RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EaioAy/RM_26565.MonDec40000252023 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: 1701676823 Database = /dev/shm/rModeler.EaioAy/GCA_030867085.1_rLiaOli1.hap2 - Sequences = 65 - Bases = 1478263624 Storage Throughput = excellent ( 1163.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047559 bp ( 40026146 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:03:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:24 (hh:mm:ss) Elapsed Time Round Time: 00:29:02 (hh:mm:ss) Elapsed Time : 337 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9121 repeats masked totaling 2243136 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000378 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10000378 bp After Masking: 7566415 bp Masked: 24.34 % -- Input Database Coverage: 10000378 bp out of 1478263624 bp ( 0.68 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:57 (hh:mm:ss) Elapsed Time, 10122 HSPs Collected Number of families returned by RECON: 1330 Round Time: 00:07:45 (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 : 00:02:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31930 repeats masked totaling 7398589 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30047178 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30025765 bp After Masking: 21969620 bp Masked: 26.83 % -- Input Database Coverage: 40047556 bp out of 1478263624 bp ( 2.71 % ) Sampling Time: 00:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:31:10 (hh:mm:ss) Elapsed Time, 41978 HSPs Collected Number of families returned by RECON: 4265 Round Time: 00:37:33 (hh:mm:ss) Elapsed Time : 99 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108312 repeats masked totaling 24627351 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90499832 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90034082 bp After Masking: 63405927 bp Masked: 29.58 % -- Input Database Coverage: 130547388 bp out of 1478263624 bp ( 8.83 % ) Sampling Time: 00:12:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 03:36:33 (hh:mm:ss) Elapsed Time, 172645 HSPs Collected Number of families returned by RECON: 13590 Round Time: 04:13:06 (hh:mm:ss) Elapsed Time : 356 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:23:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 394333 repeats masked totaling 86563996 bp(s). - TE Masking time 00:08:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270998815 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 270008967 bp After Masking: 177673544 bp Masked: 34.20 % -- Input Database Coverage: 401546203 bp out of 1478263624 bp ( 27.16 % ) Sampling Time: 00:42:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22994371 Comparison Time: 27:07:00 (hh:mm:ss) Elapsed Time, 435914 HSPs Collected Number of families returned by RECON: 49153 Round Time: 28:59:30 (hh:mm:ss) Elapsed Time : 805 families discovered. RepeatScout/RECON discovery complete: 1625 families found Classification Time: 01:08:41 (hh:mm:ss) Elapsed Time Program Time: 35:35:37 (hh:mm:ss) Elapsed Time