RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5TUL4Q/RM_6364.TueJan30117182023 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: 1672737437 Database = /dev/shm/rModeler.5TUL4Q/GCF_011004845.1_fEsoLuc1.pri - Sequences = 53 - Bases = 918748614 Storage Throughput = excellent ( 1039.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40131581 bp ( 40027386 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:32 (hh:mm:ss) Elapsed Time Round Time: 00:23:04 (hh:mm:ss) Elapsed Time : 612 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10402 repeats masked totaling 2660029 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10026834 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10026166 bp After Masking: 6824733 bp Masked: 31.93 % -- Input Database Coverage: 10026834 bp out of 918748614 bp ( 1.09 % ) Sampling Time: 00:01:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:52 (hh:mm:ss) Elapsed Time, 7961 HSPs Collected Number of families returned by RECON: 1630 Round Time: 00:07:16 (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 : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31503 repeats masked totaling 7776758 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30104667 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30001140 bp After Masking: 20460646 bp Masked: 31.80 % -- Input Database Coverage: 40131501 bp out of 918748614 bp ( 4.37 % ) Sampling Time: 00:03:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:30:08 (hh:mm:ss) Elapsed Time, 53142 HSPs Collected Number of families returned by RECON: 5791 Round Time: 00:35:21 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107103 repeats masked totaling 26033788 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90131282 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 90010282 bp After Masking: 58623171 bp Masked: 34.87 % -- Input Database Coverage: 130262783 bp out of 918748614 bp ( 14.18 % ) Sampling Time: 00:09:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:11:02 (hh:mm:ss) Elapsed Time, 308435 HSPs Collected Number of families returned by RECON: 18241 Round Time: 03:39:32 (hh:mm:ss) Elapsed Time : 606 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 401691 repeats masked totaling 95954949 bp(s). - TE Masking time 00:12:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270367749 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 270028083 bp After Masking: 157612769 bp Masked: 41.63 % -- Input Database Coverage: 400630532 bp out of 918748614 bp ( 43.61 % ) Sampling Time: 00:34:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 22:27:35 (hh:mm:ss) Elapsed Time, 891911 HSPs Collected Number of families returned by RECON: 56458 Round Time: 24:56:49 (hh:mm:ss) Elapsed Time : 1351 families discovered. RepeatScout/RECON discovery complete: 2712 families found Classification Time: 01:56:59 (hh:mm:ss) Elapsed Time Program Time: 31:39:01 (hh:mm:ss) Elapsed Time