RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.g9LhvX/RM_405650.WedMay101030222023 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: 1683739821 Database = /dev/shm/rModeler.g9LhvX/GCA_027579445.1_bAmmNel1.pri - Sequences = 77 - Bases = 1185463352 Storage Throughput = excellent ( 1208.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40115362 bp ( 40025110 non ambiguous ) - Num Contigs Represented = 62 - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:51 (hh:mm:ss) Elapsed Time Round Time: 00:25:35 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3031 repeats masked totaling 840874 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10082340 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10037185 bp After Masking: 8388137 bp Masked: 16.43 % -- Input Database Coverage: 10082340 bp out of 1185463352 bp ( 0.85 % ) Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:43 (hh:mm:ss) Elapsed Time, 892 HSPs Collected Number of families returned by RECON: 332 Round Time: 00:09:11 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8641 repeats masked totaling 2395628 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30073022 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30027925 bp After Masking: 24890983 bp Masked: 17.11 % -- Input Database Coverage: 40155362 bp out of 1185463352 bp ( 3.39 % ) Sampling Time: 00:03:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:36:20 (hh:mm:ss) Elapsed Time, 14786 HSPs Collected Number of families returned by RECON: 1818 Round Time: 00:40:08 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27423 repeats masked totaling 7777098 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90285422 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 90016600 bp After Masking: 75821596 bp Masked: 15.77 % -- Input Database Coverage: 130440784 bp out of 1185463352 bp ( 11.00 % ) Sampling Time: 00:10:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 03:55:59 (hh:mm:ss) Elapsed Time, 72514 HSPs Collected Number of families returned by RECON: 10792 Round Time: 04:11:38 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 94680 repeats masked totaling 29142282 bp(s). - TE Masking time 00:04:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271326926 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 270025754 bp After Masking: 220280072 bp Masked: 18.42 % -- Input Database Coverage: 401767710 bp out of 1185463352 bp ( 33.89 % ) Sampling Time: 00:37:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23028291 Comparison Time: 30:42:44 (hh:mm:ss) Elapsed Time, 443393 HSPs Collected Number of families returned by RECON: 70432 Round Time: 32:33:26 (hh:mm:ss) Elapsed Time : 290 families discovered. RepeatScout/RECON discovery complete: 573 families found Classification Time: 00:48:38 (hh:mm:ss) Elapsed Time Program Time: 38:48:36 (hh:mm:ss) Elapsed Time