mm:ss) Elapsed Time, 101423 HSPs Collected Number of families returned by RECON: 7957 Round Time: 02:36:18 (hh:mm:ss) Elapsed Time : 179 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:48:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 475812 repeats masked totaling 104905295 bp(s). - TE Masking time 00:04:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014492 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 270014492 bp After Masking: 144942351 bp Masked: 46.32 % -- Input Database Coverage: 400020441 bp out of 3117292070 bp ( 12.83 % ) Sampling Time: 01:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22784625 Comparison Time: 11:28:25 (hh:mm:ss) Elapsed Time, 281919 HSPs Collected Number of families returned by RECON: 29702 Round Time: 12:44:12 (hh:mm:ss) Elapsed Time : 373 families discovered. RepeatScout/RECON discovery complete: 904 families found Classification Time: 00:28:30 (hh:mm:ss) Elapsed Time Program Time: 16:59:10 (hh:mm:ss) Elapsed Time