RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4e07DS/RM_249232.FriJul121253302024 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: 1720814010 Database = /dev/shm/rModeler.4e07DS/GCF_027596085.1_Afim_UVic_2022 - Sequences = 7493 - Bases = 653543715 - N50 = 27098089 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 30791806-32991207 | [ 2 ] 28592406-30791806 | [ 5 ] 26393005-28592405 | [ 5 ] 24193605-26393005 | [ 4 ] 21994205-24193605 | [ 4 ] 19794804-21994204 | [ 2 ] 17595404-19794804 | [ 1 ] 15396003-17595403 | [ ] 13196603-15396003 | [ 1 ] 10997203-13196603 | [ ] 8797802-10997202 | [ ] 6598402-8797802 | [ ] 4399001-6598401 | [ ] 2199601-4399001 | [ ] 201-2199601 |************************************************** [ 7469 ] Storage Throughput = excellent ( 1195.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40026453 bp ( 40021214 non ambiguous ) - Num Contigs Represented = 510 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:33 (hh:mm:ss) Elapsed Time Round Time: 00:22:11 (hh:mm:ss) Elapsed Time : 320 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5962 repeats masked totaling 806886 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10024063 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 10022863 bp After Masking: 8654583 bp Masked: 13.65 % -- Input Database Coverage: 10024063 bp out of 653543715 bp ( 1.53 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 60726 Comparison Time: 00:08:00 (hh:mm:ss) Elapsed Time, 5992 HSPs Collected Number of families returned by RECON: 1298 Round Time: 00:09:53 (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 : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20873 repeats masked totaling 2947238 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042371 bp Num Contigs Represented = 401 Non ambiguous bp: Initial: 30038332 bp After Masking: 25504233 bp Masked: 15.09 % -- Input Database Coverage: 40066434 bp out of 653543715 bp ( 6.13 % ) Sampling Time: 00:05:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 595686 Comparison Time: 00:37:58 (hh:mm:ss) Elapsed Time, 48324 HSPs Collected Number of families returned by RECON: 5302 Round Time: 00:45:49 (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 : 00:01:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 74815 repeats masked totaling 10942228 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009090 bp Num Contigs Represented = 1097 Non ambiguous bp: Initial: 90000290 bp After Masking: 74223190 bp Masked: 17.53 % -- Input Database Coverage: 130075524 bp out of 653543715 bp ( 19.90 % ) Sampling Time: 00:13:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 5185810 Comparison Time: 03:41:33 (hh:mm:ss) Elapsed Time, 227552 HSPs Collected Number of families returned by RECON: 18920 Round Time: 04:05:37 (hh:mm:ss) Elapsed Time : 406 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 294543 repeats masked totaling 43874006 bp(s). - TE Masking time 00:06:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270033447 bp Num Contigs Represented = 3222 Non ambiguous bp: Initial: 270003470 bp After Masking: 211722149 bp Masked: 21.59 % -- Input Database Coverage: 400108971 bp out of 653543715 bp ( 61.22 % ) Sampling Time: 00:46:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 46459980 Comparison Time: 24:33:58 (hh:mm:ss) Elapsed Time, 725759 HSPs Collected Number of families returned by RECON: 69499 Round Time: 26:43:26 (hh:mm:ss) Elapsed Time : 1060 families discovered. RepeatScout/RECON discovery complete: 1929 families found Classification Time: 01:15:32 (hh:mm:ss) Elapsed Time Program Time: 33:22:28 (hh:mm:ss) Elapsed Time