RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ukwluL/RM_3634624.TueNov281747592023 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: 1701222478 Database = /dev/shm/rModeler.ukwluL/GCF_030435805.1_mMusLut2.pri - Sequences = 25 - Bases = 2586268927 Storage Throughput = excellent ( 1202.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002332 bp ( 40002332 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:03:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:45 (hh:mm:ss) Elapsed Time Round Time: 00:27:43 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12348 repeats masked totaling 2939988 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000263 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10000263 bp After Masking: 7018682 bp Masked: 29.82 % -- Input Database Coverage: 10000263 bp out of 2586268927 bp ( 0.39 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:53 (hh:mm:ss) Elapsed Time, 4924 HSPs Collected Number of families returned by RECON: 745 Round Time: 00:07:30 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39440 repeats masked totaling 9282880 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002067 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30002067 bp After Masking: 20590425 bp Masked: 31.37 % -- Input Database Coverage: 40002330 bp out of 2586268927 bp ( 1.55 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:27:40 (hh:mm:ss) Elapsed Time, 32837 HSPs Collected Number of families returned by RECON: 2347 Round Time: 00:33:55 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 129379 repeats masked totaling 31012329 bp(s). - TE Masking time 00:01:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004022 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90003822 bp After Masking: 58601346 bp Masked: 34.89 % -- Input Database Coverage: 130006352 bp out of 2586268927 bp ( 5.03 % ) Sampling Time: 00:12:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 02:47:27 (hh:mm:ss) Elapsed Time, 80100 HSPs Collected Number of families returned by RECON: 8825 Round Time: 03:03:24 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 430976 repeats masked totaling 100311740 bp(s). - TE Masking time 00:06:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270013631 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 270012431 bp After Masking: 168487217 bp Masked: 37.60 % -- Input Database Coverage: 400019983 bp out of 2586268927 bp ( 15.47 % ) Sampling Time: 00:37:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22777875 Comparison Time: 20:08:24 (hh:mm:ss) Elapsed Time, 186362 HSPs Collected Number of families returned by RECON: 34400 Round Time: 21:06:01 (hh:mm:ss) Elapsed Time : 347 families discovered. RepeatScout/RECON discovery complete: 763 families found Classification Time: 00:37:40 (hh:mm:ss) Elapsed Time Program Time: 25:56:13 (hh:mm:ss) Elapsed Time