RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.hZQXsP/RM_2115995.FriApr110716302025 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: 1744380989 Database = /data/tmp/rModeler.hZQXsP/GCA_965112155.1_rPodLio1.hap1.1 - Sequences = 290 - Bases = 1574020868 - N50 = 100109159 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 130145574-139441615 | [ 1 ] 120849533-130145574 | [ 2 ] 111553492-120849533 | [ ] 102257451-111553492 | [ 2 ] 92961410-102257451 | [ 2 ] 83665369-92961410 | [ 1 ] 74369328-83665369 | [ 2 ] 65073287-74369328 | [ 1 ] 55777246-65073287 | [ 2 ] 46481205-55777246 | [ 3 ] 37185164-46481205 | [ 3 ] 27889123-37185164 | [ ] 18593082-27889123 | [ ] 9297041-18593082 | [ 1 ] 1000-9297041 |************************************************** [ 270 ] Storage Throughput = excellent ( 1277.26 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019573 bp ( 40013974 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:51 (hh:mm:ss) Elapsed Time Round Time: 00:25:41 (hh:mm:ss) Elapsed Time : 588 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17177 repeats masked totaling 3210357 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010821 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10009021 bp After Masking: 6196284 bp Masked: 38.09 % -- Input Database Coverage: 10010821 bp out of 1574020868 bp ( 0.64 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:04:47 (hh:mm:ss) Elapsed Time, 7280 HSPs Collected Number of families returned by RECON: 1238 Round Time: 00:07:34 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54594 repeats masked totaling 9989720 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008740 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30004941 bp After Masking: 18466477 bp Masked: 38.46 % -- Input Database Coverage: 40019561 bp out of 1574020868 bp ( 2.54 % ) Sampling Time: 00:04:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:23:36 (hh:mm:ss) Elapsed Time, 56228 HSPs Collected Number of families returned by RECON: 4275 Round Time: 00:34:19 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 177719 repeats masked totaling 32206171 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90014197 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 90003489 bp After Masking: 52371953 bp Masked: 41.81 % -- Input Database Coverage: 130033758 bp out of 1574020868 bp ( 8.26 % ) Sampling Time: 00:14:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 02:37:38 (hh:mm:ss) Elapsed Time, 167450 HSPs Collected Number of families returned by RECON: 13101 Round Time: 03:14:57 (hh:mm:ss) Elapsed Time : 407 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 606006 repeats masked totaling 106981024 bp(s). - TE Masking time 00:07:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032455 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 270000255 bp After Masking: 148162737 bp Masked: 45.12 % -- Input Database Coverage: 400066213 bp out of 1574020868 bp ( 25.42 % ) Sampling Time: 00:38:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 19:15:09 (hh:mm:ss) Elapsed Time, 475135 HSPs Collected Number of families returned by RECON: 45500 Round Time: 22:03:22 (hh:mm:ss) Elapsed Time : 1035 families discovered. RepeatScout/RECON discovery complete: 2168 families found Classification Time: 00:59:40 (hh:mm:ss) Elapsed Time Program Time: 27:25:33 (hh:mm:ss) Elapsed Time