RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BuNtU8/RM_891601.FriJul181029262025 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: 1752859765 Database = /dev/shm/rModeler.BuNtU8/GCA_046129705.1_bLonStr1.pat - Sequences = 202 - Bases = 1195923327 - N50 = 73617835 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146600270-157070485 | [ 1 ] 136130056-146600270 | [ ] 125659841-136130055 | [ ] 115189627-125659841 | [ ] 104719413-115189627 | [ 2 ] 94249198-104719412 | [ ] 83778984-94249198 | [ 1 ] 73308769-83778983 | [ 1 ] 62838555-73308769 | [ 2 ] 52368341-62838555 | [ ] 41898126-52368340 | [ ] 31427912-41898126 | [ 3 ] 20957697-31427911 |* [ 5 ] 10487483-20957697 |** [ 9 ] 17269-10487483 |************************************************** [ 178 ] Storage Throughput = excellent ( 1134.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002019 bp ( 40000519 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:24:00 (hh:mm:ss) Elapsed Time Round Time: 00:39:11 (hh:mm:ss) Elapsed Time : 161 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3432 repeats masked totaling 1197498 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014669 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10014469 bp After Masking: 8048190 bp Masked: 19.63 % -- Input Database Coverage: 10014669 bp out of 1195923327 bp ( 0.84 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:49 (hh:mm:ss) Elapsed Time, 4361 HSPs Collected Number of families returned by RECON: 268 Round Time: 00:08:44 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9572 repeats masked totaling 3438705 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027217 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 30025917 bp After Masking: 24583382 bp Masked: 18.13 % -- Input Database Coverage: 40041886 bp out of 1195923327 bp ( 3.35 % ) Sampling Time: 00:05:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:38:09 (hh:mm:ss) Elapsed Time, 42861 HSPs Collected Number of families returned by RECON: 1322 Round Time: 00:46:20 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28470 repeats masked totaling 10206045 bp(s). - TE Masking time 00:01:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026431 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 90024174 bp After Masking: 73769249 bp Masked: 18.06 % -- Input Database Coverage: 130068317 bp out of 1195923327 bp ( 10.88 % ) Sampling Time: 00:15:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 04:48:43 (hh:mm:ss) Elapsed Time, 548875 HSPs Collected Number of families returned by RECON: 8297 Round Time: 05:12:14 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 94092 repeats masked totaling 33753820 bp(s). - TE Masking time 00:07:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026977 bp Num Contigs Represented = 149 Non ambiguous bp: Initial: 270016977 bp After Masking: 219284378 bp Masked: 18.79 % -- Input Database Coverage: 400095294 bp out of 1195923327 bp ( 33.45 % ) Sampling Time: 00:41:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 41:19:40 (hh:mm:ss) Elapsed Time, 7124084 HSPs Collected Number of families returned by RECON: 56275 Round Time: 42:51:03 (hh:mm:ss) Elapsed Time : 290 families discovered. RepeatScout/RECON discovery complete: 553 families found Classification Time: 00:56:32 (hh:mm:ss) Elapsed Time Program Time: 50:34:04 (hh:mm:ss) Elapsed Time