RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RDSfhH/RM_2126812.SatMar300426142024 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: 1711797974 Database = /dev/shm/rModeler.RDSfhH/GCA_963924715.1_fThuThy2.1 - Sequences = 120 - Bases = 799063593 - N50 = 35057343 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 39207654-42008130 |* [ 3 ] 36407179-39207654 | [ 1 ] 33606704-36407179 |**** [ 8 ] 30806228-33606703 |** [ 4 ] 28005753-30806228 |** [ 4 ] 25205278-28005753 |* [ 3 ] 22404802-25205277 | [ ] 19604327-22404802 | [ 1 ] 16803852-19604327 | [ ] 14003376-16803851 | [ ] 11202901-14003376 | [ ] 8402426-11202901 | [ ] 5601950-8402425 | [ ] 2801475-5601950 | [ ] 1000-2801475 |************************************************** [ 96 ] Storage Throughput = excellent ( 1153.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039051 bp ( 40033509 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:35 (hh:mm:ss) Elapsed Time Round Time: 00:17:31 (hh:mm:ss) Elapsed Time : 593 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9695 repeats masked totaling 1468224 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031348 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10029948 bp After Masking: 8380335 bp Masked: 16.45 % -- Input Database Coverage: 10031348 bp out of 799063593 bp ( 1.26 % ) Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:35 (hh:mm:ss) Elapsed Time, 7083 HSPs Collected Number of families returned by RECON: 1682 Round Time: 00:07:35 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30099 repeats masked totaling 4736754 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007702 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30003560 bp After Masking: 24266381 bp Masked: 19.12 % -- Input Database Coverage: 40039050 bp out of 799063593 bp ( 5.01 % ) Sampling Time: 00:02:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:31:09 (hh:mm:ss) Elapsed Time, 54986 HSPs Collected Number of families returned by RECON: 6246 Round Time: 00:35:29 (hh:mm:ss) Elapsed Time : 132 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100563 repeats masked totaling 15654293 bp(s). - TE Masking time 00:01:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045946 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 90035629 bp After Masking: 71455363 bp Masked: 20.64 % -- Input Database Coverage: 130084996 bp out of 799063593 bp ( 16.28 % ) Sampling Time: 00:08:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 03:31:04 (hh:mm:ss) Elapsed Time, 346414 HSPs Collected Number of families returned by RECON: 21621 Round Time: 03:54:38 (hh:mm:ss) Elapsed Time : 631 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 387880 repeats masked totaling 64263192 bp(s). - TE Masking time 00:10:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270068372 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 270035493 bp After Masking: 197076214 bp Masked: 27.02 % -- Input Database Coverage: 400153368 bp out of 799063593 bp ( 50.08 % ) Sampling Time: 00:32:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 25:39:30 (hh:mm:ss) Elapsed Time, 1000668 HSPs Collected Number of families returned by RECON: 73682 Round Time: 28:06:39 (hh:mm:ss) Elapsed Time : 1459 families discovered. RepeatScout/RECON discovery complete: 2830 families found Classification Time: 02:08:50 (hh:mm:ss) Elapsed Time Program Time: 35:10:42 (hh:mm:ss) Elapsed Time