RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.jkERza/RM_724754.FriJul181029592025 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: 1752859798 Database = /dev/shm/rModeler.jkERza/GCA_046562875.1_mPanOnc1_haplotype_2 - Sequences = 85 - Bases = 2487960463 Storage Throughput = excellent ( 1168.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035651 bp ( 40034851 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:03:04 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:02 (hh:mm:ss) Elapsed Time Round Time: 00:29:36 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13357 repeats masked totaling 2473586 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003013 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10003013 bp After Masking: 7432590 bp Masked: 25.70 % -- Input Database Coverage: 10003013 bp out of 2487960463 bp ( 0.40 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:58 (hh:mm:ss) Elapsed Time, 5910 HSPs Collected Number of families returned by RECON: 815 Round Time: 00:06:40 (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 : 00:02:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44414 repeats masked totaling 8290450 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032558 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30031758 bp After Masking: 21295590 bp Masked: 29.09 % -- Input Database Coverage: 40035571 bp out of 2487960463 bp ( 1.61 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:27:15 (hh:mm:ss) Elapsed Time, 26188 HSPs Collected Number of families returned by RECON: 2315 Round Time: 00:32:46 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143208 repeats masked totaling 27971781 bp(s). - TE Masking time 00:01:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90006017 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90005217 bp After Masking: 61099057 bp Masked: 32.12 % -- Input Database Coverage: 130041588 bp out of 2487960463 bp ( 5.23 % ) Sampling Time: 00:12:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:16:52 (hh:mm:ss) Elapsed Time, 71400 HSPs Collected Number of families returned by RECON: 8217 Round Time: 03:35:40 (hh:mm:ss) Elapsed Time : 159 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 460933 repeats masked totaling 90045729 bp(s). - TE Masking time 00:07:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030332 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 270025532 bp After Masking: 176971549 bp Masked: 34.46 % -- Input Database Coverage: 400071920 bp out of 2487960463 bp ( 16.08 % ) Sampling Time: 00:38:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 26:02:47 (hh:mm:ss) Elapsed Time, 170759 HSPs Collected Number of families returned by RECON: 33866 Round Time: 27:16:38 (hh:mm:ss) Elapsed Time : 346 families discovered. RepeatScout/RECON discovery complete: 804 families found Classification Time: 00:39:20 (hh:mm:ss) Elapsed Time Program Time: 32:40:40 (hh:mm:ss) Elapsed Time