RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zBzoxN/RM_57831.FriJan121056522024 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: 1705085810 Database = /dev/shm/rModeler.zBzoxN/GCA_947561715.1_kaAscMent1.1 - Sequences = 96 - Bases = 196975169 Storage Throughput = excellent ( 1059.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032948 bp ( 40031948 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:32 (hh:mm:ss) Elapsed Time Round Time: 00:18:52 (hh:mm:ss) Elapsed Time : 640 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7946 repeats masked totaling 1826510 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014587 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10014387 bp After Masking: 7333018 bp Masked: 26.78 % -- Input Database Coverage: 10014587 bp out of 196975169 bp ( 5.08 % ) Sampling Time: 00:00:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:05:43 (hh:mm:ss) Elapsed Time, 3583 HSPs Collected Number of families returned by RECON: 742 Round Time: 00:06:42 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25003 repeats masked totaling 5874033 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018329 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30017529 bp After Masking: 21670361 bp Masked: 27.81 % -- Input Database Coverage: 40032916 bp out of 196975169 bp ( 20.32 % ) Sampling Time: 00:02:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:20:46 (hh:mm:ss) Elapsed Time, 29140 HSPs Collected Number of families returned by RECON: 3341 Round Time: 00:23:35 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 78452 repeats masked totaling 17222836 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004452 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 90001652 bp After Masking: 66432733 bp Masked: 26.19 % -- Input Database Coverage: 130037368 bp out of 196975169 bp ( 66.02 % ) Sampling Time: 00:06:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 04:24:54 (hh:mm:ss) Elapsed Time, 307073 HSPs Collected Number of families returned by RECON: 12356 Round Time: 04:43:40 (hh:mm:ss) Elapsed Time : 386 families discovered. - Increasing sample size to include end piece now = 336942253 RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71420 repeats masked totaling 17232337 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 66937653 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 66935053 bp After Masking: 45503715 bp Masked: 32.02 % -- Input Database Coverage: 196975021 bp out of 196975169 bp ( 100.00 % ) Sampling Time: 00:05:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1437360 Comparison Time: 02:10:29 (hh:mm:ss) Elapsed Time, 67873 HSPs Collected Number of families returned by RECON: 7224 Round Time: 02:19:59 (hh:mm:ss) Elapsed Time : 111 families discovered. RepeatScout/RECON discovery complete: 1197 families found Classification Time: 01:04:52 (hh:mm:ss) Elapsed Time Program Time: 08:57:40 (hh:mm:ss) Elapsed Time