RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/900/634/795/GCF_900634795.3_fBetSpl5.3/trackData/repeatModeler/RM_35147.MonDec262121132022 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: 1672118472 Database = /hive/data/genomes/asmHubs/refseqBuild/GCF/900/634/795/GCF_900634795.3_fBetSpl5.3/trackData/repeatModeler/GCF_900634795.3_fBetSpl5.3 - Sequences = 70 - Bases = 441388503 Storage Throughput = good ( 837.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030077 bp ( 40026777 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:13 (hh:mm:ss) Elapsed Time Round Time: 00:21:47 (hh:mm:ss) Elapsed Time : 285 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 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4411 repeats masked totaling 1366574 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007204 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10006454 bp After Masking: 8242291 bp Masked: 17.63 % -- Input Database Coverage: 10007204 bp out of 441388503 bp ( 2.27 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:16 (hh:mm:ss) Elapsed Time, 4928 HSPs Collected Number of families returned by RECON: 588 Round Time: 00:07:15 (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 : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10853 repeats masked totaling 3801773 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022793 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30020243 bp After Masking: 25153688 bp Masked: 16.21 % -- Input Database Coverage: 40029997 bp out of 441388503 bp ( 9.07 % ) Sampling Time: 00:03:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:26:55 (hh:mm:ss) Elapsed Time, 20224 HSPs Collected Number of families returned by RECON: 2515 Round Time: 00:32:21 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34603 repeats masked totaling 11197227 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015999 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90009984 bp After Masking: 75620035 bp Masked: 15.99 % -- Input Database Coverage: 130045996 bp out of 441388503 bp ( 29.46 % ) Sampling Time: 00:07:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 03:11:27 (hh:mm:ss) Elapsed Time, 115197 HSPs Collected Number of families returned by RECON: 12207 Round Time: 03:36:17 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 126577 repeats masked totaling 40134062 bp(s). - TE Masking time 00:06:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270050477 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270032897 bp After Masking: 220745637 bp Masked: 18.25 % -- Input Database Coverage: 400096473 bp out of 441388503 bp ( 90.64 % ) Sampling Time: 00:27:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 25:06:37 (hh:mm:ss) Elapsed Time, 579423 HSPs Collected Number of families returned by RECON: 58585 Round Time: 27:21:02 (hh:mm:ss) Elapsed Time : 549 families discovered. RepeatScout/RECON discovery complete: 1047 families found Classification Time: 01:27:54 (hh:mm:ss) Elapsed Time Program Time: 33:26:36 (hh:mm:ss) Elapsed Time