RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gToc22/RM_15145.MonJun241451242024 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: 1719265882 Database = /dev/shm/rModeler.gToc22/GCF_023053635.1_rElgMul1.1.pri - Sequences = 34 - Bases = 1790500004 Storage Throughput = excellent ( 1136.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002614 bp ( 40002014 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:02:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:22 (hh:mm:ss) Elapsed Time Round Time: 00:30:03 (hh:mm:ss) Elapsed Time : 640 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (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... 22771 repeats masked totaling 3619011 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000708 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10000308 bp After Masking: 6142939 bp Masked: 38.57 % -- Input Database Coverage: 10000708 bp out of 1790500004 bp ( 0.56 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:57 (hh:mm:ss) Elapsed Time, 12394 HSPs Collected Number of families returned by RECON: 1510 Round Time: 00:06:48 (hh:mm:ss) Elapsed Time : 38 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 70507 repeats masked totaling 11355508 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001904 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30001704 bp After Masking: 17975898 bp Masked: 40.08 % -- Input Database Coverage: 40002612 bp out of 1790500004 bp ( 2.23 % ) Sampling Time: 00:04:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:25:01 (hh:mm:ss) Elapsed Time, 52886 HSPs Collected Number of families returned by RECON: 4861 Round Time: 00:31:07 (hh:mm:ss) Elapsed Time : 133 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 224543 repeats masked totaling 36349183 bp(s). - TE Masking time 00:02:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020896 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90020296 bp After Masking: 51281992 bp Masked: 43.03 % -- Input Database Coverage: 130023508 bp out of 1790500004 bp ( 7.26 % ) Sampling Time: 00:12:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:45:37 (hh:mm:ss) Elapsed Time, 227134 HSPs Collected Number of families returned by RECON: 13768 Round Time: 03:09:48 (hh:mm:ss) Elapsed Time : 493 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:17:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 753089 repeats masked totaling 123448402 bp(s). - TE Masking time 00:11:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034177 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270032477 bp After Masking: 140369126 bp Masked: 48.02 % -- Input Database Coverage: 400057685 bp out of 1790500004 bp ( 22.34 % ) Sampling Time: 00:40:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 20:13:25 (hh:mm:ss) Elapsed Time, 547369 HSPs Collected Number of families returned by RECON: 43548 Round Time: 22:06:32 (hh:mm:ss) Elapsed Time : 1089 families discovered. RepeatScout/RECON discovery complete: 2393 families found Classification Time: 01:15:16 (hh:mm:ss) Elapsed Time Program Time: 27:39:34 (hh:mm:ss) Elapsed Time