RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9GFbQW/RM_161775.WedJan111852112023 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: 1673491930 Database = /dev/shm/rModeler.9GFbQW/GCF_902500255.1_fThaAma1.1 - Sequences = 464 - Bases = 2446592878 - N50 = 118707304 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 163765488-175462960 | [ 1 ] 152068017-163765488 | [ 1 ] 140370546-152068017 | [ 2 ] 128673074-140370545 | [ 2 ] 116975603-128673074 | [ 5 ] 105278132-116975603 | [ ] 93580660-105278131 | [ 4 ] 81883189-93580660 | [ 1 ] 70185718-81883189 | [ 3 ] 58488246-70185717 | [ 1 ] 46790775-58488246 | [ ] 35093304-46790775 | [ 3 ] 23395832-35093303 | [ ] 11698361-23395832 | [ ] 890-11698361 |************************************************** [ 441 ] Storage Throughput = excellent ( 1265.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40312411 bp ( 40026737 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:11 (hh:mm:ss) Elapsed Time Round Time: 00:21:30 (hh:mm:ss) Elapsed Time : 1008 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17711 repeats masked totaling 5849128 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10054213 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10006356 bp After Masking: 3831205 bp Masked: 61.71 % -- Input Database Coverage: 10054213 bp out of 2446592878 bp ( 0.41 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:44 (hh:mm:ss) Elapsed Time, 7711 HSPs Collected Number of families returned by RECON: 1456 Round Time: 00:07:27 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54765 repeats masked totaling 17714799 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30258192 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30020375 bp After Masking: 11473693 bp Masked: 61.78 % -- Input Database Coverage: 40312405 bp out of 2446592878 bp ( 1.65 % ) Sampling Time: 00:04:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:20:39 (hh:mm:ss) Elapsed Time, 55936 HSPs Collected Number of families returned by RECON: 4536 Round Time: 00:26:37 (hh:mm:ss) Elapsed Time : 135 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 177327 repeats masked totaling 55557749 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90485626 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 90015404 bp After Masking: 32114562 bp Masked: 64.32 % -- Input Database Coverage: 130798031 bp out of 2446592878 bp ( 5.35 % ) Sampling Time: 00:12:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 01:47:06 (hh:mm:ss) Elapsed Time, 320033 HSPs Collected Number of families returned by RECON: 11071 Round Time: 02:06:38 (hh:mm:ss) Elapsed Time : 602 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 602310 repeats masked totaling 181765293 bp(s). - TE Masking time 00:09:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271363541 bp Num Contigs Represented = 136 Non ambiguous bp: Initial: 270008956 bp After Masking: 80622989 bp Masked: 70.14 % -- Input Database Coverage: 402161572 bp out of 2446592878 bp ( 16.44 % ) Sampling Time: 00:48:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23164221 Comparison Time: 08:46:17 (hh:mm:ss) Elapsed Time, 744516 HSPs Collected Number of families returned by RECON: 28167 Round Time: 10:03:37 (hh:mm:ss) Elapsed Time : 1319 families discovered. RepeatScout/RECON discovery complete: 3075 families found Classification Time: 01:24:12 (hh:mm:ss) Elapsed Time Program Time: 14:30:01 (hh:mm:ss) Elapsed Time