RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.9SaxE3/RM_3445595.SunSep130939502026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.9SaxE3/GCA_965279235.1_fBatMol1.1_alternate_haplotype, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1789317589 Database = /dev/shm/rModeler.9SaxE3/GCA_965279235.1_fBatMol1.1_alternate_haplotype - Sequences = 9961 - Bases = 1071127208 - N50 = 26722168 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 37591190-40276228 | [ 2 ] 34906152-37591190 | [ 3 ] 32221114-34906152 | [ 5 ] 29536076-32221114 | [ 3 ] 26851038-29536076 | [ 2 ] 24166000-26851038 | [ 5 ] 21480962-24166000 | [ 1 ] 18795924-21480962 | [ ] 16110886-18795924 | [ 2 ] 13425848-16110886 | [ 1 ] 10740810-13425848 | [ ] 8055772-10740810 | [ ] 5370734-8055772 | [ ] 2685696-5370734 | [ ] 658-2685696 |************************************************** [ 9937 ] Storage Throughput = excellent ( 1649.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40042768 bp ( 40005885 non ambiguous ) - Num Contigs Represented = 499 - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 874 raw families identified - RepeatScout: Running filtering stage.. 764 families remaining - RepeatScout: 00:03:38 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 734 families... 00:28:29 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 18 satellite(s), 270 contained, found in 00:00:04 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:05 (hh:mm:ss) Elapsed Time Round Time: 00:32:24 (hh:mm:ss) Elapsed Time : 446 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 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12270 repeats masked totaling 2287363 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10021146 bp Num Contigs Represented = 149 Non ambiguous bp: Initial: 10010546 bp After Masking: 6276869 bp Masked: 37.30 % -- Input Database Coverage: 10021146 bp out of 1071127208 bp ( 0.94 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 43071 Comparison Time: 00:04:04 (hh:mm:ss) Elapsed Time, 64505 HSPs Collected Number of families returned by RECON: 1852 Round Time: 00:05:44 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43841 repeats masked totaling 8441323 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30061624 bp Num Contigs Represented = 386 Non ambiguous bp: Initial: 30035141 bp After Masking: 17191777 bp Masked: 42.76 % -- Input Database Coverage: 40082770 bp out of 1071127208 bp ( 3.74 % ) Sampling Time: 00:03:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 384126 Comparison Time: 00:16:28 (hh:mm:ss) Elapsed Time, 81755 HSPs Collected Number of families returned by RECON: 4950 Round Time: 00:21:48 (hh:mm:ss) Elapsed Time : 215 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 154532 repeats masked totaling 28577214 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90093070 bp Num Contigs Represented = 1085 Non ambiguous bp: Initial: 90013194 bp After Masking: 47445387 bp Masked: 47.29 % -- Input Database Coverage: 130175840 bp out of 1071127208 bp ( 12.15 % ) Sampling Time: 00:12:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3451878 Comparison Time: 01:22:39 (hh:mm:ss) Elapsed Time, 400851 HSPs Collected Number of families returned by RECON: 12486 Round Time: 01:40:00 (hh:mm:ss) Elapsed Time : 609 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 572207 repeats masked totaling 103224172 bp(s). - TE Masking time 00:08:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270268754 bp Num Contigs Represented = 3108 Non ambiguous bp: Initial: 270008211 bp After Masking: 126532807 bp Masked: 53.14 % -- Input Database Coverage: 400444594 bp out of 1071127208 bp ( 37.39 % ) Sampling Time: 00:38:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31956015 Comparison Time: 08:24:53 (hh:mm:ss) Elapsed Time, 1039493 HSPs Collected Number of families returned by RECON: 34876 Round Time: 09:24:49 (hh:mm:ss) Elapsed Time : 1107 families discovered. RepeatScout/RECON discovery complete: 2436 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.9SaxE3/RM_3445595.SunSep130939502026 # 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: 00:04:43 (hh:mm:ss) Elapsed Time Program Time: 12:09:28 (hh:mm:ss) Elapsed Time