RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.YmKb8P/RM_3813372.ThuOct10649112026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.YmKb8P/GCA_988136345.1_bMusSti1.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: 1790862551 Database = /dev/shm/rModeler.YmKb8P/GCA_988136345.1_bMusSti1.hap1.1 - Sequences = 167 - Bases = 1516191245 - N50 = 66891566 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 149651269-160340308 | [ 1 ] 138962231-149651269 | [ ] 128273193-138962231 | [ ] 117584154-128273192 | [ 2 ] 106895116-117584154 | [ ] 96206078-106895116 | [ 1 ] 85517040-96206078 | [ ] 74828001-85517039 | [ 2 ] 64138963-74828001 | [ 1 ] 53449925-64138963 | [ ] 42760887-53449925 | [ 2 ] 32071848-42760886 |* [ 5 ] 21382810-32071848 |* [ 4 ] 10693772-21382810 |****** [ 16 ] 4734-10693772 |************************************************** [ 133 ] Storage Throughput = excellent ( 1616.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009973 bp ( 40009073 non ambiguous ) - Num Contigs Represented = 74 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 321 raw families identified - RepeatScout: Running filtering stage.. 283 families remaining - RepeatScout: 00:06:28 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 277 families... 06:17:09 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 18 satellite(s), 94 contained, found in 00:00:12 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:12 (hh:mm:ss) Elapsed Time Round Time: 06:24:22 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4652 repeats masked totaling 1977503 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039060 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 10038960 bp After Masking: 6608649 bp Masked: 34.17 % -- Input Database Coverage: 10039060 bp out of 1516191245 bp ( 0.66 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:37 (hh:mm:ss) Elapsed Time, 176810 HSPs Collected Number of families returned by RECON: 251 Round Time: 00:07:41 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (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... 12178 repeats masked totaling 4863897 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010915 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30010115 bp After Masking: 21582738 bp Masked: 28.08 % -- Input Database Coverage: 40049975 bp out of 1516191245 bp ( 2.64 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:27:01 (hh:mm:ss) Elapsed Time, 1815670 HSPs Collected Number of families returned by RECON: 1301 Round Time: 00:31:30 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38120 repeats masked totaling 15691869 bp(s). - TE Masking time 00:02:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011352 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 90010752 bp After Masking: 62713245 bp Masked: 30.33 % -- Input Database Coverage: 130061327 bp out of 1516191245 bp ( 8.58 % ) Sampling Time: 00:13:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:08:44 (hh:mm:ss) Elapsed Time, 24717480 HSPs Collected Number of families returned by RECON: 6673 Round Time: 03:33:28 (hh:mm:ss) Elapsed Time : 80 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143056 repeats masked totaling 62511279 bp(s). - TE Masking time 00:12:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031041 bp Num Contigs Represented = 142 Non ambiguous bp: Initial: 270025405 bp After Masking: 173227132 bp Masked: 35.85 % -- Input Database Coverage: 400092368 bp out of 1516191245 bp ( 26.39 % ) Sampling Time: 00:48:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 21:17:15 (hh:mm:ss) Elapsed Time, 192186932 HSPs Collected Number of families returned by RECON: 36846 Round Time: 23:55:26 (hh:mm:ss) Elapsed Time : 240 families discovered. RepeatScout/RECON discovery complete: 498 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.YmKb8P/RM_3813372.ThuOct10649112026 # 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: 00:05:11 (hh:mm:ss) Elapsed Time Program Time: 34:37:38 (hh:mm:ss) Elapsed Time