RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MRWkSa/RM_20609.MonDec40112252023 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: 1701681143 Database = /dev/shm/rModeler.MRWkSa/GCA_030867105.1_rLiaOli1.hap1 - Sequences = 43 - Bases = 1486119866 Storage Throughput = excellent ( 1166.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043160 bp ( 40002760 non ambiguous ) - Num Contigs Represented = 17 - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:40 (hh:mm:ss) Elapsed Time Round Time: 00:28:20 (hh:mm:ss) Elapsed Time : 315 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10052 repeats masked totaling 2250867 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040600 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 10000500 bp After Masking: 7539003 bp Masked: 24.61 % -- Input Database Coverage: 10040600 bp out of 1486119866 bp ( 0.68 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:53 (hh:mm:ss) Elapsed Time, 20541 HSPs Collected Number of families returned by RECON: 1421 Round Time: 00:08:12 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33017 repeats masked totaling 7223107 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002480 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 30002180 bp After Masking: 21977042 bp Masked: 26.75 % -- Input Database Coverage: 40043080 bp out of 1486119866 bp ( 2.69 % ) Sampling Time: 00:04:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:31:05 (hh:mm:ss) Elapsed Time, 43043 HSPs Collected Number of families returned by RECON: 4073 Round Time: 00:37:12 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:46 (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... 112600 repeats masked totaling 25114000 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015813 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 90004015 bp After Masking: 62636729 bp Masked: 30.41 % -- Input Database Coverage: 130058893 bp out of 1486119866 bp ( 8.75 % ) Sampling Time: 00:13:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 03:34:33 (hh:mm:ss) Elapsed Time, 157778 HSPs Collected Number of families returned by RECON: 12944 Round Time: 04:53:47 (hh:mm:ss) Elapsed Time : 343 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 397428 repeats masked totaling 87969663 bp(s). - TE Masking time 00:08:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034850 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 270017663 bp After Masking: 175031647 bp Masked: 35.18 % -- Input Database Coverage: 400093743 bp out of 1486119866 bp ( 26.92 % ) Sampling Time: 00:41:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 26:32:27 (hh:mm:ss) Elapsed Time, 393907 HSPs Collected Number of families returned by RECON: 45569 Round Time: 28:17:36 (hh:mm:ss) Elapsed Time : 771 families discovered. RepeatScout/RECON discovery complete: 1552 families found Classification Time: 01:11:16 (hh:mm:ss) Elapsed Time Program Time: 35:36:23 (hh:mm:ss) Elapsed Time