RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gr9R8L/RM_16060.MonNov271306102023 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: 1701119169 Database = /dev/shm/rModeler.gr9R8L/GCF_027579695.1_fNeoGra1.pri - Sequences = 38 - Bases = 2341916362 Storage Throughput = excellent ( 1197.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40321939 bp ( 40034433 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:11 (hh:mm:ss) Elapsed Time Round Time: 00:46:44 (hh:mm:ss) Elapsed Time : 928 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17364 repeats masked totaling 5609097 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080477 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10000446 bp After Masking: 4127855 bp Masked: 58.72 % -- Input Database Coverage: 10080477 bp out of 2341916362 bp ( 0.43 % ) Sampling Time: 00:01:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:49 (hh:mm:ss) Elapsed Time, 17287 HSPs Collected Number of families returned by RECON: 1274 Round Time: 00:07:49 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53487 repeats masked totaling 17209029 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30241457 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30033982 bp After Masking: 11385066 bp Masked: 62.09 % -- Input Database Coverage: 40321934 bp out of 2341916362 bp ( 1.72 % ) Sampling Time: 00:06:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:20:49 (hh:mm:ss) Elapsed Time, 43118 HSPs Collected Number of families returned by RECON: 4042 Round Time: 00:28:14 (hh:mm:ss) Elapsed Time : 91 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 164265 repeats masked totaling 52389677 bp(s). - TE Masking time 00:03:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90478665 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90029903 bp After Masking: 33839884 bp Masked: 62.41 % -- Input Database Coverage: 130800599 bp out of 2341916362 bp ( 5.59 % ) Sampling Time: 00:22:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 02:02:44 (hh:mm:ss) Elapsed Time, 311092 HSPs Collected Number of families returned by RECON: 10705 Round Time: 02:35:46 (hh:mm:ss) Elapsed Time : 544 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 555153 repeats masked totaling 174894962 bp(s). - TE Masking time 00:17:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271295169 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 270031636 bp After Masking: 83760278 bp Masked: 68.98 % -- Input Database Coverage: 402095768 bp out of 2341916362 bp ( 17.17 % ) Sampling Time: 01:06:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 13:19:37 (hh:mm:ss) Elapsed Time, 865647 HSPs Collected Number of families returned by RECON: 27445 Round Time: 15:17:01 (hh:mm:ss) Elapsed Time : 1279 families discovered. RepeatScout/RECON discovery complete: 2854 families found Classification Time: 02:27:08 (hh:mm:ss) Elapsed Time Program Time: 21:42:42 (hh:mm:ss) Elapsed Time