RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SF0WbP/RM_32704.MonJan160720202023 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: 1673882419 Database = /dev/shm/rModeler.SF0WbP/GCF_014108235.1_mMyoMyo1.p - Sequences = 93 - Bases = 2002797769 Storage Throughput = excellent ( 1162.54 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40608351 bp ( 40017522 non ambiguous ) - Num Contigs Represented = 48 - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:54 (hh:mm:ss) Elapsed Time Round Time: 00:30:25 (hh:mm:ss) Elapsed Time : 342 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14002 repeats masked totaling 2718354 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042312 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10001300 bp After Masking: 7105483 bp Masked: 28.95 % -- Input Database Coverage: 10042312 bp out of 2002797769 bp ( 0.50 % ) Sampling Time: 00:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:27 (hh:mm:ss) Elapsed Time, 4982 HSPs Collected Number of families returned by RECON: 811 Round Time: 00:08:08 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44042 repeats masked totaling 8464663 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30566031 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30016214 bp After Masking: 21004645 bp Masked: 30.02 % -- Input Database Coverage: 40608343 bp out of 2002797769 bp ( 2.03 % ) Sampling Time: 00:04:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:32:29 (hh:mm:ss) Elapsed Time, 25036 HSPs Collected Number of families returned by RECON: 2724 Round Time: 00:38:07 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 145908 repeats masked totaling 28248437 bp(s). - TE Masking time 00:01:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91543521 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90016859 bp After Masking: 60159469 bp Masked: 33.17 % -- Input Database Coverage: 132151864 bp out of 2002797769 bp ( 6.60 % ) Sampling Time: 00:11:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2634660 Comparison Time: 03:27:34 (hh:mm:ss) Elapsed Time, 100179 HSPs Collected Number of families returned by RECON: 8205 Round Time: 03:44:16 (hh:mm:ss) Elapsed Time : 209 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 476334 repeats masked totaling 91921518 bp(s). - TE Masking time 00:07:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273635688 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 270011339 bp After Masking: 173127509 bp Masked: 35.88 % -- Input Database Coverage: 405787552 bp out of 2002797769 bp ( 20.26 % ) Sampling Time: 00:38:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23430435 Comparison Time: 26:26:41 (hh:mm:ss) Elapsed Time, 250400 HSPs Collected Number of families returned by RECON: 35583 Round Time: 27:36:51 (hh:mm:ss) Elapsed Time : 443 families discovered. RepeatScout/RECON discovery complete: 1066 families found Classification Time: 00:39:18 (hh:mm:ss) Elapsed Time Program Time: 33:17:05 (hh:mm:ss) Elapsed Time