RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EniR9H/RM_25427.FriJan122332442024 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: 1705131161 Database = /dev/shm/rModeler.EniR9H/GCA_031878665.1_mThoBot2.hap2 - Sequences = 340 - Bases = 1879249320 - N50 = 64567486 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 96209505-103080557 | [ 3 ] 89338453-96209504 | [ ] 82467402-89338453 | [ 3 ] 75596350-82467401 | [ 1 ] 68725298-75596349 | [ 2 ] 61854247-68725298 | [ 2 ] 54983195-61854246 | [ 5 ] 48112143-54983194 | [ 2 ] 41241092-48112143 | [ 2 ] 34370040-41241091 | [ 2 ] 27498988-34370039 | [ 2 ] 20627937-27498988 | [ 3 ] 13756885-20627936 | [ 3 ] 6885833-13756884 |* [ 11 ] 14782-6885833 |************************************************* [ 299 ] Storage Throughput = excellent ( 1108.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031479 bp ( 40027479 non ambiguous ) - Num Contigs Represented = 87 - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:33 (hh:mm:ss) Elapsed Time Round Time: 00:40:01 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20477 repeats masked totaling 3358895 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010045 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10008845 bp After Masking: 6372381 bp Masked: 36.33 % -- Input Database Coverage: 10010045 bp out of 1879249320 bp ( 0.53 % ) Sampling Time: 00:02:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:17:32 (hh:mm:ss) Elapsed Time, 1870 HSPs Collected Number of families returned by RECON: 369 Round Time: 00:20:58 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57563 repeats masked totaling 10077436 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021430 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 30018630 bp After Masking: 18763768 bp Masked: 37.49 % -- Input Database Coverage: 40031475 bp out of 1879249320 bp ( 2.13 % ) Sampling Time: 00:07:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:37:02 (hh:mm:ss) Elapsed Time, 9611 HSPs Collected Number of families returned by RECON: 1455 Round Time: 00:44:58 (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 : 00:02:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 179944 repeats masked totaling 30686723 bp(s). - TE Masking time 00:03:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029107 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 90024183 bp After Masking: 56215437 bp Masked: 37.56 % -- Input Database Coverage: 130060582 bp out of 1879249320 bp ( 6.92 % ) Sampling Time: 00:20:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:46:28 (hh:mm:ss) Elapsed Time, 45392 HSPs Collected Number of families returned by RECON: 6352 Round Time: 04:09:11 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:40:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 563035 repeats masked totaling 96373844 bp(s). - TE Masking time 00:11:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270020565 bp Num Contigs Represented = 182 Non ambiguous bp: Initial: 270007165 bp After Masking: 164325915 bp Masked: 39.14 % -- Input Database Coverage: 400081147 bp out of 1879249320 bp ( 21.29 % ) Sampling Time: 01:00:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 26:54:29 (hh:mm:ss) Elapsed Time, 207843 HSPs Collected Number of families returned by RECON: 29240 Round Time: 28:17:56 (hh:mm:ss) Elapsed Time : 306 families discovered. RepeatScout/RECON discovery complete: 618 families found Classification Time: 00:41:44 (hh:mm:ss) Elapsed Time Program Time: 34:54:48 (hh:mm:ss) Elapsed Time