RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.ZyWMy8/RM_3374826.SatApr121605062025 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: 1744499105 Database = /data/tmp/rModeler.ZyWMy8/GCA_047511565.1_fPolLow2.hap1 - Sequences = 327 - Bases = 675344950 - N50 = 28759549 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35897210-38460444 | [ 1 ] 33333976-35897209 | [ 2 ] 30770742-33333975 | [ 2 ] 28207508-30770741 |* [ 8 ] 25644275-28207508 | [ 5 ] 23081041-25644274 | [ 2 ] 20517807-23081040 | [ 1 ] 17954573-20517806 | [ 2 ] 15391339-17954572 | [ 1 ] 12828106-15391339 | [ ] 10264872-12828105 | [ ] 7701638-10264871 | [ ] 5138404-7701637 | [ ] 2575170-5138403 | [ ] 11937-2575170 |************************************************** [ 303 ] Storage Throughput = excellent ( 1694.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011892 bp ( 40003265 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:10 (hh:mm:ss) Elapsed Time Round Time: 00:11:14 (hh:mm:ss) Elapsed Time : 522 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6603 repeats masked totaling 953730 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002252 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10000052 bp After Masking: 8115444 bp Masked: 18.85 % -- Input Database Coverage: 10002252 bp out of 675344950 bp ( 1.48 % ) Sampling Time: 00:01:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:55 (hh:mm:ss) Elapsed Time, 7305 HSPs Collected Number of families returned by RECON: 1736 Round Time: 00:05:08 (hh:mm:ss) Elapsed Time : 14 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 00:02:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20957 repeats masked totaling 3248293 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009560 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30003133 bp After Masking: 23745372 bp Masked: 20.86 % -- Input Database Coverage: 40011812 bp out of 675344950 bp ( 5.92 % ) Sampling Time: 00:03:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:17:36 (hh:mm:ss) Elapsed Time, 43939 HSPs Collected Number of families returned by RECON: 5934 Round Time: 00:21:40 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71425 repeats masked totaling 10919641 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040463 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 90019201 bp After Masking: 69574813 bp Masked: 22.71 % -- Input Database Coverage: 130052275 bp out of 675344950 bp ( 19.26 % ) Sampling Time: 00:11:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 01:52:06 (hh:mm:ss) Elapsed Time, 272267 HSPs Collected Number of families returned by RECON: 20549 Round Time: 02:10:17 (hh:mm:ss) Elapsed Time : 515 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 283002 repeats masked totaling 45901890 bp(s). - TE Masking time 00:05:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270070906 bp Num Contigs Represented = 179 Non ambiguous bp: Initial: 270010712 bp After Masking: 196580503 bp Masked: 27.20 % -- Input Database Coverage: 400123181 bp out of 675344950 bp ( 59.25 % ) Sampling Time: 00:37:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23157415 Comparison Time: 13:51:01 (hh:mm:ss) Elapsed Time, 997522 HSPs Collected Number of families returned by RECON: 71393 Round Time: 15:29:46 (hh:mm:ss) Elapsed Time : 1303 families discovered. RepeatScout/RECON discovery complete: 2462 families found Classification Time: 01:05:27 (hh:mm:ss) Elapsed Time Program Time: 19:23:32 (hh:mm:ss) Elapsed Time