RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.HB4fbo/RM_3048716.FriJul181028512025 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: 1752859730 Database = /dev/shm/rModeler.HB4fbo/GCA_048129085.1_fCenGer3.hap2.cur.20231027 - Sequences = 204 - Bases = 774057239 - N50 = 31787880 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35482226-38015964 |* [ 4 ] 32948489-35482226 |* [ 6 ] 30414752-32948489 |* [ 6 ] 27881015-30414752 | [ 3 ] 25347278-27881015 | [ 1 ] 22813540-25347277 |* [ 4 ] 20279803-22813540 | [ ] 17746066-20279803 | [ ] 15212329-17746066 | [ ] 12678592-15212329 | [ ] 10144854-12678591 | [ ] 7611117-10144854 | [ ] 5077380-7611117 | [ 1 ] 2543643-5077380 | [ ] 9906-2543643 |************************************************** [ 179 ] Storage Throughput = excellent ( 1174.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011420 bp ( 40005620 non ambiguous ) - Num Contigs Represented = 49 - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:10 (hh:mm:ss) Elapsed Time Round Time: 00:31:45 (hh:mm:ss) Elapsed Time : 682 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11511 repeats masked totaling 1419564 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006734 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10005934 bp After Masking: 7907999 bp Masked: 20.97 % -- Input Database Coverage: 10006734 bp out of 774057239 bp ( 1.29 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:21 (hh:mm:ss) Elapsed Time, 9547 HSPs Collected Number of families returned by RECON: 1983 Round Time: 00:07:04 (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 : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35031 repeats masked totaling 4649351 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30045169 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30040169 bp After Masking: 22946936 bp Masked: 23.61 % -- Input Database Coverage: 40051903 bp out of 774057239 bp ( 5.17 % ) Sampling Time: 00:04:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:30:51 (hh:mm:ss) Elapsed Time, 65263 HSPs Collected Number of families returned by RECON: 7080 Round Time: 00:38:19 (hh:mm:ss) Elapsed Time : 155 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118894 repeats masked totaling 16005246 bp(s). - TE Masking time 00:02:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023093 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 90009493 bp After Masking: 66413774 bp Masked: 26.21 % -- Input Database Coverage: 130074996 bp out of 774057239 bp ( 16.80 % ) Sampling Time: 00:14:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:46:45 (hh:mm:ss) Elapsed Time, 339447 HSPs Collected Number of families returned by RECON: 22506 Round Time: 04:22:34 (hh:mm:ss) Elapsed Time : 628 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 449040 repeats masked totaling 64817020 bp(s). - TE Masking time 00:13:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062370 bp Num Contigs Represented = 120 Non ambiguous bp: Initial: 270016834 bp After Masking: 182317004 bp Masked: 32.48 % -- Input Database Coverage: 400137366 bp out of 774057239 bp ( 51.69 % ) Sampling Time: 00:50:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 28:32:07 (hh:mm:ss) Elapsed Time, 1083815 HSPs Collected Number of families returned by RECON: 72959 Round Time: 32:24:21 (hh:mm:ss) Elapsed Time : 1514 families discovered. RepeatScout/RECON discovery complete: 2996 families found Classification Time: 01:56:23 (hh:mm:ss) Elapsed Time Program Time: 40:00:26 (hh:mm:ss) Elapsed Time