RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Su0KjW/RM_140560.ThuJan121038542023 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: 1673548733 Database = /dev/shm/rModeler.Su0KjW/GCA_015220805.1_bPogPus1.pri - Sequences = 253 - Bases = 1272358903 - N50 = 34651362 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 110049264-117909544 | [ 1 ] 102188985-110049264 | [ ] 94328706-102188985 | [ ] 86468427-94328706 | [ ] 78608148-86468427 | [ ] 70747869-78608148 | [ ] 62887590-70747869 | [ ] 55027311-62887590 | [ ] 47167032-55027311 |* [ 6 ] 39306753-47167032 | [ 4 ] 31446474-39306753 | [ 4 ] 23586195-31446474 |* [ 6 ] 15725916-23586195 |** [ 12 ] 7865637-15725916 |** [ 9 ] 5358-7865637 |************************************************** [ 211 ] Storage Throughput = excellent ( 1166.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40256402 bp ( 40036238 non ambiguous ) - Num Contigs Represented = 67 - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:33 (hh:mm:ss) Elapsed Time Round Time: 00:22:43 (hh:mm:ss) Elapsed Time : 214 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11601 repeats masked totaling 3147030 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10088744 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10008406 bp After Masking: 6536296 bp Masked: 34.69 % -- Input Database Coverage: 10088744 bp out of 1272358903 bp ( 0.79 % ) Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:21 (hh:mm:ss) Elapsed Time, 800 HSPs Collected Number of families returned by RECON: 234 Round Time: 00:07:24 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35520 repeats masked totaling 9366033 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30167578 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30027752 bp After Masking: 19734937 bp Masked: 34.28 % -- Input Database Coverage: 40256322 bp out of 1272358903 bp ( 3.16 % ) Sampling Time: 00:02:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:27:22 (hh:mm:ss) Elapsed Time, 7563 HSPs Collected Number of families returned by RECON: 1302 Round Time: 00:30:55 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102013 repeats masked totaling 27260802 bp(s). - TE Masking time 00:01:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90367412 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 90001596 bp After Masking: 59534202 bp Masked: 33.85 % -- Input Database Coverage: 130623734 bp out of 1272358903 bp ( 10.27 % ) Sampling Time: 00:09:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 02:59:29 (hh:mm:ss) Elapsed Time, 44233 HSPs Collected Number of families returned by RECON: 7849 Round Time: 03:17:15 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 322466 repeats masked totaling 85912856 bp(s). - TE Masking time 00:05:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271288959 bp Num Contigs Represented = 136 Non ambiguous bp: Initial: 270016511 bp After Masking: 175384149 bp Masked: 35.05 % -- Input Database Coverage: 401912693 bp out of 1272358903 bp ( 31.59 % ) Sampling Time: 00:32:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23171028 Comparison Time: 23:48:14 (hh:mm:ss) Elapsed Time, 167248 HSPs Collected Number of families returned by RECON: 50625 Round Time: 24:55:02 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatScout/RECON discovery complete: 484 families found Classification Time: 00:25:07 (hh:mm:ss) Elapsed Time Program Time: 29:38:26 (hh:mm:ss) Elapsed Time