RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UEysS1/RM_640209.MonApr211255582025 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: 1745265358 Database = /dev/shm/rModeler.UEysS1/GCA_965226115.1_fAulStu2.1 - Sequences = 23 - Bases = 945383024 Storage Throughput = excellent ( 1710.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033478 bp ( 40033278 non ambiguous ) - Num Contigs Represented = 22 - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:21 (hh:mm:ss) Elapsed Time Round Time: 00:10:47 (hh:mm:ss) Elapsed Time : 650 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10029 repeats masked totaling 2711709 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001261 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10001261 bp After Masking: 7082628 bp Masked: 29.18 % -- Input Database Coverage: 10001261 bp out of 945383024 bp ( 1.06 % ) Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 5992 HSPs Collected Number of families returned by RECON: 1169 Round Time: 00:03:19 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31279 repeats masked totaling 8282006 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032137 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30031937 bp After Masking: 20469344 bp Masked: 31.84 % -- Input Database Coverage: 40033398 bp out of 945383024 bp ( 4.23 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:11:56 (hh:mm:ss) Elapsed Time, 48239 HSPs Collected Number of families returned by RECON: 3947 Round Time: 00:14:07 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100801 repeats masked totaling 24981164 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011992 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 90011592 bp After Masking: 61617445 bp Masked: 31.54 % -- Input Database Coverage: 130045390 bp out of 945383024 bp ( 13.76 % ) Sampling Time: 00:04:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:16:11 (hh:mm:ss) Elapsed Time, 216596 HSPs Collected Number of families returned by RECON: 13300 Round Time: 01:24:20 (hh:mm:ss) Elapsed Time : 415 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 358553 repeats masked totaling 88428084 bp(s). - TE Masking time 00:04:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028643 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 270027243 bp After Masking: 172086579 bp Masked: 36.27 % -- Input Database Coverage: 400074033 bp out of 945383024 bp ( 42.32 % ) Sampling Time: 00:15:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22811635 Comparison Time: 09:02:37 (hh:mm:ss) Elapsed Time, 684693 HSPs Collected Number of families returned by RECON: 47868 Round Time: 09:44:57 (hh:mm:ss) Elapsed Time : 1030 families discovered. RepeatScout/RECON discovery complete: 2178 families found Classification Time: 01:04:05 (hh:mm:ss) Elapsed Time Program Time: 12:41:35 (hh:mm:ss) Elapsed Time