RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7VmIVI/RM_376626.WedJan101930472024 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: 1704943845 Database = /dev/shm/rModeler.7VmIVI/GCF_025265405.1_mMesDen1_primary_haplotype - Sequences = 74 - Bases = 2683391478 Storage Throughput = excellent ( 1480.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036510 bp ( 40035810 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:01:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:46 (hh:mm:ss) Elapsed Time Round Time: 00:23:12 (hh:mm:ss) Elapsed Time : 194 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10188 repeats masked totaling 3081195 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001729 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10001729 bp After Masking: 6501824 bp Masked: 34.99 % -- Input Database Coverage: 10001729 bp out of 2683391478 bp ( 0.37 % ) Sampling Time: 00:01:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:52 (hh:mm:ss) Elapsed Time, 137963 HSPs Collected Number of families returned by RECON: 702 Round Time: 00:08:45 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35221 repeats masked totaling 10552872 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034778 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30034078 bp After Masking: 18657791 bp Masked: 37.88 % -- Input Database Coverage: 40036507 bp out of 2683391478 bp ( 1.49 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:18:46 (hh:mm:ss) Elapsed Time, 32770 HSPs Collected Number of families returned by RECON: 2480 Round Time: 00:22:12 (hh:mm:ss) Elapsed Time : 62 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 00:04:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 115833 repeats masked totaling 33348805 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039413 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 90032207 bp After Masking: 53567133 bp Masked: 40.50 % -- Input Database Coverage: 130075920 bp out of 2683391478 bp ( 4.85 % ) Sampling Time: 00:09:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:36:56 (hh:mm:ss) Elapsed Time, 171281 HSPs Collected Number of families returned by RECON: 7859 Round Time: 01:51:10 (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 : 00:13:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 393747 repeats masked totaling 108577046 bp(s). - TE Masking time 00:03:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270133303 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 270009987 bp After Masking: 151565631 bp Masked: 43.87 % -- Input Database Coverage: 400209223 bp out of 2683391478 bp ( 14.91 % ) Sampling Time: 00:28:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 11:01:30 (hh:mm:ss) Elapsed Time, 305938 HSPs Collected Number of families returned by RECON: 30561 Round Time: 11:55:35 (hh:mm:ss) Elapsed Time : 340 families discovered. RepeatScout/RECON discovery complete: 778 families found Classification Time: 00:25:32 (hh:mm:ss) Elapsed Time Program Time: 15:06:26 (hh:mm:ss) Elapsed Time