RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5W4cwz/RM_60212.FriJul182239202025 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: 1752903558 Database = /dev/shm/rModeler.5W4cwz/GCA_048301475.1_ASM4830147v1 - Sequences = 248 - Bases = 669846493 - N50 = 28837212 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32728092-35065742 | [ 1 ] 30390443-32728092 | [ 3 ] 28052793-30390442 |* [ 7 ] 25715144-28052793 | [ 4 ] 23377494-25715143 |* [ 5 ] 21039845-23377494 | [ 2 ] 18702195-21039844 | [ ] 16364546-18702195 | [ 1 ] 14026896-16364545 | [ ] 11689247-14026896 | [ ] 9351597-11689246 | [ 1 ] 7013948-9351597 | [ ] 4676298-7013947 | [ 1 ] 2338649-4676298 | [ ] 1000-2338649 |************************************************** [ 223 ] Storage Throughput = excellent ( 1681.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023682 bp ( 40022782 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:01 (hh:mm:ss) Elapsed Time Round Time: 00:09:32 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4427 repeats masked totaling 789625 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018616 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10018516 bp After Masking: 8607964 bp Masked: 14.08 % -- Input Database Coverage: 10018616 bp out of 669846493 bp ( 1.50 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:00 (hh:mm:ss) Elapsed Time, 6267 HSPs Collected Number of families returned by RECON: 1328 Round Time: 00:04:02 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14849 repeats masked totaling 2568502 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005059 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30004259 bp After Masking: 25129536 bp Masked: 16.25 % -- Input Database Coverage: 40023675 bp out of 669846493 bp ( 5.98 % ) Sampling Time: 00:02:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:14:05 (hh:mm:ss) Elapsed Time, 37958 HSPs Collected Number of families returned by RECON: 5397 Round Time: 00:17:21 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55856 repeats masked totaling 10037772 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025013 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 90022213 bp After Masking: 73144214 bp Masked: 18.75 % -- Input Database Coverage: 130048688 bp out of 669846493 bp ( 19.41 % ) Sampling Time: 00:09:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:19:11 (hh:mm:ss) Elapsed Time, 229458 HSPs Collected Number of families returned by RECON: 19932 Round Time: 01:33:34 (hh:mm:ss) Elapsed Time : 374 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 222564 repeats masked totaling 41338056 bp(s). - TE Masking time 00:02:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270008261 bp Num Contigs Represented = 169 Non ambiguous bp: Initial: 270001561 bp After Masking: 207836310 bp Masked: 23.02 % -- Input Database Coverage: 400056949 bp out of 669846493 bp ( 59.72 % ) Sampling Time: 00:25:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23184645 Comparison Time: 09:30:56 (hh:mm:ss) Elapsed Time, 677526 HSPs Collected Number of families returned by RECON: 75406 Round Time: 10:39:11 (hh:mm:ss) Elapsed Time : 1010 families discovered. RepeatScout/RECON discovery complete: 1702 families found Classification Time: 00:42:14 (hh:mm:ss) Elapsed Time Program Time: 13:25:54 (hh:mm:ss) Elapsed Time