RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.uLFsAi/RM_134170.SatNov11138462025 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: 1762022325 Database = /dev/shm/rModeler.uLFsAi/GCA_036186865.1_ASM3618686v1 - Sequences = 100 - Bases = 1324827894 Storage Throughput = excellent ( 1120.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036592 bp ( 40026332 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:00:41 (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.. 490 families remaining - RepeatScout: 00:10:06 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 487 families... 00:12:54 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 7 satellite(s), 175 contained, found in 00:00:18 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:19 (hh:mm:ss) Elapsed Time Round Time: 00:24:10 (hh:mm:ss) Elapsed Time : 308 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10089 repeats masked totaling 6754332 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023782 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10021432 bp After Masking: 3180637 bp Masked: 68.26 % -- Input Database Coverage: 10023782 bp out of 1324827894 bp ( 0.76 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:51 (hh:mm:ss) Elapsed Time, 38589 HSPs Collected Number of families returned by RECON: 906 Round Time: 00:06:03 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30529 repeats masked totaling 21235243 bp(s). - TE Masking time 00:02:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012797 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30004887 bp After Masking: 8534348 bp Masked: 71.56 % -- Input Database Coverage: 40036579 bp out of 1324827894 bp ( 3.02 % ) Sampling Time: 00:04:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:16:30 (hh:mm:ss) Elapsed Time, 230040 HSPs Collected Number of families returned by RECON: 2754 Round Time: 00:22:52 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 98402 repeats masked totaling 65955164 bp(s). - TE Masking time 00:08:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034160 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 90010105 bp After Masking: 23308518 bp Masked: 74.10 % -- Input Database Coverage: 130070739 bp out of 1324827894 bp ( 9.82 % ) Sampling Time: 00:13:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:28:56 (hh:mm:ss) Elapsed Time, 210615 HSPs Collected Number of families returned by RECON: 7816 Round Time: 01:48:31 (hh:mm:ss) Elapsed Time : 255 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 317762 repeats masked totaling 207125849 bp(s). - TE Masking time 00:37:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270073862 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 270005059 bp After Masking: 60578939 bp Masked: 77.56 % -- Input Database Coverage: 400144601 bp out of 1324827894 bp ( 30.20 % ) Sampling Time: 00:51:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 09:08:40 (hh:mm:ss) Elapsed Time, 1071977 HSPs Collected Number of families returned by RECON: 25025 Round Time: 10:27:16 (hh:mm:ss) Elapsed Time : 449 families discovered. RepeatScout/RECON discovery complete: 1083 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.uLFsAi/RM_134170.SatNov11138462025 # 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: 00:12:00 (hh:mm:ss) Elapsed Time Program Time: 13:20:52 (hh:mm:ss) Elapsed Time