RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.sdraDf/RM_3953376.WedMar130345452024 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: 1710326744 Database = /dev/shm/rModeler.sdraDf/GCA_035083965.1_klBraLanc5.hap2 - Sequences = 34 - Bases = 458287516 Storage Throughput = excellent ( 1348.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019847 bp ( 40019147 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:53 (hh:mm:ss) Elapsed Time Round Time: 00:20:24 (hh:mm:ss) Elapsed Time : 815 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 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14510 repeats masked totaling 2440290 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024571 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10024571 bp After Masking: 6933679 bp Masked: 30.83 % -- Input Database Coverage: 10024571 bp out of 458287516 bp ( 2.19 % ) Sampling Time: 00:02:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 5852 HSPs Collected Number of families returned by RECON: 1088 Round Time: 00:07:49 (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 : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42883 repeats masked totaling 7221556 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035276 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30034576 bp After Masking: 20994173 bp Masked: 30.10 % -- Input Database Coverage: 40059847 bp out of 458287516 bp ( 8.74 % ) Sampling Time: 00:03:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:24:37 (hh:mm:ss) Elapsed Time, 39267 HSPs Collected Number of families returned by RECON: 4440 Round Time: 00:28:46 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 132802 repeats masked totaling 21844778 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90031179 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 90028079 bp After Masking: 63263927 bp Masked: 29.73 % -- Input Database Coverage: 130091026 bp out of 458287516 bp ( 28.39 % ) Sampling Time: 00:07:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 02:49:20 (hh:mm:ss) Elapsed Time, 281289 HSPs Collected Number of families returned by RECON: 14613 Round Time: 03:05:52 (hh:mm:ss) Elapsed Time : 453 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 450088 repeats masked totaling 77270629 bp(s). - TE Masking time 00:08:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028868 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 270019468 bp After Masking: 177811095 bp Masked: 34.15 % -- Input Database Coverage: 400119894 bp out of 458287516 bp ( 87.31 % ) Sampling Time: 00:28:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 18:22:09 (hh:mm:ss) Elapsed Time, 1054091 HSPs Collected Number of families returned by RECON: 49514 Round Time: 19:58:14 (hh:mm:ss) Elapsed Time : 1251 families discovered. RepeatScout/RECON discovery complete: 2597 families found Classification Time: 01:53:12 (hh:mm:ss) Elapsed Time Program Time: 25:54:17 (hh:mm:ss) Elapsed Time