RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.CduDYe/RM_77403.SatDec312247282022 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: 1672555647 Database = /dev/shm/rModeler.CduDYe/GCF_009829125.1_fPerMag1.pri - Sequences = 124 - Bases = 752621858 - N50 = 33436419 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34523101-36988977 |*** [ 6 ] 32057225-34523100 |*** [ 7 ] 29591349-32057224 |* [ 3 ] 27125473-29591348 |** [ 5 ] 24659597-27125472 | [ ] 22193721-24659596 | [ 1 ] 19727845-22193720 | [ ] 17261969-19727844 |* [ 2 ] 14796093-17261968 | [ ] 12330217-14796092 | [ ] 9864341-12330216 | [ ] 7398465-9864340 | [ ] 4932589-7398464 | [ ] 2466713-4932588 | [ ] 838-2466713 |************************************************** [ 100 ] Storage Throughput = excellent ( 1022.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40301209 bp ( 40018840 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:20 (hh:mm:ss) Elapsed Time Round Time: 00:19:49 (hh:mm:ss) Elapsed Time : 656 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 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21457 repeats masked totaling 3161100 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10071863 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10003078 bp After Masking: 6341842 bp Masked: 36.60 % -- Input Database Coverage: 10071863 bp out of 752621858 bp ( 1.34 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:39 (hh:mm:ss) Elapsed Time, 4615 HSPs Collected Number of families returned by RECON: 956 Round Time: 00:07:15 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64623 repeats masked totaling 9695288 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30229322 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30015738 bp After Masking: 18530072 bp Masked: 38.27 % -- Input Database Coverage: 40301185 bp out of 752621858 bp ( 5.35 % ) Sampling Time: 00:04:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:26:19 (hh:mm:ss) Elapsed Time, 34247 HSPs Collected Number of families returned by RECON: 3432 Round Time: 00:32:03 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 202081 repeats masked totaling 29947970 bp(s). - TE Masking time 00:01:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91278258 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90003410 bp After Masking: 55001660 bp Masked: 38.89 % -- Input Database Coverage: 131579443 bp out of 752621858 bp ( 17.48 % ) Sampling Time: 00:14:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2616328 Comparison Time: 02:51:19 (hh:mm:ss) Elapsed Time, 158789 HSPs Collected Number of families returned by RECON: 11230 Round Time: 03:12:52 (hh:mm:ss) Elapsed Time : 379 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 664982 repeats masked totaling 98832971 bp(s). - TE Masking time 00:08:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272553709 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 270034299 bp After Masking: 156338309 bp Masked: 42.10 % -- Input Database Coverage: 404133152 bp out of 752621858 bp ( 53.70 % ) Sampling Time: 00:48:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23423590 Comparison Time: 22:27:00 (hh:mm:ss) Elapsed Time, 441235 HSPs Collected Number of families returned by RECON: 40368 Round Time: 24:20:45 (hh:mm:ss) Elapsed Time : 816 families discovered. RepeatScout/RECON discovery complete: 1966 families found Classification Time: 01:27:43 (hh:mm:ss) Elapsed Time Program Time: 30:00:27 (hh:mm:ss) Elapsed Time