RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.67i5DP/RM_1343856.SunNov171553522024 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: 1731887631 Database = /scratch/tmp/rModeler.67i5DP/GCA_037038545.1_mRhyNas2.hap1 - Sequences = 41 - Bases = 2455066473 Storage Throughput = excellent ( 1248.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005814 bp ( 40005614 non ambiguous ) - Num Contigs Represented = 12 - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:14 (hh:mm:ss) Elapsed Time Round Time: 00:14:12 (hh:mm:ss) Elapsed Time : 255 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9971 repeats masked totaling 3178368 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000123 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10000123 bp After Masking: 6743275 bp Masked: 32.57 % -- Input Database Coverage: 10000123 bp out of 2455066473 bp ( 0.41 % ) Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:07 (hh:mm:ss) Elapsed Time, 11928 HSPs Collected Number of families returned by RECON: 842 Round Time: 00:04:14 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33165 repeats masked totaling 10387461 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005611 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 30005411 bp After Masking: 19428320 bp Masked: 35.25 % -- Input Database Coverage: 40005734 bp out of 2455066473 bp ( 1.63 % ) Sampling Time: 00:02:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:14:52 (hh:mm:ss) Elapsed Time, 37668 HSPs Collected Number of families returned by RECON: 1920 Round Time: 00:18:14 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 106827 repeats masked totaling 32927274 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90001901 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 90001501 bp After Masking: 56481034 bp Masked: 37.24 % -- Input Database Coverage: 130007635 bp out of 2455066473 bp ( 5.30 % ) Sampling Time: 00:08:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 01:28:58 (hh:mm:ss) Elapsed Time, 473228 HSPs Collected Number of families returned by RECON: 6612 Round Time: 01:38:51 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 347537 repeats masked totaling 104953645 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032091 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 270030191 bp After Masking: 163324050 bp Masked: 39.52 % -- Input Database Coverage: 400039726 bp out of 2455066473 bp ( 16.29 % ) Sampling Time: 00:25:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 08:56:32 (hh:mm:ss) Elapsed Time, 3197616 HSPs Collected Number of families returned by RECON: 29173 Round Time: 09:30:47 (hh:mm:ss) Elapsed Time : 343 families discovered. RepeatScout/RECON discovery complete: 833 families found Classification Time: 00:17:54 (hh:mm:ss) Elapsed Time Program Time: 12:04:13 (hh:mm:ss) Elapsed Time