RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1CAmNr/RM_27642.WedDec282306002022 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: 1672297559 Database = /dev/shm/rModeler.1CAmNr/GCF_020382885.2_fScaArg1.pri - Sequences = 48 - Bases = 570802272 Storage Throughput = excellent ( 1022.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40085766 bp ( 40002944 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:58 (hh:mm:ss) Elapsed Time Round Time: 00:25:02 (hh:mm:ss) Elapsed Time : 196 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (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... 3324 repeats masked totaling 669073 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035890 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10033133 bp After Masking: 9229640 bp Masked: 8.01 % -- Input Database Coverage: 10035890 bp out of 570802272 bp ( 1.76 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:40 (hh:mm:ss) Elapsed Time, 6557 HSPs Collected Number of families returned by RECON: 1514 Round Time: 00:07:40 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11968 repeats masked totaling 2217588 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30089875 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30009810 bp After Masking: 27508057 bp Masked: 8.34 % -- Input Database Coverage: 40125765 bp out of 570802272 bp ( 7.03 % ) Sampling Time: 00:01:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:39:12 (hh:mm:ss) Elapsed Time, 42195 HSPs Collected Number of families returned by RECON: 5984 Round Time: 00:42:41 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45722 repeats masked totaling 8086520 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90291672 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90029338 bp After Masking: 81019364 bp Masked: 10.01 % -- Input Database Coverage: 130417437 bp out of 570802272 bp ( 22.85 % ) Sampling Time: 00:05:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 04:45:32 (hh:mm:ss) Elapsed Time, 189276 HSPs Collected Number of families returned by RECON: 22964 Round Time: 05:05:30 (hh:mm:ss) Elapsed Time : 297 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 186860 repeats masked totaling 33040630 bp(s). - TE Masking time 00:06:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271165951 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 270009996 bp After Masking: 234152261 bp Masked: 13.28 % -- Input Database Coverage: 401583388 bp out of 570802272 bp ( 70.35 % ) Sampling Time: 00:19:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 37:48:31 (hh:mm:ss) Elapsed Time, 892625 HSPs Collected Number of families returned by RECON: 97820 Round Time: 41:35:20 (hh:mm:ss) Elapsed Time : 892 families discovered. RepeatScout/RECON discovery complete: 1495 families found Classification Time: 01:08:04 (hh:mm:ss) Elapsed Time Program Time: 49:04:17 (hh:mm:ss) Elapsed Time