RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.QXOYy2/RM_335806.ThuSep102200242026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.QXOYy2/GCF_951640355.1_mEptNil1.1, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1789102823 Database = /dev/shm/rModeler.QXOYy2/GCF_951640355.1_mEptNil1.1 - Sequences = 206 - Bases = 2064102006 - N50 = 103318240 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 124240326-133114493 | [ 1 ] 115366160-124240326 | [ 2 ] 106491994-115366160 |* [ 4 ] 97617828-106491994 | [ 3 ] 88743662-97617828 | [ 2 ] 79869495-88743661 | [ 3 ] 70995329-79869495 | [ 1 ] 62121163-70995329 | [ 1 ] 53246997-62121163 | [ 2 ] 44372831-53246997 | [ 3 ] 35498664-44372830 | [ ] 26624498-35498664 | [ 1 ] 17750332-26624498 | [ 1 ] 8876166-17750332 | [ 2 ] 2000-8876166 |************************************************** [ 180 ] Storage Throughput = excellent ( 1115.54 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028373 bp ( 40023173 non ambiguous ) - Num Contigs Represented = 35 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 322 raw families identified - RepeatScout: Running filtering stage.. 278 families remaining - RepeatScout: 00:05:59 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 272 families... 01:55:18 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 3 satellite(s), 129 contained, found in 00:00:05 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:05 (hh:mm:ss) Elapsed Time Round Time: 02:03:08 (hh:mm:ss) Elapsed Time : 140 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13264 repeats masked totaling 2574043 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040735 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10039335 bp After Masking: 7121477 bp Masked: 29.06 % -- Input Database Coverage: 10040735 bp out of 2064102006 bp ( 0.49 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:48 (hh:mm:ss) Elapsed Time, 28756 HSPs Collected Number of families returned by RECON: 920 Round Time: 00:07:57 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46383 repeats masked totaling 8908560 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027643 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30023643 bp After Masking: 19773176 bp Masked: 34.14 % -- Input Database Coverage: 40068378 bp out of 2064102006 bp ( 1.94 % ) Sampling Time: 00:03:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:30:29 (hh:mm:ss) Elapsed Time, 64068 HSPs Collected Number of families returned by RECON: 2050 Round Time: 00:35:16 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:43 (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... 151205 repeats masked totaling 28457338 bp(s). - TE Masking time 00:02:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017194 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 90006594 bp After Masking: 58093252 bp Masked: 35.46 % -- Input Database Coverage: 130085572 bp out of 2064102006 bp ( 6.30 % ) Sampling Time: 00:10:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:43:58 (hh:mm:ss) Elapsed Time, 1217061 HSPs Collected Number of families returned by RECON: 6411 Round Time: 03:57:54 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 492474 repeats masked totaling 93906298 bp(s). - TE Masking time 00:10:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270061151 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 270026044 bp After Masking: 166086902 bp Masked: 38.49 % -- Input Database Coverage: 400146723 bp out of 2064102006 bp ( 19.39 % ) Sampling Time: 00:34:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 28:13:04 (hh:mm:ss) Elapsed Time, 9212067 HSPs Collected Number of families returned by RECON: 26727 Round Time: 29:13:13 (hh:mm:ss) Elapsed Time : 383 families discovered. RepeatScout/RECON discovery complete: 775 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.QXOYy2/RM_335806.ThuSep102200242026 # 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: 00:05:35 (hh:mm:ss) Elapsed Time Program Time: 36:03:03 (hh:mm:ss) Elapsed Time