RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.upQDJb/RM_45129.MonJan21738462023 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: 1672709926 Database = /dev/shm/rModeler.upQDJb/GCF_018492685.1_fAloSap1.pri - Sequences = 74 - Bases = 903581644 Storage Throughput = excellent ( 1039.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40165789 bp ( 40022527 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:56 (hh:mm:ss) Elapsed Time Round Time: 00:32:43 (hh:mm:ss) Elapsed Time : 835 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9763 repeats masked totaling 2187486 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10100863 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10039254 bp After Masking: 6848211 bp Masked: 31.79 % -- Input Database Coverage: 10100863 bp out of 903581644 bp ( 1.12 % ) Sampling Time: 00:03:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:00 (hh:mm:ss) Elapsed Time, 4873 HSPs Collected Number of families returned by RECON: 1342 Round Time: 00:10:24 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30809 repeats masked totaling 7079892 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30104780 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30023127 bp After Masking: 19998923 bp Masked: 33.39 % -- Input Database Coverage: 40205643 bp out of 903581644 bp ( 4.45 % ) Sampling Time: 00:08:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:35:32 (hh:mm:ss) Elapsed Time, 125140 HSPs Collected Number of families returned by RECON: 5110 Round Time: 00:46:52 (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 : 00:02:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 96413 repeats masked totaling 21749698 bp(s). - TE Masking time 00:02:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90687073 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 90036862 bp After Masking: 59754426 bp Masked: 33.63 % -- Input Database Coverage: 130892716 bp out of 903581644 bp ( 14.49 % ) Sampling Time: 00:24:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 03:33:47 (hh:mm:ss) Elapsed Time, 369164 HSPs Collected Number of families returned by RECON: 17233 Round Time: 04:18:13 (hh:mm:ss) Elapsed Time : 597 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 359958 repeats masked totaling 80938453 bp(s). - TE Masking time 00:16:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271742491 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 270022170 bp After Masking: 164059922 bp Masked: 39.24 % -- Input Database Coverage: 402635207 bp out of 903581644 bp ( 44.56 % ) Sampling Time: 01:23:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23150610 Comparison Time: 21:39:36 (hh:mm:ss) Elapsed Time, 1155379 HSPs Collected Number of families returned by RECON: 58920 Round Time: 25:21:50 (hh:mm:ss) Elapsed Time : 1341 families discovered. RepeatScout/RECON discovery complete: 2849 families found Classification Time: 02:14:18 (hh:mm:ss) Elapsed Time Program Time: 33:24:20 (hh:mm:ss) Elapsed Time