RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Dfnpep/RM_744323.SatDec20227302023 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: 1701512849 Database = /dev/shm/rModeler.Dfnpep/GCF_027579445.1_bAmmNel1.pri - Sequences = 77 - Bases = 1185463352 Storage Throughput = excellent ( 1316.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40289679 bp ( 40032754 non ambiguous ) - Num Contigs Represented = 59 - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:11 (hh:mm:ss) Elapsed Time Round Time: 00:21:27 (hh:mm:ss) Elapsed Time : 180 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3179 repeats masked totaling 837563 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10082057 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10032323 bp After Masking: 8125804 bp Masked: 19.00 % -- Input Database Coverage: 10082057 bp out of 1185463352 bp ( 0.85 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:22 (hh:mm:ss) Elapsed Time, 1137 HSPs Collected Number of families returned by RECON: 329 Round Time: 00:08:06 (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 : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9705 repeats masked totaling 2668660 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30207619 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 30000428 bp After Masking: 25247759 bp Masked: 15.84 % -- Input Database Coverage: 40289676 bp out of 1185463352 bp ( 3.40 % ) Sampling Time: 00:03:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:32:50 (hh:mm:ss) Elapsed Time, 10667 HSPs Collected Number of families returned by RECON: 1749 Round Time: 00:37:23 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30409 repeats masked totaling 8352693 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90379749 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 90016515 bp After Masking: 74716217 bp Masked: 17.00 % -- Input Database Coverage: 130669425 bp out of 1185463352 bp ( 11.02 % ) Sampling Time: 00:11:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:35:50 (hh:mm:ss) Elapsed Time, 82876 HSPs Collected Number of families returned by RECON: 10884 Round Time: 03:51:42 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 98618 repeats masked totaling 28973711 bp(s). - TE Masking time 00:05:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270970372 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 270011226 bp After Masking: 220327329 bp Masked: 18.40 % -- Input Database Coverage: 401639797 bp out of 1185463352 bp ( 33.88 % ) Sampling Time: 00:37:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 29:00:53 (hh:mm:ss) Elapsed Time, 244231 HSPs Collected Number of families returned by RECON: 70076 Round Time: 30:31:27 (hh:mm:ss) Elapsed Time : 300 families discovered. RepeatScout/RECON discovery complete: 612 families found Classification Time: 00:41:35 (hh:mm:ss) Elapsed Time Program Time: 36:11:40 (hh:mm:ss) Elapsed Time