RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.F3XlxZ/RM_31410.WedJan41950092023 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: 1672890608 Database = /dev/shm/rModeler.F3XlxZ/GCA_009764595.1_bGeoTri1.pri - Sequences = 278 - Bases = 1078128490 - N50 = 74170629 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 142881920-153087655 | [ 1 ] 132676185-142881919 | [ ] 122470450-132676184 | [ ] 112264715-122470449 | [ 2 ] 102058981-112264715 | [ ] 91853246-102058980 | [ ] 81647511-91853245 | [ ] 71441776-81647510 | [ 3 ] 61236041-71441775 | [ 1 ] 51030307-61236041 | [ ] 40824572-51030306 | [ ] 30618837-40824571 | [ 3 ] 20413102-30618836 | [ 4 ] 10207367-20413101 |* [ 9 ] 1633-10207367 |************************************************** [ 255 ] Storage Throughput = excellent ( 1102.50 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40698287 bp ( 40035093 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:07 (hh:mm:ss) Elapsed Time Round Time: 00:26:30 (hh:mm:ss) Elapsed Time : 153 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (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... 2824 repeats masked totaling 730309 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10146648 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10017836 bp After Masking: 9105783 bp Masked: 9.10 % -- Input Database Coverage: 10146648 bp out of 1078128490 bp ( 0.94 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:07:21 (hh:mm:ss) Elapsed Time, 853 HSPs Collected Number of families returned by RECON: 309 Round Time: 00:08:27 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9226 repeats masked totaling 2369148 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30551638 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30017256 bp After Masking: 26988161 bp Masked: 10.09 % -- Input Database Coverage: 40698286 bp out of 1078128490 bp ( 3.77 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:40:05 (hh:mm:ss) Elapsed Time, 7151 HSPs Collected Number of families returned by RECON: 1933 Round Time: 00:43:14 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26993 repeats masked totaling 6542334 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91208155 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 90017421 bp After Masking: 81692025 bp Masked: 9.25 % -- Input Database Coverage: 131906441 bp out of 1078128490 bp ( 12.23 % ) Sampling Time: 00:08:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2627778 Comparison Time: 04:59:20 (hh:mm:ss) Elapsed Time, 45820 HSPs Collected Number of families returned by RECON: 12240 Round Time: 05:11:16 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 87849 repeats masked totaling 22402208 bp(s). - TE Masking time 00:03:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273603788 bp Num Contigs Represented = 139 Non ambiguous bp: Initial: 270039502 bp After Masking: 241883310 bp Masked: 10.43 % -- Input Database Coverage: 405510229 bp out of 1078128490 bp ( 37.61 % ) Sampling Time: 00:25:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23615628 Comparison Time: 40:23:37 (hh:mm:ss) Elapsed Time, 265415 HSPs Collected Number of families returned by RECON: 82751 Round Time: 42:30:39 (hh:mm:ss) Elapsed Time : 317 families discovered. RepeatScout/RECON discovery complete: 555 families found Classification Time: 00:40:24 (hh:mm:ss) Elapsed Time Program Time: 49:40:30 (hh:mm:ss) Elapsed Time