RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ksKZIg/RM_8710.WedJun261939142024 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: 1719455953 Database = /dev/shm/rModeler.ksKZIg/GCF_030014295.1_mLoxAfr1.hap2 - Sequences = 879 - Bases = 3540876381 - N50 = 135789635 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 225734151-241857137 | [ 2 ] 209611165-225734150 | [ 1 ] 193488180-209611165 | [ 1 ] 177365194-193488179 | [ 1 ] 161242209-177365194 | [ 1 ] 145119223-161242208 | [ ] 128996238-145119223 | [ 3 ] 112873252-128996237 | [ 2 ] 96750267-112873252 | [ 2 ] 80627281-96750266 | [ 8 ] 64504296-80627281 | [ 5 ] 48381310-64504295 | [ 1 ] 32258325-48381310 | [ 1 ] 16135339-32258324 | [ 1 ] 12354-16135339 |************************************************** [ 850 ] Storage Throughput = excellent ( 1081.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047363 bp ( 40007150 non ambiguous ) - Num Contigs Represented = 96 - Sequence extraction : 00:02:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:28 (hh:mm:ss) Elapsed Time Round Time: 00:35:32 (hh:mm:ss) Elapsed Time : 283 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16364 repeats masked totaling 4439183 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005324 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10005311 bp After Masking: 5216101 bp Masked: 47.87 % -- Input Database Coverage: 10005324 bp out of 3540876381 bp ( 0.28 % ) Sampling Time: 00:02:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:45 (hh:mm:ss) Elapsed Time, 54895 HSPs Collected Number of families returned by RECON: 657 Round Time: 00:10:15 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52516 repeats masked totaling 14301101 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041959 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 30001759 bp After Masking: 14746168 bp Masked: 50.85 % -- Input Database Coverage: 40047283 bp out of 3540876381 bp ( 1.13 % ) Sampling Time: 00:07:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:34:40 (hh:mm:ss) Elapsed Time, 408812 HSPs Collected Number of families returned by RECON: 1805 Round Time: 00:42:38 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 166061 repeats masked totaling 44634097 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90112151 bp Num Contigs Represented = 162 Non ambiguous bp: Initial: 90013129 bp After Masking: 42561944 bp Masked: 52.72 % -- Input Database Coverage: 130159434 bp out of 3540876381 bp ( 3.68 % ) Sampling Time: 00:17:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:59:56 (hh:mm:ss) Elapsed Time, 1345252 HSPs Collected Number of families returned by RECON: 6103 Round Time: 03:24:33 (hh:mm:ss) Elapsed Time : 158 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 522591 repeats masked totaling 139899504 bp(s). - TE Masking time 00:09:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270154371 bp Num Contigs Represented = 308 Non ambiguous bp: Initial: 270007821 bp After Masking: 122027190 bp Masked: 54.81 % -- Input Database Coverage: 400313805 bp out of 3540876381 bp ( 11.31 % ) Sampling Time: 01:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 22:04:30 (hh:mm:ss) Elapsed Time, 13513170 HSPs Collected Number of families returned by RECON: 22805 Round Time: 23:32:16 (hh:mm:ss) Elapsed Time : 371 families discovered. RepeatScout/RECON discovery complete: 875 families found Classification Time: 00:45:06 (hh:mm:ss) Elapsed Time Program Time: 29:10:20 (hh:mm:ss) Elapsed Time