RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.H1eD0p/RM_3837892.ThuSep110929032025 Search Engine = rmblast 2.14.1+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1757608142 Database = /dev/shm/rModeler.H1eD0p/GCA_023105745.2_Au3_v3_hapA - Sequences = 20 - Bases = 1073584748 Storage Throughput = excellent ( 1123.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003861 bp ( 40002361 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 170 raw families identified - RepeatScout: Running filtering stage.. 147 families remaining - RepeatScout: 00:14:52 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 147 families... 00:30:21 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 5 satellite(s), 51 contained, found in 00:00:08 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:09 (hh:mm:ss) Elapsed Time Round Time: 00:46:29 (hh:mm:ss) Elapsed Time : 92 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5050 repeats masked totaling 7349953 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000880 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10000880 bp After Masking: 2524542 bp Masked: 74.76 % -- Input Database Coverage: 10000880 bp out of 1073584748 bp ( 0.93 % ) Sampling Time: 00:02:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:38 (hh:mm:ss) Elapsed Time, 49099 HSPs Collected Number of families returned by RECON: 394 Round Time: 00:16:37 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15043 repeats masked totaling 23914995 bp(s). - TE Masking time 00:02:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002901 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 30001401 bp After Masking: 5806668 bp Masked: 80.65 % -- Input Database Coverage: 40003781 bp out of 1073584748 bp ( 3.73 % ) Sampling Time: 00:05:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:17:42 (hh:mm:ss) Elapsed Time, 16187 HSPs Collected Number of families returned by RECON: 1012 Round Time: 00:24:28 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46958 repeats masked totaling 74200093 bp(s). - TE Masking time 00:08:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009390 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 90007390 bp After Masking: 14815285 bp Masked: 83.54 % -- Input Database Coverage: 130013171 bp out of 1073584748 bp ( 12.11 % ) Sampling Time: 00:19:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:28:58 (hh:mm:ss) Elapsed Time, 112643 HSPs Collected Number of families returned by RECON: 2642 Round Time: 01:53:16 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155970 repeats masked totaling 231619582 bp(s). - TE Masking time 00:55:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039175 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 270032175 bp After Masking: 35472758 bp Masked: 86.86 % -- Input Database Coverage: 400052346 bp out of 1073584748 bp ( 37.26 % ) Sampling Time: 01:27:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 08:37:41 (hh:mm:ss) Elapsed Time, 232030 HSPs Collected Number of families returned by RECON: 6733 Round Time: 10:21:57 (hh:mm:ss) Elapsed Time : 277 families discovered. RepeatScout/RECON discovery complete: 503 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.H1eD0p/RM_3837892.ThuSep110929032025 # Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib # - 26292 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: 00:09:27 (hh:mm:ss) Elapsed Time Program Time: 13:52:14 (hh:mm:ss) Elapsed Time