RepeatModeler Version 2.0.9 =========================== Using output directory = /dev/shm/rModeler.UH4k84/RM_3092078.ThuOct220828472026 Search Engine = rmblast 2.17.1+ Threads = 32 Dependencies: TRF 4.09, RECON /dev/shm/rModeler.UH4k84/GCA_037349215.2_rGraGeo1_p1.2, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1792682926 Database = /dev/shm/rModeler.UH4k84/GCA_037349215.2_rGraGeo1_p1.2 - Sequences = 59 - Bases = 2225189681 Storage Throughput = excellent ( 1161.27 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030526 bp ( 40029826 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:03:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 513 raw families identified - RepeatScout: Running filtering stage.. 468 families remaining - RepeatScout: 00:04:19 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 457 families... 00:39:44 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 2 satellite(s), 177 contained, found in 00:00:09 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:09 (hh:mm:ss) Elapsed Time Round Time: 00:47:33 (hh:mm:ss) Elapsed Time : 278 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11917 repeats masked totaling 2990515 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001415 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10001315 bp After Masking: 6908622 bp Masked: 30.92 % -- Input Database Coverage: 10001415 bp out of 2225189681 bp ( 0.45 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:27 (hh:mm:ss) Elapsed Time, 27556 HSPs Collected Number of families returned by RECON: 1824 Round Time: 00:07:44 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44518 repeats masked totaling 10250765 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029111 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30028511 bp After Masking: 19546192 bp Masked: 34.91 % -- Input Database Coverage: 40030526 bp out of 2225189681 bp ( 1.80 % ) Sampling Time: 00:04:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:28:59 (hh:mm:ss) Elapsed Time, 72396 HSPs Collected Number of families returned by RECON: 4454 Round Time: 00:35:58 (hh:mm:ss) Elapsed Time : 147 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 158408 repeats masked totaling 35116034 bp(s). - TE Masking time 00:04:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029887 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 90027426 bp After Masking: 54150810 bp Masked: 39.85 % -- Input Database Coverage: 130060413 bp out of 2225189681 bp ( 5.84 % ) Sampling Time: 00:14:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:09:40 (hh:mm:ss) Elapsed Time, 207487 HSPs Collected Number of families returned by RECON: 11873 Round Time: 03:34:12 (hh:mm:ss) Elapsed Time : 405 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 562485 repeats masked totaling 121127977 bp(s). - TE Masking time 00:22:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032745 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 270026645 bp After Masking: 146724303 bp Masked: 45.66 % -- Input Database Coverage: 400093158 bp out of 2225189681 bp ( 17.98 % ) Sampling Time: 00:54:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 23:08:03 (hh:mm:ss) Elapsed Time, 415945 HSPs Collected Number of families returned by RECON: 34602 Round Time: 24:48:35 (hh:mm:ss) Elapsed Time : 900 families discovered. RepeatScout/RECON discovery complete: 1777 families found # # RepeatClassifier # # Version 2.0.9 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.UH4k84/RM_3092078.ThuOct220828472026 # 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: 00:09:23 (hh:mm:ss) Elapsed Time Program Time: 30:03:25 (hh:mm:ss) Elapsed Time