RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6smeqi/RM_2513813.SatJul60756572024 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: 1720277817 Database = /dev/shm/rModeler.6smeqi/GCF_033978795.1_RoL_Noph_v1.0 - Sequences = 473 - Bases = 1845757181 - N50 = 69978453 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 86891772-93097911 | [ 3 ] 80685633-86891771 | [ 2 ] 74479494-80685632 | [ 4 ] 68273355-74479493 | [ 2 ] 62067217-68273355 | [ 2 ] 55861078-62067216 | [ 1 ] 49654939-55861077 | [ 4 ] 43448800-49654938 | [ 4 ] 37242661-43448799 | [ 4 ] 31036523-37242661 | [ 3 ] 24830384-31036522 | [ ] 18624245-24830383 | [ ] 12418106-18624244 | [ ] 6211967-12418105 | [ ] 5829-6211967 |************************************************* [ 444 ] Storage Throughput = excellent ( 1421.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015095 bp ( 40014515 non ambiguous ) - Num Contigs Represented = 76 - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:07 (hh:mm:ss) Elapsed Time Round Time: 00:55:12 (hh:mm:ss) Elapsed Time : 1035 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24059 repeats masked totaling 5691291 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029218 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10029138 bp After Masking: 2948076 bp Masked: 70.60 % -- Input Database Coverage: 10029218 bp out of 1845757181 bp ( 0.54 % ) Sampling Time: 00:02:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:16 (hh:mm:ss) Elapsed Time, 17358 HSPs Collected Number of families returned by RECON: 1017 Round Time: 00:07:40 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75721 repeats masked totaling 17431162 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025950 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30025450 bp After Masking: 8682319 bp Masked: 71.08 % -- Input Database Coverage: 40055168 bp out of 1845757181 bp ( 2.17 % ) Sampling Time: 00:09:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:18:10 (hh:mm:ss) Elapsed Time, 53846 HSPs Collected Number of families returned by RECON: 2924 Round Time: 00:28:17 (hh:mm:ss) Elapsed Time : 140 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 235124 repeats masked totaling 53504890 bp(s). - TE Masking time 00:02:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037620 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 90036340 bp After Masking: 23996105 bp Masked: 73.35 % -- Input Database Coverage: 130092788 bp out of 1845757181 bp ( 7.05 % ) Sampling Time: 00:26:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:31:04 (hh:mm:ss) Elapsed Time, 211239 HSPs Collected Number of families returned by RECON: 6895 Round Time: 02:01:56 (hh:mm:ss) Elapsed Time : 426 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:59:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 770067 repeats masked totaling 171720230 bp(s). - TE Masking time 00:11:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038379 bp Num Contigs Represented = 236 Non ambiguous bp: Initial: 270035239 bp After Masking: 62359337 bp Masked: 76.91 % -- Input Database Coverage: 400131167 bp out of 1845757181 bp ( 21.68 % ) Sampling Time: 01:18:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 09:03:54 (hh:mm:ss) Elapsed Time, 418719 HSPs Collected Number of families returned by RECON: 18321 Round Time: 10:42:02 (hh:mm:ss) Elapsed Time : 885 families discovered. RepeatScout/RECON discovery complete: 2508 families found Classification Time: 01:27:36 (hh:mm:ss) Elapsed Time Program Time: 15:42:43 (hh:mm:ss) Elapsed Time