RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ZxDYye/RM_47218.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.ZxDYye/GCA_947034865.1_fBarBar1.1 - Sequences = 100 - Bases = 617663352 Storage Throughput = excellent ( 1528.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020816 bp ( 40010616 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:18 (hh:mm:ss) Elapsed Time Round Time: 00:24:01 (hh:mm:ss) Elapsed Time : 577 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9470 repeats masked totaling 1897411 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008762 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10006362 bp After Masking: 7073643 bp Masked: 29.31 % -- Input Database Coverage: 10008762 bp out of 617663352 bp ( 1.62 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:04 (hh:mm:ss) Elapsed Time, 7985 HSPs Collected Number of families returned by RECON: 1280 Round Time: 00:06:49 (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 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30992 repeats masked totaling 6218215 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012036 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30004236 bp After Masking: 21881366 bp Masked: 27.07 % -- Input Database Coverage: 40020798 bp out of 617663352 bp ( 6.48 % ) Sampling Time: 00:03:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:27:19 (hh:mm:ss) Elapsed Time, 47935 HSPs Collected Number of families returned by RECON: 4646 Round Time: 00:32:11 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102250 repeats masked totaling 20923273 bp(s). - TE Masking time 00:01:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041112 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90018004 bp After Masking: 62675357 bp Masked: 30.37 % -- Input Database Coverage: 130061910 bp out of 617663352 bp ( 21.06 % ) Sampling Time: 00:11:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 03:13:11 (hh:mm:ss) Elapsed Time, 319596 HSPs Collected Number of families returned by RECON: 14237 Round Time: 04:21:14 (hh:mm:ss) Elapsed Time : 538 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 370910 repeats masked totaling 77916830 bp(s). - TE Masking time 00:11:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270110711 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 270036546 bp After Masking: 172019346 bp Masked: 36.30 % -- Input Database Coverage: 400172621 bp out of 617663352 bp ( 64.79 % ) Sampling Time: 00:43:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 22:07:55 (hh:mm:ss) Elapsed Time, 870018 HSPs Collected Number of families returned by RECON: 46291 Round Time: 24:04:10 (hh:mm:ss) Elapsed Time : 1162 families discovered. RepeatScout/RECON discovery complete: 2414 families found Classification Time: 02:15:05 (hh:mm:ss) Elapsed Time Program Time: 31:43:30 (hh:mm:ss) Elapsed Time