RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DQkfVP/RM_21902.TueJan101419382023 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: 1673389178 Database = /dev/shm/rModeler.DQkfVP/GCF_900496995.4_bAquChr1.4 - Sequences = 144 - Bases = 1233704830 - N50 = 47779391 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 82335456-88216475 |* [ 3 ] 76454438-82335456 |* [ 3 ] 70573420-76454438 | [ ] 64692402-70573420 | [ ] 58811384-64692402 | [ ] 52930366-58811384 | [ 1 ] 47049348-52930366 | [ 1 ] 41168329-47049347 |** [ 6 ] 35287311-41168329 | [ ] 29406293-35287311 |* [ 4 ] 23525275-29406293 |* [ 4 ] 17644257-23525275 |** [ 5 ] 11763239-17644257 | [ ] 5882221-11763239 |* [ 3 ] 1203-5882221 |************************************************** [ 114 ] Storage Throughput = good ( 986.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40149066 bp ( 40015348 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:36 (hh:mm:ss) Elapsed Time Round Time: 00:24:17 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1216 repeats masked totaling 576200 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003062 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10002812 bp After Masking: 9401999 bp Masked: 6.01 % -- Input Database Coverage: 10003062 bp out of 1233704830 bp ( 0.81 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:07:26 (hh:mm:ss) Elapsed Time, 826 HSPs Collected Number of families returned by RECON: 321 Round Time: 00:08:19 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3693 repeats masked totaling 1812695 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30145924 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30012456 bp After Masking: 28103485 bp Masked: 6.36 % -- Input Database Coverage: 40148986 bp out of 1233704830 bp ( 3.25 % ) Sampling Time: 00:02:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:40:59 (hh:mm:ss) Elapsed Time, 7764 HSPs Collected Number of families returned by RECON: 1664 Round Time: 00:43:44 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13444 repeats masked totaling 5692415 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90291464 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90017390 bp After Masking: 84047881 bp Masked: 6.63 % -- Input Database Coverage: 130440450 bp out of 1233704830 bp ( 10.57 % ) Sampling Time: 00:06:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 04:44:41 (hh:mm:ss) Elapsed Time, 51199 HSPs Collected Number of families returned by RECON: 9932 Round Time: 04:54:31 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51520 repeats masked totaling 19610226 bp(s). - TE Masking time 00:02:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271121229 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270028534 bp After Masking: 249566699 bp Masked: 7.58 % -- Input Database Coverage: 401561679 bp out of 1233704830 bp ( 32.55 % ) Sampling Time: 00:25:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23075821 Comparison Time: 35:56:27 (hh:mm:ss) Elapsed Time, 186874 HSPs Collected Number of families returned by RECON: 61928 Round Time: 37:11:08 (hh:mm:ss) Elapsed Time : 239 families discovered. RepeatScout/RECON discovery complete: 377 families found Classification Time: 00:25:33 (hh:mm:ss) Elapsed Time Program Time: 43:47:32 (hh:mm:ss) Elapsed Time