RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.nDBKGO/RM_3456.TueMay161958252023 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: 1684292304 Database = /dev/shm/rModeler.nDBKGO/GCF_027887155.1_rMalTer1.hap1 - Sequences = 76 - Bases = 2211221380 Storage Throughput = excellent ( 1203.95 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40004188 bp ( 40003988 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:03:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:13 (hh:mm:ss) Elapsed Time Round Time: 00:34:04 (hh:mm:ss) Elapsed Time : 605 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14752 repeats masked totaling 2946598 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002472 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10002472 bp After Masking: 6988894 bp Masked: 30.13 % -- Input Database Coverage: 10002472 bp out of 2211221380 bp ( 0.45 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:56 (hh:mm:ss) Elapsed Time, 10892 HSPs Collected Number of families returned by RECON: 1603 Round Time: 00:08:52 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46313 repeats masked totaling 9651356 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001636 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30001436 bp After Masking: 20070709 bp Masked: 33.10 % -- Input Database Coverage: 40004108 bp out of 2211221380 bp ( 1.81 % ) Sampling Time: 00:04:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:31:52 (hh:mm:ss) Elapsed Time, 62229 HSPs Collected Number of families returned by RECON: 5013 Round Time: 00:39:17 (hh:mm:ss) Elapsed Time : 130 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155315 repeats masked totaling 33025503 bp(s). - TE Masking time 00:02:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90145190 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90024590 bp After Masking: 56208650 bp Masked: 37.56 % -- Input Database Coverage: 130149298 bp out of 2211221380 bp ( 5.89 % ) Sampling Time: 00:14:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2543640 Comparison Time: 03:06:35 (hh:mm:ss) Elapsed Time, 241431 HSPs Collected Number of families returned by RECON: 14392 Round Time: 03:34:58 (hh:mm:ss) Elapsed Time : 460 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:24:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 536307 repeats masked totaling 112532502 bp(s). - TE Masking time 00:12:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270154473 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 270010168 bp After Masking: 154785013 bp Masked: 42.67 % -- Input Database Coverage: 400303771 bp out of 2211221380 bp ( 18.10 % ) Sampling Time: 00:49:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 22:21:39 (hh:mm:ss) Elapsed Time, 612284 HSPs Collected Number of families returned by RECON: 44273 Round Time: 24:34:20 (hh:mm:ss) Elapsed Time : 1056 families discovered. RepeatScout/RECON discovery complete: 2277 families found Classification Time: 01:34:00 (hh:mm:ss) Elapsed Time Program Time: 31:05:31 (hh:mm:ss) Elapsed Time