RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mLb5pZ/RM_22107.WedNov290641042023 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: 1701268862 Database = /dev/shm/rModeler.mLb5pZ/GCA_028571685.1_mHetBru1.pri - Sequences = 62 - Bases = 3488059404 Storage Throughput = excellent ( 1179.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006590 bp ( 40006390 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:03:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:45 (hh:mm:ss) Elapsed Time Round Time: 00:30:28 (hh:mm:ss) Elapsed Time : 228 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14024 repeats masked totaling 4445145 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005526 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10005526 bp After Masking: 4894355 bp Masked: 51.08 % -- Input Database Coverage: 10005526 bp out of 3488059404 bp ( 0.29 % ) Sampling Time: 00:01:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:47 (hh:mm:ss) Elapsed Time, 4437 HSPs Collected Number of families returned by RECON: 625 Round Time: 00:06:41 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45243 repeats masked totaling 13819800 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001063 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30000863 bp After Masking: 14670208 bp Masked: 51.10 % -- Input Database Coverage: 40006589 bp out of 3488059404 bp ( 1.15 % ) Sampling Time: 00:04:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:22:15 (hh:mm:ss) Elapsed Time, 17601 HSPs Collected Number of families returned by RECON: 1590 Round Time: 00:27:06 (hh:mm:ss) Elapsed Time : 49 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140144 repeats masked totaling 41383730 bp(s). - TE Masking time 00:01:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016027 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90015627 bp After Masking: 43776666 bp Masked: 51.37 % -- Input Database Coverage: 130022616 bp out of 3488059404 bp ( 3.73 % ) Sampling Time: 00:13:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:26:56 (hh:mm:ss) Elapsed Time, 66751 HSPs Collected Number of families returned by RECON: 5975 Round Time: 02:43:23 (hh:mm:ss) Elapsed Time : 139 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 459735 repeats masked totaling 129952918 bp(s). - TE Masking time 00:05:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270025872 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 270018724 bp After Masking: 123408781 bp Masked: 54.30 % -- Input Database Coverage: 400048488 bp out of 3488059404 bp ( 11.47 % ) Sampling Time: 00:45:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 17:35:55 (hh:mm:ss) Elapsed Time, 201768 HSPs Collected Number of families returned by RECON: 23600 Round Time: 18:40:47 (hh:mm:ss) Elapsed Time : 332 families discovered. RepeatScout/RECON discovery complete: 767 families found Classification Time: 00:31:54 (hh:mm:ss) Elapsed Time Program Time: 23:00:19 (hh:mm:ss) Elapsed Time