RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.S1v3Wk/RM_973066.FriSep182106352026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.S1v3Wk/GCA_060551615.1_aCryAll3.hap1, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1789790794 Database = /dev/shm/rModeler.S1v3Wk/GCA_060551615.1_aCryAll3.hap1 - Sequences = 15812 - Bases = 49388744164 - N50 = 1545643803 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1923158825-2060526829 | [ 6 ] 1785790822-1923158825 | [ 3 ] 1648422819-1785790822 | [ 2 ] 1511054815-1648422818 | [ 3 ] 1373686812-1511054815 | [ 4 ] 1236318809-1373686812 | [ 1 ] 1098950805-1236318808 | [ 1 ] 961582802-1098950805 | [ 3 ] 824214799-961582802 | [ 2 ] 686846795-824214798 | [ 2 ] 549478792-686846795 | [ 2 ] 412110789-549478792 | [ 1 ] 274742785-412110788 | [ 2 ] 137374782-274742785 | [ 11 ] 6779-137374782 |************************************************** [ 15769 ] Storage Throughput = excellent ( 1751.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033899 bp ( 40031382 non ambiguous ) - Num Contigs Represented = 133 - Sequence extraction : 00:09:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 615 raw families identified - RepeatScout: Running filtering stage.. 498 families remaining - RepeatScout: 00:07:58 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 492 families... 00:13:44 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 11 satellite(s), 173 contained, found in 00:00:06 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:06 (hh:mm:ss) Elapsed Time Round Time: 00:31:39 (hh:mm:ss) Elapsed Time : 313 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9508 repeats masked totaling 5020387 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003864 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 10003464 bp After Masking: 2994777 bp Masked: 70.06 % -- Input Database Coverage: 10003864 bp out of 49388744164 bp ( 0.02 % ) Sampling Time: 00:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:12 (hh:mm:ss) Elapsed Time, 23369 HSPs Collected Number of families returned by RECON: 909 Round Time: 00:09:18 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29707 repeats masked totaling 15964115 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030035 bp Num Contigs Represented = 112 Non ambiguous bp: Initial: 30027918 bp After Masking: 9144425 bp Masked: 69.55 % -- Input Database Coverage: 40033899 bp out of 49388744164 bp ( 0.08 % ) Sampling Time: 00:13:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:14:40 (hh:mm:ss) Elapsed Time, 72558 HSPs Collected Number of families returned by RECON: 3035 Round Time: 00:30:52 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:22:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90249 repeats masked totaling 52090412 bp(s). - TE Masking time 00:02:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017977 bp Num Contigs Represented = 243 Non ambiguous bp: Initial: 90014377 bp After Masking: 21895396 bp Masked: 75.68 % -- Input Database Coverage: 130051876 bp out of 49388744164 bp ( 0.26 % ) Sampling Time: 00:42:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 00:56:22 (hh:mm:ss) Elapsed Time, 228610 HSPs Collected Number of families returned by RECON: 7534 Round Time: 01:42:21 (hh:mm:ss) Elapsed Time : 276 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:12:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:52:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 303233 repeats masked totaling 173347570 bp(s). - TE Masking time 00:12:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041476 bp Num Contigs Represented = 544 Non ambiguous bp: Initial: 270028976 bp After Masking: 48698105 bp Masked: 81.97 % -- Input Database Coverage: 400093352 bp out of 49388744164 bp ( 0.81 % ) Sampling Time: 02:18:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 04:11:26 (hh:mm:ss) Elapsed Time, 607044 HSPs Collected Number of families returned by RECON: 17884 Round Time: 06:59:51 (hh:mm:ss) Elapsed Time : 824 families discovered. RepeatScout/RECON discovery complete: 1504 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.S1v3Wk/RM_973066.FriSep182106352026 # 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: 00:08:25 (hh:mm:ss) Elapsed Time Program Time: 10:02:26 (hh:mm:ss) Elapsed Time