RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.sH3ZdZ/RM_3963571.SunFeb232337172025 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: 1740382636 Database = /dev/shm/rModeler.sH3ZdZ/GCA_043748645.1_ASM4374864v1 - Sequences = 38 - Bases = 2209024231 Storage Throughput = excellent ( 1909.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001698 bp ( 40001698 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:23 (hh:mm:ss) Elapsed Time Round Time: 00:11:52 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11808 repeats masked totaling 2784324 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000467 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10000467 bp After Masking: 7069353 bp Masked: 29.31 % -- Input Database Coverage: 10000467 bp out of 2209024231 bp ( 0.45 % ) Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:50 (hh:mm:ss) Elapsed Time, 5951 HSPs Collected Number of families returned by RECON: 857 Round Time: 00:03:51 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36679 repeats masked totaling 8708711 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001226 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30001226 bp After Masking: 20833084 bp Masked: 30.56 % -- Input Database Coverage: 40001693 bp out of 2209024231 bp ( 1.81 % ) Sampling Time: 00:02:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:12:22 (hh:mm:ss) Elapsed Time, 23503 HSPs Collected Number of families returned by RECON: 2370 Round Time: 00:14:57 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118505 repeats masked totaling 27926763 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034438 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 90033438 bp After Masking: 60778440 bp Masked: 32.49 % -- Input Database Coverage: 130036131 bp out of 2209024231 bp ( 5.89 % ) Sampling Time: 00:07:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:08:07 (hh:mm:ss) Elapsed Time, 86805 HSPs Collected Number of families returned by RECON: 8274 Round Time: 01:16:38 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 390565 repeats masked totaling 92607138 bp(s). - TE Masking time 00:01:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026852 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 270020112 bp After Masking: 173608865 bp Masked: 35.71 % -- Input Database Coverage: 400062983 bp out of 2209024231 bp ( 18.11 % ) Sampling Time: 00:20:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 07:43:29 (hh:mm:ss) Elapsed Time, 269822 HSPs Collected Number of families returned by RECON: 34236 Round Time: 08:13:07 (hh:mm:ss) Elapsed Time : 405 families discovered. RepeatScout/RECON discovery complete: 836 families found Classification Time: 00:16:25 (hh:mm:ss) Elapsed Time Program Time: 10:16:50 (hh:mm:ss) Elapsed Time