RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.XpC868/RM_31779.WedJan101935142024 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: 1704944113 Database = /dev/shm/rModeler.XpC868/GCA_023053635.1_rElgMul1.0.p - Sequences = 85 - Bases = 1790509355 Storage Throughput = excellent ( 1133.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006898 bp ( 40006898 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:34 (hh:mm:ss) Elapsed Time Round Time: 00:28:38 (hh:mm:ss) Elapsed Time : 615 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (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... 22280 repeats masked totaling 3609783 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002424 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10002424 bp After Masking: 6085615 bp Masked: 39.16 % -- Input Database Coverage: 10002424 bp out of 1790509355 bp ( 0.56 % ) Sampling Time: 00:01:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:15 (hh:mm:ss) Elapsed Time, 13972 HSPs Collected Number of families returned by RECON: 1487 Round Time: 00:07:21 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67319 repeats masked totaling 11305858 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004394 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30004394 bp After Masking: 18123571 bp Masked: 39.60 % -- Input Database Coverage: 40006818 bp out of 1790509355 bp ( 2.23 % ) Sampling Time: 00:03:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:25:33 (hh:mm:ss) Elapsed Time, 53140 HSPs Collected Number of families returned by RECON: 4812 Round Time: 00:30:29 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 219796 repeats masked totaling 36535306 bp(s). - TE Masking time 00:02:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90006544 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 90006444 bp After Masking: 51325039 bp Masked: 42.98 % -- Input Database Coverage: 130013362 bp out of 1790509355 bp ( 7.26 % ) Sampling Time: 00:10:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:45:54 (hh:mm:ss) Elapsed Time, 210163 HSPs Collected Number of families returned by RECON: 13753 Round Time: 03:07:49 (hh:mm:ss) Elapsed Time : 466 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 732379 repeats masked totaling 122155917 bp(s). - TE Masking time 00:11:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270000860 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 270000660 bp After Masking: 141398437 bp Masked: 47.63 % -- Input Database Coverage: 400014222 bp out of 1790509355 bp ( 22.34 % ) Sampling Time: 00:34:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 20:32:36 (hh:mm:ss) Elapsed Time, 627094 HSPs Collected Number of families returned by RECON: 44333 Round Time: 22:24:31 (hh:mm:ss) Elapsed Time : 1103 families discovered. RepeatScout/RECON discovery complete: 2361 families found Classification Time: 01:16:16 (hh:mm:ss) Elapsed Time Program Time: 27:55:04 (hh:mm:ss) Elapsed Time