RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DZk9Cd/RM_19971.SatJul62235512024 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: 1720330549 Database = /dev/shm/rModeler.DZk9Cd/GCF_001266775.1_Austrofundulus_limnaeus-1.0 - Sequences = 29784 - Bases = 866963076 - N50 = 1098656 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 10443137-11189062 | [ 2 ] 9697213-10443137 | [ 1 ] 8951289-9697213 | [ 1 ] 8205365-8951289 | [ ] 7459441-8205365 | [ ] 6713517-7459441 | [ ] 5967593-6713517 | [ 3 ] 5221668-5967592 | [ 3 ] 4475744-5221668 | [ 5 ] 3729820-4475744 | [ 4 ] 2983896-3729820 | [ 16 ] 2237972-2983896 | [ 32 ] 1492048-2237972 | [ 61 ] 746124-1492048 | [ 147 ] 200-746124 |************************************************** [ 29509 ] Storage Throughput = excellent ( 1064.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 50130889 bp ( 40028996 non ambiguous ) - Num Contigs Represented = 2245 - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:52 (hh:mm:ss) Elapsed Time Round Time: 00:24:06 (hh:mm:ss) Elapsed Time : 875 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15585 repeats masked totaling 2840082 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 12491115 bp Num Contigs Represented = 627 Non ambiguous bp: Initial: 10001488 bp After Masking: 6855635 bp Masked: 31.45 % -- Input Database Coverage: 12491115 bp out of 866963076 bp ( 1.44 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 236328 Comparison Time: 00:08:20 (hh:mm:ss) Elapsed Time, 10605 HSPs Collected Number of families returned by RECON: 1369 Round Time: 00:09:33 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48809 repeats masked totaling 8635176 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 37639763 bp Num Contigs Represented = 1750 Non ambiguous bp: Initial: 30027497 bp After Masking: 20430382 bp Masked: 31.96 % -- Input Database Coverage: 50130878 bp out of 866963076 bp ( 5.78 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2301585 Comparison Time: 00:43:20 (hh:mm:ss) Elapsed Time, 65879 HSPs Collected Number of families returned by RECON: 4644 Round Time: 00:50:09 (hh:mm:ss) Elapsed Time : 132 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157865 repeats masked totaling 28348657 bp(s). - TE Masking time 00:03:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 112475885 bp Num Contigs Represented = 4737 Non ambiguous bp: Initial: 90008835 bp After Masking: 58917591 bp Masked: 34.54 % -- Input Database Coverage: 162606763 bp out of 866963076 bp ( 18.76 % ) Sampling Time: 00:07:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 21258460 Comparison Time: 04:35:13 (hh:mm:ss) Elapsed Time, 237460 HSPs Collected Number of families returned by RECON: 14217 Round Time: 04:54:48 (hh:mm:ss) Elapsed Time : 517 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 548013 repeats masked totaling 97214922 bp(s). - TE Masking time 00:14:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 336310379 bp Num Contigs Represented = 12294 Non ambiguous bp: Initial: 270016108 bp After Masking: 164711669 bp Masked: 39.00 % -- Input Database Coverage: 498917142 bp out of 866963076 bp ( 57.55 % ) Sampling Time: 00:28:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 180984825 Comparison Time: 33:25:08 (hh:mm:ss) Elapsed Time, 561889 HSPs Collected Number of families returned by RECON: 50699 Round Time: 35:17:03 (hh:mm:ss) Elapsed Time : 1163 families discovered. RepeatScout/RECON discovery complete: 2709 families found Classification Time: 01:32:31 (hh:mm:ss) Elapsed Time Program Time: 43:08:10 (hh:mm:ss) Elapsed Time