RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.P0Um4C/RM_1148439.TueNov121153312024 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: 1731441211 Database = /scratch/tmp/rModeler.P0Um4C/GCA_036784965.1_fSalAlp2_p1.0 - Sequences = 1169 - Bases = 2129031653 - N50 = 68839419 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204338842-218933541 | [ 1 ] 189744144-204338842 | [ ] 175149446-189744144 | [ ] 160554747-175149445 | [ ] 145960049-160554747 | [ ] 131365351-145960049 | [ ] 116770653-131365351 | [ 2 ] 102175954-116770652 | [ 2 ] 87581256-102175954 | [ 1 ] 72986558-87581256 | [ 1 ] 58391860-72986558 | [ 3 ] 43797161-58391859 | [ 8 ] 29202463-43797161 | [ 7 ] 14607765-29202463 | [ 2 ] 13067-14607765 |************************************************** [ 1142 ] Storage Throughput = excellent ( 1624.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014557 bp ( 40000469 non ambiguous ) - Num Contigs Represented = 147 - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:10 (hh:mm:ss) Elapsed Time Round Time: 00:12:42 (hh:mm:ss) Elapsed Time : 795 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12654 repeats masked totaling 3666593 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018870 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 10016093 bp After Masking: 3983479 bp Masked: 60.23 % -- Input Database Coverage: 10018870 bp out of 2129031653 bp ( 0.47 % ) Sampling Time: 00:02:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:36 (hh:mm:ss) Elapsed Time, 6705 HSPs Collected Number of families returned by RECON: 1010 Round Time: 00:05:00 (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 : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38642 repeats masked totaling 11020865 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035600 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 30024289 bp After Masking: 11756388 bp Masked: 60.84 % -- Input Database Coverage: 40054470 bp out of 2129031653 bp ( 1.88 % ) Sampling Time: 00:07:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:09:57 (hh:mm:ss) Elapsed Time, 65558 HSPs Collected Number of families returned by RECON: 3570 Round Time: 00:18:18 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121150 repeats masked totaling 34701929 bp(s). - TE Masking time 00:00:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034302 bp Num Contigs Represented = 245 Non ambiguous bp: Initial: 90009502 bp After Masking: 34163655 bp Masked: 62.04 % -- Input Database Coverage: 130088772 bp out of 2129031653 bp ( 6.11 % ) Sampling Time: 00:25:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 00:52:20 (hh:mm:ss) Elapsed Time, 265192 HSPs Collected Number of families returned by RECON: 9878 Round Time: 01:22:57 (hh:mm:ss) Elapsed Time : 451 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:03:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 422292 repeats masked totaling 117017244 bp(s). - TE Masking time 00:03:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270087364 bp Num Contigs Represented = 474 Non ambiguous bp: Initial: 270001920 bp After Masking: 90717990 bp Masked: 66.40 % -- Input Database Coverage: 400176136 bp out of 2129031653 bp ( 18.80 % ) Sampling Time: 01:12:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23327865 Comparison Time: 05:21:26 (hh:mm:ss) Elapsed Time, 861003 HSPs Collected Number of families returned by RECON: 31406 Round Time: 06:51:58 (hh:mm:ss) Elapsed Time : 999 families discovered. RepeatScout/RECON discovery complete: 2342 families found Classification Time: 00:50:14 (hh:mm:ss) Elapsed Time Program Time: 09:41:09 (hh:mm:ss) Elapsed Time