RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wDFnGm/RM_1241.SatDec90116312023 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: 1702113389 Database = /dev/shm/rModeler.wDFnGm/GCA_951802725.1_fRutRut2.1 - Sequences = 85 - Bases = 1100195650 Storage Throughput = excellent ( 1192.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035599 bp ( 40032599 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:31 (hh:mm:ss) Elapsed Time Round Time: 00:47:10 (hh:mm:ss) Elapsed Time : 1291 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15892 repeats masked totaling 3345212 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002369 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10001369 bp After Masking: 5980203 bp Masked: 40.21 % -- Input Database Coverage: 10002369 bp out of 1100195650 bp ( 0.91 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:39 (hh:mm:ss) Elapsed Time, 21827 HSPs Collected Number of families returned by RECON: 1763 Round Time: 00:08:12 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50586 repeats masked totaling 10306545 bp(s). - TE Masking time 00:01:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033224 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30031224 bp After Masking: 18091002 bp Masked: 39.76 % -- Input Database Coverage: 40035593 bp out of 1100195650 bp ( 3.64 % ) Sampling Time: 00:05:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:29:35 (hh:mm:ss) Elapsed Time, 82422 HSPs Collected Number of families returned by RECON: 6161 Round Time: 00:37:15 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 159019 repeats masked totaling 32538819 bp(s). - TE Masking time 00:04:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031555 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90022755 bp After Masking: 52588214 bp Masked: 41.58 % -- Input Database Coverage: 130067148 bp out of 1100195650 bp ( 11.82 % ) Sampling Time: 00:18:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:19:42 (hh:mm:ss) Elapsed Time, 573925 HSPs Collected Number of families returned by RECON: 17344 Round Time: 03:58:53 (hh:mm:ss) Elapsed Time : 739 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:32:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 562784 repeats masked totaling 117963688 bp(s). - TE Masking time 00:23:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270045830 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 270020153 bp After Masking: 136946271 bp Masked: 49.28 % -- Input Database Coverage: 400112978 bp out of 1100195650 bp ( 36.37 % ) Sampling Time: 01:02:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 22:50:05 (hh:mm:ss) Elapsed Time, 2019699 HSPs Collected Number of families returned by RECON: 45148 Round Time: 25:44:01 (hh:mm:ss) Elapsed Time : 1802 families discovered. RepeatScout/RECON discovery complete: 3988 families found Classification Time: 03:00:38 (hh:mm:ss) Elapsed Time Program Time: 34:16:09 (hh:mm:ss) Elapsed Time