RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Xnpjcz/RM_4094940.TueJul162153492024 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: 1721192021 Database = /dev/shm/rModeler.Xnpjcz/GCF_024500385.1_UOR_Ptae_1.2 - Sequences = 1259 - Bases = 652173514 - N50 = 31990137 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 47677512-51083034 | [ 1 ] 44271990-47677511 | [ ] 40866469-44271990 | [ 1 ] 37460947-40866468 | [ ] 34055425-37460946 | [ ] 30649904-34055425 | [ 8 ] 27244382-30649903 | [ 2 ] 23838860-27244381 | [ 3 ] 20433339-23838860 | [ 2 ] 17027817-20433338 | [ 4 ] 13622295-17027816 | [ ] 10216774-13622295 | [ 1 ] 6811252-10216773 | [ 1 ] 3405730-6811251 | [ 1 ] 209-3405730 |************************************************** [ 1235 ] Storage Throughput = good ( 829.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006731 bp ( 40006451 non ambiguous ) - Num Contigs Represented = 123 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:02 (hh:mm:ss) Elapsed Time Round Time: 00:33:44 (hh:mm:ss) Elapsed Time : 885 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18720 repeats masked totaling 3304333 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020458 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10020298 bp After Masking: 6385929 bp Masked: 36.27 % -- Input Database Coverage: 10020458 bp out of 652173514 bp ( 1.54 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 36585 Comparison Time: 00:33:46 (hh:mm:ss) Elapsed Time, 14323 HSPs Collected Number of families returned by RECON: 1822 Round Time: 00:36:38 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61132 repeats masked totaling 10958469 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026204 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 30026084 bp After Masking: 18063047 bp Masked: 39.84 % -- Input Database Coverage: 40046662 bp out of 652173514 bp ( 6.14 % ) Sampling Time: 00:03:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 318801 Comparison Time: 01:51:36 (hh:mm:ss) Elapsed Time, 70822 HSPs Collected Number of families returned by RECON: 5521 Round Time: 02:00:48 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 195714 repeats masked totaling 34402446 bp(s). - TE Masking time 00:02:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009591 bp Num Contigs Represented = 243 Non ambiguous bp: Initial: 90009051 bp After Masking: 52905866 bp Masked: 41.22 % -- Input Database Coverage: 130056253 bp out of 652173514 bp ( 19.94 % ) Sampling Time: 00:11:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2907666 Comparison Time: 07:32:51 (hh:mm:ss) Elapsed Time, 300738 HSPs Collected Number of families returned by RECON: 15775 Round Time: 08:07:12 (hh:mm:ss) Elapsed Time : 542 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 688424 repeats masked totaling 119687116 bp(s). - TE Masking time 00:09:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031455 bp Num Contigs Represented = 554 Non ambiguous bp: Initial: 270029875 bp After Masking: 142583674 bp Masked: 47.20 % -- Input Database Coverage: 400087708 bp out of 652173514 bp ( 61.35 % ) Sampling Time: 00:38:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25657866 Comparison Time: 40:58:03 (hh:mm:ss) Elapsed Time, 650400 HSPs Collected Number of families returned by RECON: 48745 Round Time: 42:39:02 (hh:mm:ss) Elapsed Time : 1073 families discovered. RepeatScout/RECON discovery complete: 2731 families found Classification Time: 01:13:34 (hh:mm:ss) Elapsed Time Program Time: 55:10:58 (hh:mm:ss) Elapsed Time