RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KPpF45/RM_401948.ThuJan121211322023 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: 1673554290 Database = /dev/shm/rModeler.KPpF45/GCF_007474595.2_mLynCan4.pri.v2 - Sequences = 54 - Bases = 2407810255 Storage Throughput = excellent ( 1687.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041151 bp ( 40010757 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:04:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:39 (hh:mm:ss) Elapsed Time Round Time: 00:22:41 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:01 (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... 11188 repeats masked totaling 2429117 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040286 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10010397 bp After Masking: 7498588 bp Masked: 25.09 % -- Input Database Coverage: 10040286 bp out of 2407810255 bp ( 0.42 % ) Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:20 (hh:mm:ss) Elapsed Time, 7201 HSPs Collected Number of families returned by RECON: 922 Round Time: 00:09:10 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36133 repeats masked totaling 7734762 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000860 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 30000355 bp After Masking: 22006100 bp Masked: 26.65 % -- Input Database Coverage: 40041146 bp out of 2407810255 bp ( 1.66 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:25:39 (hh:mm:ss) Elapsed Time, 24855 HSPs Collected Number of families returned by RECON: 2375 Round Time: 00:30:35 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125509 repeats masked totaling 26984569 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90115838 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 90021365 bp After Masking: 62317267 bp Masked: 30.78 % -- Input Database Coverage: 130156984 bp out of 2407810255 bp ( 5.41 % ) Sampling Time: 00:11:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:21:38 (hh:mm:ss) Elapsed Time, 71736 HSPs Collected Number of families returned by RECON: 8148 Round Time: 02:35:54 (hh:mm:ss) Elapsed Time : 161 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:24:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 399182 repeats masked totaling 86833879 bp(s). - TE Masking time 00:03:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270345868 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 270018513 bp After Masking: 180927906 bp Masked: 32.99 % -- Input Database Coverage: 400502852 bp out of 2407810255 bp ( 16.63 % ) Sampling Time: 00:37:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 14:56:04 (hh:mm:ss) Elapsed Time, 157021 HSPs Collected Number of families returned by RECON: 35867 Round Time: 15:48:10 (hh:mm:ss) Elapsed Time : 327 families discovered. RepeatScout/RECON discovery complete: 751 families found Classification Time: 00:16:31 (hh:mm:ss) Elapsed Time Program Time: 19:43:01 (hh:mm:ss) Elapsed Time