RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Kk5Uh1/RM_30835.MonNov271819082023 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: 1701137947 Database = /dev/shm/rModeler.Kk5Uh1/GCA_027887205.1_rMalTer1.hap2 - Sequences = 59 - Bases = 2212837039 Storage Throughput = excellent ( 1184.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045995 bp ( 40032641 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:03:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:09 (hh:mm:ss) Elapsed Time Round Time: 00:31:07 (hh:mm:ss) Elapsed Time : 575 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13571 repeats masked totaling 2997272 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040639 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10027985 bp After Masking: 6972069 bp Masked: 30.47 % -- Input Database Coverage: 10040639 bp out of 2212837039 bp ( 0.45 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:29 (hh:mm:ss) Elapsed Time, 14300 HSPs Collected Number of families returned by RECON: 1583 Round Time: 00:07:30 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:44 (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... 44052 repeats masked totaling 9296324 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005346 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30004646 bp After Masking: 20453077 bp Masked: 31.83 % -- Input Database Coverage: 40045985 bp out of 2212837039 bp ( 1.81 % ) Sampling Time: 00:04:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:27:42 (hh:mm:ss) Elapsed Time, 63755 HSPs Collected Number of families returned by RECON: 5249 Round Time: 00:34:17 (hh:mm:ss) Elapsed Time : 135 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 152206 repeats masked totaling 32131680 bp(s). - TE Masking time 00:02:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90050261 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90034948 bp After Masking: 57051350 bp Masked: 36.63 % -- Input Database Coverage: 130096246 bp out of 2212837039 bp ( 5.88 % ) Sampling Time: 00:14:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:24:47 (hh:mm:ss) Elapsed Time, 267709 HSPs Collected Number of families returned by RECON: 14547 Round Time: 03:53:45 (hh:mm:ss) Elapsed Time : 457 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:24:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 534171 repeats masked totaling 112274136 bp(s). - TE Masking time 00:12:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270047830 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 270037959 bp After Masking: 155528887 bp Masked: 42.40 % -- Input Database Coverage: 400144076 bp out of 2212837039 bp ( 18.08 % ) Sampling Time: 00:46:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 22:02:36 (hh:mm:ss) Elapsed Time, 645763 HSPs Collected Number of families returned by RECON: 44914 Round Time: 24:10:28 (hh:mm:ss) Elapsed Time : 1148 families discovered. RepeatScout/RECON discovery complete: 2347 families found Classification Time: 01:38:47 (hh:mm:ss) Elapsed Time Program Time: 30:55:54 (hh:mm:ss) Elapsed Time