RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.dtSVDb/RM_59816.SunJan11104032023 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: 1672599842 Database = /dev/shm/rModeler.dtSVDb/GCA_946808225.1_fSilAri3.1 - Sequences = 241 - Bases = 800118513 - N50 = 30789638 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 41123262-44060567 | [ 1 ] 38185958-41123262 | [ 1 ] 35248653-38185957 | [ 3 ] 32311349-35248653 | [ 1 ] 29374044-32311348 |* [ 8 ] 26436740-29374044 | [ ] 23499435-26436739 |* [ 5 ] 20562131-23499435 | [ 2 ] 17624826-20562130 |* [ 7 ] 14687522-17624826 | [ ] 11750217-14687521 | [ 1 ] 8812913-11750217 | [ ] 5875608-8812912 | [ ] 2938304-5875608 | [ ] 1000-2938304 |************************************************** [ 212 ] Storage Throughput = excellent ( 1550.96 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025503 bp ( 40019703 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:21 (hh:mm:ss) Elapsed Time Round Time: 00:21:23 (hh:mm:ss) Elapsed Time : 537 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12228 repeats masked totaling 2694734 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006231 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10005431 bp After Masking: 6396751 bp Masked: 36.07 % -- Input Database Coverage: 10006231 bp out of 800118513 bp ( 1.25 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:28 (hh:mm:ss) Elapsed Time, 5724 HSPs Collected Number of families returned by RECON: 950 Round Time: 00:09:30 (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 : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38024 repeats masked totaling 8403919 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019192 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30014192 bp After Masking: 18819140 bp Masked: 37.30 % -- Input Database Coverage: 40025423 bp out of 800118513 bp ( 5.00 % ) Sampling Time: 00:05:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:23:49 (hh:mm:ss) Elapsed Time, 32078 HSPs Collected Number of families returned by RECON: 3135 Round Time: 00:30:24 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 114799 repeats masked totaling 24224116 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023815 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90002787 bp After Masking: 56530879 bp Masked: 37.19 % -- Input Database Coverage: 130049238 bp out of 800118513 bp ( 16.25 % ) Sampling Time: 00:21:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:19:41 (hh:mm:ss) Elapsed Time, 240076 HSPs Collected Number of families returned by RECON: 10977 Round Time: 02:45:37 (hh:mm:ss) Elapsed Time : 289 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:54:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 390083 repeats masked totaling 82647074 bp(s). - TE Masking time 00:04:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270052479 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 270002079 bp After Masking: 160835555 bp Masked: 40.43 % -- Input Database Coverage: 400101717 bp out of 800118513 bp ( 50.01 % ) Sampling Time: 01:02:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 15:43:28 (hh:mm:ss) Elapsed Time, 2235847 HSPs Collected Number of families returned by RECON: 41236 Round Time: 17:14:46 (hh:mm:ss) Elapsed Time : 769 families discovered. RepeatScout/RECON discovery complete: 1680 families found Classification Time: 00:48:48 (hh:mm:ss) Elapsed Time Program Time: 21:50:28 (hh:mm:ss) Elapsed Time