RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/008/658/365/GCA_008658365.1_bAlcTor1_primary/trackData/repeatModeler/RM_16011.SatDec241330032022 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: 1671917401 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/008/658/365/GCA_008658365.1_bAlcTor1_primary/trackData/repeatModeler/GCA_008658365.1_bAlcTor1_primary - Sequences = 95 - Bases = 1178492568 Storage Throughput = fair ( 580.83 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40093554 bp ( 40000501 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:02:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:24 (hh:mm:ss) Elapsed Time Round Time: 00:20:11 (hh:mm:ss) Elapsed Time : 43 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1383 repeats masked totaling 549038 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002087 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10001987 bp After Masking: 9407371 bp Masked: 5.94 % -- Input Database Coverage: 10002087 bp out of 1178492568 bp ( 0.85 % ) Sampling Time: 00:00:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:08 (hh:mm:ss) Elapsed Time, 579 HSPs Collected Number of families returned by RECON: 244 Round Time: 00:07:19 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4534 repeats masked totaling 1760898 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30131396 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30038443 bp After Masking: 28138886 bp Masked: 6.32 % -- Input Database Coverage: 40133483 bp out of 1178492568 bp ( 3.41 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:31:12 (hh:mm:ss) Elapsed Time, 3847 HSPs Collected Number of families returned by RECON: 1366 Round Time: 00:34:55 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13709 repeats masked totaling 5044556 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90264637 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 90024672 bp After Masking: 84355986 bp Masked: 6.30 % -- Input Database Coverage: 130398120 bp out of 1178492568 bp ( 11.06 % ) Sampling Time: 00:07:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:42:48 (hh:mm:ss) Elapsed Time, 30610 HSPs Collected Number of families returned by RECON: 8913 Round Time: 03:56:12 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53689 repeats masked totaling 17917256 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270980346 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 270026307 bp After Masking: 250414174 bp Masked: 7.26 % -- Input Database Coverage: 401378466 bp out of 1178492568 bp ( 34.06 % ) Sampling Time: 00:28:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 29:36:30 (hh:mm:ss) Elapsed Time, 140885 HSPs Collected Number of families returned by RECON: 56158 Round Time: 31:07:02 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatScout/RECON discovery complete: 303 families found Classification Time: 00:12:39 (hh:mm:ss) Elapsed Time Program Time: 36:18:18 (hh:mm:ss) Elapsed Time