RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.g2Lq87/RM_4111340.TueApr81834562025 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: 1744162493 Database = /dev/shm/rModeler.g2Lq87/GCA_965231255.1_bVanVan1.hap1.1 - Sequences = 2408 - Bases = 1476623026 - N50 = 86090893 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 208169168-223038323 | [ 1 ] 193300013-208169167 | [ ] 178430858-193300012 | [ ] 163561703-178430857 | [ 1 ] 148692548-163561702 | [ ] 133823393-148692547 | [ ] 118954238-133823392 | [ 1 ] 104085084-118954238 | [ ] 89215929-104085083 | [ 1 ] 74346774-89215928 | [ 2 ] 59477619-74346773 | [ 1 ] 44608464-59477618 | [ ] 29739309-44608463 | [ 2 ] 14870154-29739308 | [ 9 ] 1000-14870154 |************************************************** [ 2390 ] Storage Throughput = excellent ( 1715.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016236 bp ( 40010636 non ambiguous ) - Num Contigs Represented = 214 - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:18 (hh:mm:ss) Elapsed Time Round Time: 00:10:59 (hh:mm:ss) Elapsed Time : 103 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2275 repeats masked totaling 809709 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041068 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 10039868 bp After Masking: 7705276 bp Masked: 23.25 % -- Input Database Coverage: 10041068 bp out of 1476623026 bp ( 0.68 % ) Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34453 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 923 HSPs Collected Number of families returned by RECON: 194 Round Time: 00:03:54 (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 : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9354 repeats masked totaling 3508895 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015163 bp Num Contigs Represented = 167 Non ambiguous bp: Initial: 30010763 bp After Masking: 23149889 bp Masked: 22.86 % -- Input Database Coverage: 40056231 bp out of 1476623026 bp ( 2.71 % ) Sampling Time: 00:01:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 300700 Comparison Time: 00:14:01 (hh:mm:ss) Elapsed Time, 5351 HSPs Collected Number of families returned by RECON: 1145 Round Time: 00:15:56 (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 : 00:02:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26973 repeats masked totaling 9358185 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018497 bp Num Contigs Represented = 406 Non ambiguous bp: Initial: 90004779 bp After Masking: 70165295 bp Masked: 22.04 % -- Input Database Coverage: 130074728 bp out of 1476623026 bp ( 8.81 % ) Sampling Time: 00:06:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2715615 Comparison Time: 01:21:40 (hh:mm:ss) Elapsed Time, 34495 HSPs Collected Number of families returned by RECON: 6560 Round Time: 01:30:06 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 93832 repeats masked totaling 33155937 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062759 bp Num Contigs Represented = 912 Non ambiguous bp: Initial: 270029265 bp After Masking: 206048969 bp Masked: 23.69 % -- Input Database Coverage: 400137487 bp out of 1476623026 bp ( 27.10 % ) Sampling Time: 00:18:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24454521 Comparison Time: 09:55:53 (hh:mm:ss) Elapsed Time, 187407 HSPs Collected Number of families returned by RECON: 39778 Round Time: 10:47:55 (hh:mm:ss) Elapsed Time : 233 families discovered. RepeatScout/RECON discovery complete: 413 families found Classification Time: 00:18:59 (hh:mm:ss) Elapsed Time Program Time: 13:07:49 (hh:mm:ss) Elapsed Time