RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.fo4otm/RM_541117.TueSep290835152026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.fo4otm/GCA_988281055.1_fPhyBle1.1, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1790696115 Database = /dev/shm/rModeler.fo4otm/GCA_988281055.1_fPhyBle1.1 - Sequences = 52 - Bases = 589436901 Storage Throughput = excellent ( 1654.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009228 bp ( 40008728 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 378 raw families identified - RepeatScout: Running filtering stage.. 317 families remaining - RepeatScout: 00:15:24 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 301 families... 00:09:35 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 10 satellite(s), 90 contained, found in 00:00:03 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:25:11 (hh:mm:ss) Elapsed Time : 201 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4768 repeats masked totaling 937833 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001326 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10001026 bp After Masking: 7521249 bp Masked: 24.80 % -- Input Database Coverage: 10001326 bp out of 589436901 bp ( 1.70 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:57 (hh:mm:ss) Elapsed Time, 7542 HSPs Collected Number of families returned by RECON: 863 Round Time: 00:06:49 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16900 repeats masked totaling 3457168 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007902 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30007702 bp After Masking: 22194535 bp Masked: 26.04 % -- Input Database Coverage: 40009228 bp out of 589436901 bp ( 6.79 % ) Sampling Time: 00:05:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:22:08 (hh:mm:ss) Elapsed Time, 35015 HSPs Collected Number of families returned by RECON: 3817 Round Time: 00:27:49 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58404 repeats masked totaling 10457445 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90006759 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90006059 bp After Masking: 66463967 bp Masked: 26.16 % -- Input Database Coverage: 130015987 bp out of 589436901 bp ( 22.06 % ) Sampling Time: 00:12:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:21:49 (hh:mm:ss) Elapsed Time, 114644 HSPs Collected Number of families returned by RECON: 14332 Round Time: 02:37:02 (hh:mm:ss) Elapsed Time : 225 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 228980 repeats masked totaling 40095852 bp(s). - TE Masking time 00:05:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027206 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 270025606 bp After Masking: 190445236 bp Masked: 29.47 % -- Input Database Coverage: 400043193 bp out of 589436901 bp ( 67.87 % ) Sampling Time: 00:40:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 17:05:06 (hh:mm:ss) Elapsed Time, 565003 HSPs Collected Number of families returned by RECON: 54757 Round Time: 18:12:11 (hh:mm:ss) Elapsed Time : 726 families discovered. RepeatScout/RECON discovery complete: 1235 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.fo4otm/RM_541117.TueSep290835152026 # 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: 00:03:57 (hh:mm:ss) Elapsed Time Program Time: 21:52:59 (hh:mm:ss) Elapsed Time