RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VN3Vno/RM_9069.WedJan101934212024 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: 1704944061 Database = /dev/shm/rModeler.VN3Vno/GCA_019207075.1_Bb-hap - Sequences = 79 - Bases = 405532174 Storage Throughput = excellent ( 1170.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40088805 bp ( 40019288 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:58 (hh:mm:ss) Elapsed Time Round Time: 00:24:08 (hh:mm:ss) Elapsed Time : 747 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15626 repeats masked totaling 2361933 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042725 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10026102 bp After Masking: 6996884 bp Masked: 30.21 % -- Input Database Coverage: 10042725 bp out of 405532174 bp ( 2.48 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 5298 HSPs Collected Number of families returned by RECON: 1203 Round Time: 00:06:41 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46376 repeats masked totaling 7003045 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30086080 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30033186 bp After Masking: 21519859 bp Masked: 28.35 % -- Input Database Coverage: 40128805 bp out of 405532174 bp ( 9.90 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:26:08 (hh:mm:ss) Elapsed Time, 39842 HSPs Collected Number of families returned by RECON: 4469 Round Time: 00:31:02 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 145672 repeats masked totaling 21596669 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90178795 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90037176 bp After Masking: 63511880 bp Masked: 29.46 % -- Input Database Coverage: 130307600 bp out of 405532174 bp ( 32.13 % ) Sampling Time: 00:10:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 03:00:32 (hh:mm:ss) Elapsed Time, 309102 HSPs Collected Number of families returned by RECON: 15389 Round Time: 03:24:51 (hh:mm:ss) Elapsed Time : 489 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 492091 repeats masked totaling 77565426 bp(s). - TE Masking time 00:11:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270310793 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 270031900 bp After Masking: 177770441 bp Masked: 34.17 % -- Input Database Coverage: 400618393 bp out of 405532174 bp ( 98.79 % ) Sampling Time: 00:40:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 23:09:28 (hh:mm:ss) Elapsed Time, 1215086 HSPs Collected Number of families returned by RECON: 53151 Round Time: 25:44:30 (hh:mm:ss) Elapsed Time : 1297 families discovered. RepeatScout/RECON discovery complete: 2624 families found Classification Time: 02:09:40 (hh:mm:ss) Elapsed Time Program Time: 32:20:52 (hh:mm:ss) Elapsed Time