RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Wm0oZI/RM_111945.ThuJan50906212023 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: 1672938381 Database = /dev/shm/rModeler.Wm0oZI/GCA_023851605.1_mTamTet1.pri - Sequences = 201 - Bases = 3205741135 - N50 = 175609909 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 218797232-234425570 | [ 2 ] 203168895-218797232 | [ 1 ] 187540558-203168895 | [ 2 ] 171912221-187540558 | [ 3 ] 156283884-171912221 | [ ] 140655547-156283884 | [ ] 125027210-140655547 | [ 1 ] 109398872-125027209 | [ 2 ] 93770535-109398872 |* [ 4 ] 78142198-93770535 |* [ 4 ] 62513861-78142198 | [ 2 ] 46885524-62513861 |* [ 5 ] 31257187-46885524 | [ 1 ] 15628850-31257187 | [ 1 ] 513-15628850 |************************************************** [ 173 ] Storage Throughput = excellent ( 1284.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40192560 bp ( 40023151 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:03:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:18 (hh:mm:ss) Elapsed Time Round Time: 00:35:59 (hh:mm:ss) Elapsed Time : 230 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9942 repeats masked totaling 3610829 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040237 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10039625 bp After Masking: 6392425 bp Masked: 36.33 % -- Input Database Coverage: 10040237 bp out of 3205741135 bp ( 0.31 % ) Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:53 (hh:mm:ss) Elapsed Time, 4988 HSPs Collected Number of families returned by RECON: 782 Round Time: 00:07:48 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33547 repeats masked totaling 12367251 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30192244 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30023447 bp After Masking: 17503213 bp Masked: 41.70 % -- Input Database Coverage: 40232481 bp out of 3205741135 bp ( 1.26 % ) Sampling Time: 00:05:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:27:14 (hh:mm:ss) Elapsed Time, 36402 HSPs Collected Number of families returned by RECON: 2149 Round Time: 00:33:14 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109467 repeats masked totaling 38226677 bp(s). - TE Masking time 00:01:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90487392 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 90013414 bp After Masking: 51423200 bp Masked: 42.87 % -- Input Database Coverage: 130719873 bp out of 3205741135 bp ( 4.08 % ) Sampling Time: 00:14:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:44:12 (hh:mm:ss) Elapsed Time, 75844 HSPs Collected Number of families returned by RECON: 7453 Round Time: 03:03:06 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:27:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 355038 repeats masked totaling 122617900 bp(s). - TE Masking time 00:06:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271450179 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 270037683 bp After Masking: 146253090 bp Masked: 45.84 % -- Input Database Coverage: 402170052 bp out of 3205741135 bp ( 12.55 % ) Sampling Time: 00:46:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23075821 Comparison Time: 17:58:39 (hh:mm:ss) Elapsed Time, 174458 HSPs Collected Number of families returned by RECON: 29515 Round Time: 19:08:44 (hh:mm:ss) Elapsed Time : 343 families discovered. RepeatScout/RECON discovery complete: 812 families found Classification Time: 00:44:37 (hh:mm:ss) Elapsed Time Program Time: 24:13:28 (hh:mm:ss) Elapsed Time