RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GYjrfi/RM_17444.FriJul262118002024 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: 1722053870 Database = /dev/shm/rModeler.GYjrfi/GCF_019802595.1_ASM1980259v1 - Sequences = 143 - Bases = 636535704 - N50 = 32634731 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 41304983-44255145 | [ 1 ] 38354821-41304982 | [ 1 ] 35404660-38354821 | [ 1 ] 32454498-35404659 |** [ 5 ] 29504336-32454497 |* [ 3 ] 26554175-29504336 | [ 2 ] 23604013-26554174 |* [ 3 ] 20653851-23604012 | [ 1 ] 17703690-20653851 |* [ 3 ] 14753528-17703689 | [ 2 ] 11803366-14753527 | [ ] 8853205-11803366 | [ ] 5903043-8853204 | [ 1 ] 2952881-5903042 | [ ] 2720-2952881 |************************************************** [ 120 ] Storage Throughput = excellent ( 1042.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015597 bp ( 40014697 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:30 (hh:mm:ss) Elapsed Time Round Time: 00:36:05 (hh:mm:ss) Elapsed Time : 582 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16332 repeats masked totaling 3579418 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001198 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000998 bp After Masking: 6307857 bp Masked: 36.93 % -- Input Database Coverage: 10001198 bp out of 636535704 bp ( 1.57 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:48:53 (hh:mm:ss) Elapsed Time, 8968 HSPs Collected Number of families returned by RECON: 1370 Round Time: 00:52:02 (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 : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49493 repeats masked totaling 10751140 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014319 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30013619 bp After Masking: 18933548 bp Masked: 36.92 % -- Input Database Coverage: 40015517 bp out of 636535704 bp ( 6.29 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 02:29:55 (hh:mm:ss) Elapsed Time, 51586 HSPs Collected Number of families returned by RECON: 4771 Round Time: 02:39:40 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 165088 repeats masked totaling 35054047 bp(s). - TE Masking time 00:02:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025400 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90023300 bp After Masking: 54027106 bp Masked: 39.99 % -- Input Database Coverage: 130040917 bp out of 636535704 bp ( 20.43 % ) Sampling Time: 00:07:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 06:10:32 (hh:mm:ss) Elapsed Time, 174959 HSPs Collected Number of families returned by RECON: 13896 Round Time: 06:29:04 (hh:mm:ss) Elapsed Time : 416 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 568757 repeats masked totaling 116878681 bp(s). - TE Masking time 00:11:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012711 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 270007011 bp After Masking: 150186867 bp Masked: 44.38 % -- Input Database Coverage: 400053628 bp out of 636535704 bp ( 62.85 % ) Sampling Time: 00:26:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23062236 Comparison Time: 29:07:30 (hh:mm:ss) Elapsed Time, 475845 HSPs Collected Number of families returned by RECON: 47359 Round Time: 30:41:58 (hh:mm:ss) Elapsed Time : 868 families discovered. RepeatScout/RECON discovery complete: 2040 families found Classification Time: 01:17:47 (hh:mm:ss) Elapsed Time Program Time: 42:36:36 (hh:mm:ss) Elapsed Time