RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.qlnd6L/RM_1538245.SatSep191009332026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.qlnd6L/GCF_965119305.1_aPelLes1.hap1.1, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1789837772 Database = /dev/shm/rModeler.qlnd6L/GCF_965119305.1_aPelLes1.hap1.1 - Sequences = 1328 - Bases = 5811246175 - N50 = 688568912 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 836871209-896647653 | [ 1 ] 777094765-836871208 | [ ] 717318322-777094765 | [ 1 ] 657541878-717318321 | [ 2 ] 597765435-657541878 | [ ] 537988991-597765434 | [ 1 ] 478212548-537988991 | [ ] 418436104-478212547 | [ ] 358659661-418436104 | [ ] 298883217-358659660 | [ 3 ] 239106774-298883217 | [ 2 ] 179330330-239106773 | [ 3 ] 119553887-179330330 | [ ] 59777443-119553886 | [ ] 1000-59777443 |************************************************** [ 1315 ] Storage Throughput = excellent ( 1842.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029437 bp ( 40026037 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:04:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 740 raw families identified - RepeatScout: Running filtering stage.. 620 families remaining - RepeatScout: 00:03:50 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 612 families... 03:15:47 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 25 satellite(s), 243 contained, found in 00:00:05 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:05 (hh:mm:ss) Elapsed Time Round Time: 03:23:45 (hh:mm:ss) Elapsed Time : 351 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12764 repeats masked totaling 4062205 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031303 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10030703 bp After Masking: 4909436 bp Masked: 51.06 % -- Input Database Coverage: 10031303 bp out of 5811246175 bp ( 0.17 % ) Sampling Time: 00:01:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:53 (hh:mm:ss) Elapsed Time, 81699 HSPs Collected Number of families returned by RECON: 2019 Round Time: 00:06:39 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46576 repeats masked totaling 14423992 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038134 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30035334 bp After Masking: 12738333 bp Masked: 57.59 % -- Input Database Coverage: 40069437 bp out of 5811246175 bp ( 0.69 % ) Sampling Time: 00:05:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:14:19 (hh:mm:ss) Elapsed Time, 102982 HSPs Collected Number of families returned by RECON: 4829 Round Time: 00:21:05 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 159698 repeats masked totaling 48515782 bp(s). - TE Masking time 00:01:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009456 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90000856 bp After Masking: 32910502 bp Masked: 63.43 % -- Input Database Coverage: 130078893 bp out of 5811246175 bp ( 2.24 % ) Sampling Time: 00:16:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:06:13 (hh:mm:ss) Elapsed Time, 343930 HSPs Collected Number of families returned by RECON: 12102 Round Time: 01:27:50 (hh:mm:ss) Elapsed Time : 515 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:27:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 571481 repeats masked totaling 167113861 bp(s). - TE Masking time 00:09:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270033782 bp Num Contigs Represented = 153 Non ambiguous bp: Initial: 270004675 bp After Masking: 75797208 bp Masked: 71.93 % -- Input Database Coverage: 400112675 bp out of 5811246175 bp ( 6.89 % ) Sampling Time: 00:55:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 05:49:23 (hh:mm:ss) Elapsed Time, 772611 HSPs Collected Number of families returned by RECON: 27515 Round Time: 07:06:57 (hh:mm:ss) Elapsed Time : 1302 families discovered. RepeatScout/RECON discovery complete: 2399 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.qlnd6L/RM_1538245.SatSep191009332026 # 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: 00:05:18 (hh:mm:ss) Elapsed Time Program Time: 12:31:34 (hh:mm:ss) Elapsed Time