RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.rUYBSa/RM_654675.TueNov31512282026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.rUYBSa/GCA_976338635.1_cbUloPhyl1.1, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1793747547 Database = /dev/shm/rModeler.rUYBSa/GCA_976338635.1_cbUloPhyl1.1 - Sequences = 13 - Bases = 263917262 Storage Throughput = excellent ( 1621.54 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40007363 bp ( 40003063 non ambiguous ) - Num Contigs Represented = 11 - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 450 raw families identified - RepeatScout: Running filtering stage.. 435 families remaining - RepeatScout: 00:02:02 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 428 families... 00:15:11 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 3 satellite(s), 155 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:17:31 (hh:mm:ss) Elapsed Time : 270 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14050 repeats masked totaling 3885108 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001885 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 10000885 bp After Masking: 6044558 bp Masked: 39.56 % -- Input Database Coverage: 10001885 bp out of 263917262 bp ( 3.79 % ) Sampling Time: 00:00:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:38 (hh:mm:ss) Elapsed Time, 67758 HSPs Collected Number of families returned by RECON: 1156 Round Time: 00:04:55 (hh:mm:ss) Elapsed Time : 36 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48207 repeats masked totaling 13695741 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005478 bp Num Contigs Represented = 11 Non ambiguous bp: Initial: 30002178 bp After Masking: 16122433 bp Masked: 46.26 % -- Input Database Coverage: 40007363 bp out of 263917262 bp ( 15.16 % ) Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:14:19 (hh:mm:ss) Elapsed Time, 38767 HSPs Collected Number of families returned by RECON: 3419 Round Time: 00:16:01 (hh:mm:ss) Elapsed Time : 110 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 163511 repeats masked totaling 44978258 bp(s). - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041518 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 90026594 bp After Masking: 44503552 bp Masked: 50.57 % -- Input Database Coverage: 130048881 bp out of 263917262 bp ( 49.28 % ) Sampling Time: 00:03:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 01:12:54 (hh:mm:ss) Elapsed Time, 132503 HSPs Collected Number of families returned by RECON: 11628 Round Time: 01:19:00 (hh:mm:ss) Elapsed Time : 301 families discovered. - Increasing sample size to include end piece now = 403909899 RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 273106 repeats masked totaling 72288252 bp(s). - TE Masking time 00:03:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 133868381 bp Num Contigs Represented = 13 Non ambiguous bp: Initial: 133848446 bp After Masking: 60836703 bp Masked: 54.55 % -- Input Database Coverage: 263917262 bp out of 263917262 bp ( 100.00 % ) Sampling Time: 00:06:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 5609575 Comparison Time: 02:11:03 (hh:mm:ss) Elapsed Time, 97874 HSPs Collected Number of families returned by RECON: 16030 Round Time: 02:20:27 (hh:mm:ss) Elapsed Time : 186 families discovered. RepeatScout/RECON discovery complete: 903 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.rUYBSa/RM_654675.TueNov31512282026 # FamDB: # Database: Dfam # Version: 4.0 # Date: 2026-05-22 # Protein Library: /hive/data/outside/RepeatModeler-2.0.9/Libraries/PROT-Dfam_4.0/repeatpeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatModeler-2.0.9/Libraries/CONS-Dfam_4.0/reference.fa # - 30659 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:02:08 (hh:mm:ss) Elapsed Time Program Time: 04:20:02 (hh:mm:ss) Elapsed Time