RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.vjO5tW/RM_3806337.MonApr210731182025 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: 1745245878 Database = /data/tmp/rModeler.vjO5tW/GCA_031216445.1_YSFRI_Lmacu_1.1 - Sequences = 109 - Bases = 632510465 - N50 = 28002630 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 30734333-32929622 |* [ 2 ] 28539044-30734333 |** [ 5 ] 26343755-28539044 |**** [ 7 ] 24148466-26343755 |* [ 3 ] 21953177-24148466 |* [ 3 ] 19757888-21953177 |* [ 3 ] 17562599-19757888 | [ ] 15367310-17562599 | [ ] 13172021-15367310 | [ 1 ] 10976732-13172021 | [ ] 8781443-10976732 | [ ] 6586154-8781443 | [ ] 4390865-6586154 | [ ] 2195576-4390865 | [ ] 287-2195576 |************************************************** [ 85 ] Storage Throughput = excellent ( 1003.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40034476 bp ( 40034476 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:32 (hh:mm:ss) Elapsed Time Round Time: 00:22:55 (hh:mm:ss) Elapsed Time : 280 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5787 repeats masked totaling 834450 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033251 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10033251 bp After Masking: 8900182 bp Masked: 11.29 % -- Input Database Coverage: 10033251 bp out of 632510465 bp ( 1.59 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:35 (hh:mm:ss) Elapsed Time, 7220 HSPs Collected Number of families returned by RECON: 1371 Round Time: 00:08:44 (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 : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19890 repeats masked totaling 3382786 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001145 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30001145 bp After Masking: 25898944 bp Masked: 13.67 % -- Input Database Coverage: 40034396 bp out of 632510465 bp ( 6.33 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:31:42 (hh:mm:ss) Elapsed Time, 44856 HSPs Collected Number of families returned by RECON: 5763 Round Time: 00:40:38 (hh:mm:ss) Elapsed Time : 107 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 70354 repeats masked totaling 11787675 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028985 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 90028985 bp After Masking: 75861190 bp Masked: 15.74 % -- Input Database Coverage: 130063381 bp out of 632510465 bp ( 20.56 % ) Sampling Time: 00:10:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 03:46:38 (hh:mm:ss) Elapsed Time, 219751 HSPs Collected Number of families returned by RECON: 21317 Round Time: 04:46:58 (hh:mm:ss) Elapsed Time : 382 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 268187 repeats masked totaling 44932200 bp(s). - TE Masking time 00:06:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022073 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 270022073 bp After Masking: 218422516 bp Masked: 19.11 % -- Input Database Coverage: 400085454 bp out of 632510465 bp ( 63.25 % ) Sampling Time: 00:30:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 27:22:29 (hh:mm:ss) Elapsed Time, 748274 HSPs Collected Number of families returned by RECON: 81436 Round Time: 33:26:28 (hh:mm:ss) Elapsed Time : 1087 families discovered. RepeatScout/RECON discovery complete: 1873 families found Classification Time: 01:30:59 (hh:mm:ss) Elapsed Time Program Time: 40:56:42 (hh:mm:ss) Elapsed Time