RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LDdLAO/RM_15991.SatJan142335032023 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: 1673768102 Database = /dev/shm/rModeler.LDdLAO/GCA_947247035.1_rVipUrs1.1 - Sequences = 384 - Bases = 1625023540 - N50 = 294454259 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 335770459-359753992 | [ 1 ] 311786926-335770458 | [ ] 287803393-311786925 | [ 1 ] 263819860-287803392 | [ ] 239836328-263819860 | [ ] 215852795-239836327 | [ ] 191869262-215852794 | [ 1 ] 167885729-191869261 | [ ] 143902196-167885728 | [ ] 119918664-143902196 | [ 2 ] 95935131-119918663 | [ 1 ] 71951598-95935130 | [ 2 ] 47968065-71951597 | [ ] 23984532-47968064 | [ 3 ] 1000-23984532 |************************************************** [ 373 ] Storage Throughput = excellent ( 1102.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022544 bp ( 40012140 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:04:10 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:22 (hh:mm:ss) Elapsed Time Round Time: 00:31:16 (hh:mm:ss) Elapsed Time : 519 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15527 repeats masked totaling 3884089 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012227 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10009427 bp After Masking: 5697803 bp Masked: 43.08 % -- Input Database Coverage: 10012227 bp out of 1625023540 bp ( 0.62 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:27 (hh:mm:ss) Elapsed Time, 3841 HSPs Collected Number of families returned by RECON: 798 Round Time: 00:08:40 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45035 repeats masked totaling 11409863 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010316 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30002712 bp After Masking: 17054829 bp Masked: 43.16 % -- Input Database Coverage: 40022543 bp out of 1625023540 bp ( 2.46 % ) Sampling Time: 00:07:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:29:32 (hh:mm:ss) Elapsed Time, 28994 HSPs Collected Number of families returned by RECON: 2940 Round Time: 00:38:05 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143821 repeats masked totaling 35809101 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022406 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 90000738 bp After Masking: 49549554 bp Masked: 44.95 % -- Input Database Coverage: 130044949 bp out of 1625023540 bp ( 8.00 % ) Sampling Time: 00:22:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 03:03:36 (hh:mm:ss) Elapsed Time, 144086 HSPs Collected Number of families returned by RECON: 9577 Round Time: 03:32:45 (hh:mm:ss) Elapsed Time : 297 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:27:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 473344 repeats masked totaling 117360051 bp(s). - TE Masking time 00:09:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270066915 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 270012516 bp After Masking: 139472092 bp Masked: 48.35 % -- Input Database Coverage: 400111864 bp out of 1625023540 bp ( 24.62 % ) Sampling Time: 01:05:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22974031 Comparison Time: 22:05:50 (hh:mm:ss) Elapsed Time, 439653 HSPs Collected Number of families returned by RECON: 29966 Round Time: 23:48:07 (hh:mm:ss) Elapsed Time : 692 families discovered. RepeatScout/RECON discovery complete: 1572 families found Classification Time: 01:08:17 (hh:mm:ss) Elapsed Time Program Time: 29:47:10 (hh:mm:ss) Elapsed Time