RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.MMpn0L/RM_1102868.MonNov182132472024 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: 1731994366 Database = /scratch/tmp/rModeler.MMpn0L/GCA_964273705.1_rNatHel1.hap1.1 - Sequences = 487 - Bases = 1777516490 - N50 = 298881593 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 351695050-376816054 | [ 1 ] 326574046-351695049 | [ ] 301453043-326574046 | [ ] 276332039-301453042 | [ 1 ] 251211036-276332039 | [ ] 226090032-251211035 | [ ] 200969028-226090031 | [ ] 175848025-200969028 | [ 1 ] 150727021-175848024 | [ 2 ] 125606018-150727021 | [ 1 ] 100485014-125606017 | [ ] 75364010-100485013 | [ 3 ] 50243007-75364010 | [ ] 25122003-50243006 | [ 2 ] 1000-25122003 |************************************************** [ 476 ] Storage Throughput = excellent ( 1419.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40049270 bp ( 40039670 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:14 (hh:mm:ss) Elapsed Time Round Time: 00:12:49 (hh:mm:ss) Elapsed Time : 649 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17384 repeats masked totaling 3988320 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030420 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10028220 bp After Masking: 5577037 bp Masked: 44.39 % -- Input Database Coverage: 10030420 bp out of 1777516490 bp ( 0.56 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:57 (hh:mm:ss) Elapsed Time, 7232 HSPs Collected Number of families returned by RECON: 945 Round Time: 00:04:32 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52135 repeats masked totaling 11795437 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018849 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30011449 bp After Masking: 16175535 bp Masked: 46.10 % -- Input Database Coverage: 40049269 bp out of 1777516490 bp ( 2.25 % ) Sampling Time: 00:04:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:12:09 (hh:mm:ss) Elapsed Time, 36314 HSPs Collected Number of families returned by RECON: 2998 Round Time: 00:17:31 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 166157 repeats masked totaling 37166144 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90058386 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90038345 bp After Masking: 47505146 bp Masked: 47.24 % -- Input Database Coverage: 130107655 bp out of 1777516490 bp ( 7.32 % ) Sampling Time: 00:10:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 01:03:26 (hh:mm:ss) Elapsed Time, 175387 HSPs Collected Number of families returned by RECON: 8632 Round Time: 01:17:10 (hh:mm:ss) Elapsed Time : 340 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 554866 repeats masked totaling 122776038 bp(s). - TE Masking time 00:03:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270076703 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 270018204 bp After Masking: 131795974 bp Masked: 51.19 % -- Input Database Coverage: 400184358 bp out of 1777516490 bp ( 22.51 % ) Sampling Time: 00:34:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23116600 Comparison Time: 06:52:19 (hh:mm:ss) Elapsed Time, 690025 HSPs Collected Number of families returned by RECON: 29355 Round Time: 07:41:42 (hh:mm:ss) Elapsed Time : 804 families discovered. RepeatScout/RECON discovery complete: 1883 families found Classification Time: 00:38:57 (hh:mm:ss) Elapsed Time Program Time: 10:12:41 (hh:mm:ss) Elapsed Time