RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fyMCd8/RM_956778.FriApr111107292025 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1744394848 Database = /dev/shm/rModeler.fyMCd8/GCA_049354715.1_calJac240_pri - Sequences = 24 - Bases = 2933409465 Storage Throughput = excellent ( 1842.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000801 bp ( 40000801 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:33 (hh:mm:ss) Elapsed Time Round Time: 00:11:44 (hh:mm:ss) Elapsed Time : 251 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13160 repeats masked totaling 3117741 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000136 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000136 bp After Masking: 6534022 bp Masked: 34.66 % -- Input Database Coverage: 10000136 bp out of 2933409465 bp ( 0.34 % ) Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:43 (hh:mm:ss) Elapsed Time, 6575 HSPs Collected Number of families returned by RECON: 886 Round Time: 00:03:33 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43868 repeats masked totaling 10299493 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000585 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30000585 bp After Masking: 18689898 bp Masked: 37.70 % -- Input Database Coverage: 40000721 bp out of 2933409465 bp ( 1.36 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:11:21 (hh:mm:ss) Elapsed Time, 22053 HSPs Collected Number of families returned by RECON: 2348 Round Time: 00:13:16 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135907 repeats masked totaling 32390852 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041814 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90001814 bp After Masking: 53594547 bp Masked: 40.45 % -- Input Database Coverage: 130042535 bp out of 2933409465 bp ( 4.43 % ) Sampling Time: 00:04:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 01:03:20 (hh:mm:ss) Elapsed Time, 84742 HSPs Collected Number of families returned by RECON: 7907 Round Time: 01:09:08 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 441163 repeats masked totaling 104442126 bp(s). - TE Masking time 00:02:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017242 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 270009742 bp After Masking: 154500631 bp Masked: 42.78 % -- Input Database Coverage: 400059777 bp out of 2933409465 bp ( 13.64 % ) Sampling Time: 00:14:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22784625 Comparison Time: 07:32:21 (hh:mm:ss) Elapsed Time, 237279 HSPs Collected Number of families returned by RECON: 32221 Round Time: 07:57:04 (hh:mm:ss) Elapsed Time : 409 families discovered. RepeatScout/RECON discovery complete: 918 families found Classification Time: 00:17:48 (hh:mm:ss) Elapsed Time Program Time: 09:52:33 (hh:mm:ss) Elapsed Time