RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VcPmJP/RM_47215.FriDec301411462022 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: 1672438306 Database = /dev/shm/rModeler.VcPmJP/GCF_017976425.1_fToxJac2.pri - Sequences = 96 - Bases = 621503431 Storage Throughput = excellent ( 1205.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40075661 bp ( 40016424 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:13 (hh:mm:ss) Elapsed Time Round Time: 00:53:18 (hh:mm:ss) Elapsed Time : 211 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3915 repeats masked totaling 592790 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022106 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10022106 bp After Masking: 8664637 bp Masked: 13.54 % -- Input Database Coverage: 10022106 bp out of 621503431 bp ( 1.61 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:27 (hh:mm:ss) Elapsed Time, 20895 HSPs Collected Number of families returned by RECON: 1367 Round Time: 00:09:17 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13906 repeats masked totaling 2013510 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30093540 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30034303 bp After Masking: 25820097 bp Masked: 14.03 % -- Input Database Coverage: 40115646 bp out of 621503431 bp ( 6.45 % ) Sampling Time: 00:08:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:35:48 (hh:mm:ss) Elapsed Time, 72576 HSPs Collected Number of families returned by RECON: 5547 Round Time: 00:45:56 (hh:mm:ss) Elapsed Time : 90 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50687 repeats masked totaling 7490578 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90195209 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90016165 bp After Masking: 75942691 bp Masked: 15.63 % -- Input Database Coverage: 130310855 bp out of 621503431 bp ( 20.97 % ) Sampling Time: 00:22:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 04:00:26 (hh:mm:ss) Elapsed Time, 261156 HSPs Collected Number of families returned by RECON: 21716 Round Time: 04:44:27 (hh:mm:ss) Elapsed Time : 315 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:06:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 212019 repeats masked totaling 34534033 bp(s). - TE Masking time 00:09:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270472630 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270006475 bp After Masking: 214423063 bp Masked: 20.59 % -- Input Database Coverage: 400783485 bp out of 621503431 bp ( 64.49 % ) Sampling Time: 01:19:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 29:23:52 (hh:mm:ss) Elapsed Time, 811895 HSPs Collected Number of families returned by RECON: 90301 Round Time: 33:33:46 (hh:mm:ss) Elapsed Time : 873 families discovered. RepeatScout/RECON discovery complete: 1501 families found Classification Time: 01:26:11 (hh:mm:ss) Elapsed Time Program Time: 41:32:55 (hh:mm:ss) Elapsed Time