RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.0NrJIv/RM_31050.MonJun241450072024 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: 1719265804 Database = /dev/shm/rModeler.0NrJIv/GCF_015220805.1_bPogPus1.pri - Sequences = 252 - Bases = 1272338968 - 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 |************************************************** [ 210 ] Storage Throughput = excellent ( 1028.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40285868 bp ( 40016296 non ambiguous ) - Num Contigs Represented = 72 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:25 (hh:mm:ss) Elapsed Time Round Time: 00:27:44 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11049 repeats masked totaling 2974522 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10120886 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 10040667 bp After Masking: 6629777 bp Masked: 33.97 % -- Input Database Coverage: 10120886 bp out of 1272338968 bp ( 0.80 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:04:59 (hh:mm:ss) Elapsed Time, 1061 HSPs Collected Number of families returned by RECON: 198 Round Time: 00:06:27 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36356 repeats masked totaling 9734416 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30204976 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 30015623 bp After Masking: 19151050 bp Masked: 36.20 % -- Input Database Coverage: 40325862 bp out of 1272338968 bp ( 3.17 % ) Sampling Time: 00:03:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:26:03 (hh:mm:ss) Elapsed Time, 5692 HSPs Collected Number of families returned by RECON: 1086 Round Time: 00:30:03 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 106013 repeats masked totaling 28110658 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90466751 bp Num Contigs Represented = 84 Non ambiguous bp: Initial: 90029964 bp After Masking: 59178573 bp Masked: 34.27 % -- Input Database Coverage: 130792613 bp out of 1272338968 bp ( 10.28 % ) Sampling Time: 00:08:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 03:12:38 (hh:mm:ss) Elapsed Time, 49863 HSPs Collected Number of families returned by RECON: 7535 Round Time: 03:23:08 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 323198 repeats masked totaling 85729627 bp(s). - TE Masking time 00:06:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271428586 bp Num Contigs Represented = 140 Non ambiguous bp: Initial: 270014738 bp After Masking: 175445184 bp Masked: 35.02 % -- Input Database Coverage: 402221199 bp out of 1272338968 bp ( 31.61 % ) Sampling Time: 00:29:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23218705 Comparison Time: 25:50:46 (hh:mm:ss) Elapsed Time, 153702 HSPs Collected Number of families returned by RECON: 50713 Round Time: 26:58:43 (hh:mm:ss) Elapsed Time : 206 families discovered. RepeatScout/RECON discovery complete: 489 families found Classification Time: 00:26:20 (hh:mm:ss) Elapsed Time Program Time: 31:52:25 (hh:mm:ss) Elapsed Time