RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DwX3iL/RM_25175.SatNov252138152023 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: 1700977092 Database = /dev/shm/rModeler.DwX3iL/GCA_008822115.3_bTaeGut2.mat.v3 - Sequences = 206 - Bases = 995952786 - N50 = 73152851 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 141330076-151424995 | [ 1 ] 131235158-141330076 | [ ] 121140240-131235158 | [ ] 111045322-121140240 | [ 2 ] 100950404-111045322 | [ ] 90855486-100950404 | [ ] 80760568-90855486 | [ ] 70665650-80760568 | [ 2 ] 60570732-70665650 | [ 1 ] 50475814-60570732 | [ ] 40380896-50475814 | [ ] 30285978-40380896 | [ 3 ] 20191060-30285978 |* [ 5 ] 10096142-20191060 |** [ 8 ] 1224-10096142 |************************************************** [ 184 ] Storage Throughput = excellent ( 1183.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40628725 bp ( 40010913 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:28 (hh:mm:ss) Elapsed Time Round Time: 00:27:28 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2547 repeats masked totaling 655461 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10150939 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10013557 bp After Masking: 9130138 bp Masked: 8.82 % -- Input Database Coverage: 10150939 bp out of 995952786 bp ( 1.02 % ) Sampling Time: 00:00:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:07:08 (hh:mm:ss) Elapsed Time, 1035 HSPs Collected Number of families returned by RECON: 324 Round Time: 00:08:16 (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 : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7520 repeats masked totaling 1830400 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30517706 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30037276 bp After Masking: 27562566 bp Masked: 8.24 % -- Input Database Coverage: 40668645 bp out of 995952786 bp ( 4.08 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:41:19 (hh:mm:ss) Elapsed Time, 6789 HSPs Collected Number of families returned by RECON: 1781 Round Time: 00:45:21 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23484 repeats masked totaling 5673529 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91070077 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 90027155 bp After Masking: 82272958 bp Masked: 8.61 % -- Input Database Coverage: 131738722 bp out of 995952786 bp ( 13.23 % ) Sampling Time: 00:09:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2607186 Comparison Time: 05:09:01 (hh:mm:ss) Elapsed Time, 49813 HSPs Collected Number of families returned by RECON: 11587 Round Time: 05:23:10 (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 : 00:10:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80420 repeats masked totaling 20928895 bp(s). - TE Masking time 00:03:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274539740 bp Num Contigs Represented = 110 Non ambiguous bp: Initial: 270010182 bp After Masking: 244013578 bp Masked: 9.63 % -- Input Database Coverage: 406278462 bp out of 995952786 bp ( 40.79 % ) Sampling Time: 00:26:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23746386 Comparison Time: 42:38:29 (hh:mm:ss) Elapsed Time, 264847 HSPs Collected Number of families returned by RECON: 75859 Round Time: 44:28:25 (hh:mm:ss) Elapsed Time : 268 families discovered. RepeatScout/RECON discovery complete: 478 families found Classification Time: 00:37:23 (hh:mm:ss) Elapsed Time Program Time: 51:50:03 (hh:mm:ss) Elapsed Time