RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wnJOa2/RM_454512.SunMay140023392023 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: 1684049018 Database = /dev/shm/rModeler.wnJOa2/GCA_900963305.2_fEcheNa1.2 - Sequences = 38 - Bases = 544229243 Storage Throughput = excellent ( 1351.54 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40094028 bp ( 40036737 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:09 (hh:mm:ss) Elapsed Time Round Time: 00:19:04 (hh:mm:ss) Elapsed Time : 263 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 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3584 repeats masked totaling 636711 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037228 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10037128 bp After Masking: 9304710 bp Masked: 7.30 % -- Input Database Coverage: 10037228 bp out of 544229243 bp ( 1.84 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:08:16 (hh:mm:ss) Elapsed Time, 3129 HSPs Collected Number of families returned by RECON: 1008 Round Time: 00:09:10 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10748 repeats masked totaling 1966205 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30096666 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30039475 bp After Masking: 27746244 bp Masked: 7.63 % -- Input Database Coverage: 40133894 bp out of 544229243 bp ( 7.37 % ) Sampling Time: 00:01:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:42:26 (hh:mm:ss) Elapsed Time, 23230 HSPs Collected Number of families returned by RECON: 4509 Round Time: 00:45:09 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36562 repeats masked totaling 6286858 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90091382 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90008261 bp After Masking: 82744295 bp Masked: 8.07 % -- Input Database Coverage: 130225276 bp out of 544229243 bp ( 23.93 % ) Sampling Time: 00:05:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 05:01:19 (hh:mm:ss) Elapsed Time, 167052 HSPs Collected Number of families returned by RECON: 19732 Round Time: 05:18:15 (hh:mm:ss) Elapsed Time : 257 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 142293 repeats masked totaling 27143243 bp(s). - TE Masking time 00:07:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270314825 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 270008441 bp After Masking: 239805266 bp Masked: 11.19 % -- Input Database Coverage: 400540101 bp out of 544229243 bp ( 73.60 % ) Sampling Time: 00:22:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 37:17:52 (hh:mm:ss) Elapsed Time, 813547 HSPs Collected Number of families returned by RECON: 90927 Round Time: 40:23:17 (hh:mm:ss) Elapsed Time : 730 families discovered. RepeatScout/RECON discovery complete: 1313 families found Classification Time: 01:33:13 (hh:mm:ss) Elapsed Time Program Time: 48:28:08 (hh:mm:ss) Elapsed Time