RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/902/459/465/GCF_902459465.1_eAstRub1.3/trackData/repeatModeler/RM_35145.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/902/459/465/GCF_902459465.1_eAstRub1.3/trackData/repeatModeler/GCF_902459465.1_eAstRub1.3 - Sequences = 150 - Bases = 417601740 - N50 = 21693562 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 31571771-33825921 | [ 1 ] 29317622-31571771 | [ ] 27063473-29317622 | [ ] 24809324-27063473 | [ 1 ] 22555175-24809324 |* [ 4 ] 20301025-22555174 |* [ 4 ] 18046876-20301025 | [ 1 ] 15792727-18046876 | [ 1 ] 13538578-15792727 |* [ 4 ] 11284429-13538578 |* [ 5 ] 9030279-11284428 | [ 1 ] 6776130-9030279 | [ ] 4521981-6776130 | [ ] 2267832-4521981 | [ ] 13683-2267832 |************************************************** [ 128 ] Storage Throughput = good ( 837.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028224 bp ( 40009848 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:44 (hh:mm:ss) Elapsed Time Round Time: 00:17:58 (hh:mm:ss) Elapsed Time : 783 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 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24138 repeats masked totaling 3516167 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036457 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10031640 bp After Masking: 5990200 bp Masked: 40.29 % -- Input Database Coverage: 10036457 bp out of 417601740 bp ( 2.40 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:09 (hh:mm:ss) Elapsed Time, 7273 HSPs Collected Number of families returned by RECON: 1117 Round Time: 00:06:51 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73530 repeats masked totaling 10480108 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031687 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30018128 bp After Masking: 18090127 bp Masked: 39.74 % -- Input Database Coverage: 40068144 bp out of 417601740 bp ( 9.59 % ) Sampling Time: 00:02:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:25:35 (hh:mm:ss) Elapsed Time, 39066 HSPs Collected Number of families returned by RECON: 4024 Round Time: 00:31:54 (hh:mm:ss) Elapsed Time : 97 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 232718 repeats masked totaling 32336456 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90064706 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 90031261 bp After Masking: 53464940 bp Masked: 40.62 % -- Input Database Coverage: 130132850 bp out of 417601740 bp ( 31.16 % ) Sampling Time: 00:07:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 02:55:28 (hh:mm:ss) Elapsed Time, 258364 HSPs Collected Number of families returned by RECON: 12277 Round Time: 03:28:23 (hh:mm:ss) Elapsed Time : 548 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 765313 repeats masked totaling 108274116 bp(s). - TE Masking time 00:10:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270124410 bp Num Contigs Represented = 127 Non ambiguous bp: Initial: 270032674 bp After Masking: 149887582 bp Masked: 44.49 % -- Input Database Coverage: 400257260 bp out of 417601740 bp ( 95.85 % ) Sampling Time: 00:27:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 22:15:54 (hh:mm:ss) Elapsed Time, 783363 HSPs Collected Number of families returned by RECON: 36718 Round Time: 24:42:47 (hh:mm:ss) Elapsed Time : 1208 families discovered. RepeatScout/RECON discovery complete: 2651 families found Classification Time: 01:52:28 (hh:mm:ss) Elapsed Time Program Time: 31:00:21 (hh:mm:ss) Elapsed Time