RepeatModeler Version 2.0.7 =========================== Using output directory = /data/tmp/rModeler.z1wmeV/RM_3396917.WedSep101235582025 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: 1757532957 Database = /data/tmp/rModeler.z1wmeV/GCA_017654865.1_FW16 - Sequences = 9 - Bases = 47436558 Storage Throughput = excellent ( 1266.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029605 bp ( 40018229 non ambiguous ) - Num Contigs Represented = 9 - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 43 raw families identified - RepeatScout: Running filtering stage.. 29 families remaining - RepeatScout: 00:00:48 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 27 families... 00:02:13 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 7 contained, found in 00:00:06 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:06 (hh:mm:ss) Elapsed Time Round Time: 00:03:13 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 250 repeats masked totaling 123567 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007722 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 10007721 bp After Masking: 9872321 bp Masked: 1.35 % -- Input Database Coverage: 10007722 bp out of 47436558 bp ( 21.10 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:28 (hh:mm:ss) Elapsed Time, 1867 HSPs Collected Number of families returned by RECON: 672 Round Time: 00:26:46 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1022 repeats masked totaling 324609 bp(s). - TE Masking time 00:01:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021836 bp Num Contigs Represented = 9 Non ambiguous bp: Initial: 30010461 bp After Masking: 29634733 bp Masked: 1.25 % -- Input Database Coverage: 40029558 bp out of 47436558 bp ( 84.39 % ) Sampling Time: 00:02:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 01:00:26 (hh:mm:ss) Elapsed Time, 25433 HSPs Collected Number of families returned by RECON: 3626 Round Time: 05:00:44 (hh:mm:ss) Elapsed Time : 18 families discovered. - Increasing sample size to include end piece now = 97428836 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 97428836 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 531 repeats masked totaling 268022 bp(s). - TE Masking time 00:07:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 7406830 bp Num Contigs Represented = 9 Non ambiguous bp: Initial: 7406830 bp After Masking: 7131318 bp Masked: 3.72 % -- Input Database Coverage: 47436388 bp out of 47436558 bp ( 100.00 % ) Sampling Time: 00:07:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 17020 Comparison Time: 00:03:04 (hh:mm:ss) Elapsed Time, 922 HSPs Collected Number of families returned by RECON: 412 Round Time: 00:10:59 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 40 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /data/tmp/rModeler.z1wmeV/RM_3396917.WedSep101235582025 # 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: 00:00:38 (hh:mm:ss) Elapsed Time Program Time: 05:42:20 (hh:mm:ss) Elapsed Time