RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SsWUG2/RM_1601103.ThuMar280829102024 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: 1711639750 Database = /dev/shm/rModeler.SsWUG2/GCA_963921805.1_bPhaCar2.1 - Sequences = 351 - Bases = 1283643005 - N50 = 129753630 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204318147-218912229 | [ 1 ] 189724065-204318146 | [ ] 175129983-189724064 | [ ] 160535901-175129982 | [ 1 ] 145941819-160535900 | [ ] 131347737-145941818 | [ ] 116753655-131347736 | [ 1 ] 102159573-116753654 | [ ] 87565491-102159572 | [ ] 72971409-87565490 | [ 2 ] 58377327-72971408 | [ 2 ] 43783245-58377326 | [ 2 ] 29189163-43783244 | [ 1 ] 14595081-29189162 |* [ 7 ] 1000-14595081 |************************************************** [ 334 ] Storage Throughput = excellent ( 1390.95 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008911 bp ( 40005216 non ambiguous ) - Num Contigs Represented = 70 - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:08 (hh:mm:ss) Elapsed Time Round Time: 00:23:06 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1484 repeats masked totaling 861559 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021135 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10020040 bp After Masking: 8988779 bp Masked: 10.29 % -- Input Database Coverage: 10021135 bp out of 1283643005 bp ( 0.78 % ) Sampling Time: 00:01:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:52 (hh:mm:ss) Elapsed Time, 729 HSPs Collected Number of families returned by RECON: 240 Round Time: 00:08:20 (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 : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4331 repeats masked totaling 2197879 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027776 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 30025176 bp After Masking: 27119482 bp Masked: 9.68 % -- Input Database Coverage: 40048911 bp out of 1283643005 bp ( 3.12 % ) Sampling Time: 00:04:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:33:36 (hh:mm:ss) Elapsed Time, 4576 HSPs Collected Number of families returned by RECON: 1284 Round Time: 00:38:47 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15751 repeats masked totaling 7594491 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042916 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 90034516 bp After Masking: 80173952 bp Masked: 10.95 % -- Input Database Coverage: 130091827 bp out of 1283643005 bp ( 10.13 % ) Sampling Time: 00:13:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 03:34:06 (hh:mm:ss) Elapsed Time, 41535 HSPs Collected Number of families returned by RECON: 8136 Round Time: 03:49:54 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60529 repeats masked totaling 26061076 bp(s). - TE Masking time 00:02:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035535 bp Num Contigs Represented = 180 Non ambiguous bp: Initial: 270013358 bp After Masking: 235579078 bp Masked: 12.75 % -- Input Database Coverage: 400127362 bp out of 1283643005 bp ( 31.17 % ) Sampling Time: 00:41:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 28:58:46 (hh:mm:ss) Elapsed Time, 197864 HSPs Collected Number of families returned by RECON: 53226 Round Time: 30:20:17 (hh:mm:ss) Elapsed Time : 211 families discovered. RepeatScout/RECON discovery complete: 359 families found Classification Time: 00:30:01 (hh:mm:ss) Elapsed Time Program Time: 35:50:25 (hh:mm:ss) Elapsed Time