RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.im75NA/RM_2080368.MonNov180538022024 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: 1731937082 Database = /scratch/tmp/rModeler.im75NA/GCF_040937935.1_aHypRig1.pri - Sequences = 477 - Bases = 4915935452 - N50 = 503132392 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 645634893-691750716 | [ 1 ] 599519071-645634893 | [ ] 553403249-599519071 | [ 1 ] 507287427-553403249 | [ 1 ] 461171605-507287427 | [ 1 ] 415055782-461171604 | [ 1 ] 368939960-415055782 | [ 1 ] 322824138-368939960 | [ 1 ] 276708316-322824138 | [ 3 ] 230592494-276708316 | [ 2 ] 184476671-230592493 | [ ] 138360849-184476671 | [ ] 92245027-138360849 | [ ] 46129205-92245027 | [ ] 13383-46129205 |************************************************* [ 465 ] Storage Throughput = excellent ( 1581.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036159 bp ( 40030457 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:04:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:40 (hh:mm:ss) Elapsed Time Round Time: 00:21:24 (hh:mm:ss) Elapsed Time : 1177 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21401 repeats masked totaling 5083695 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005142 bp Num Contigs Represented = 14 Non ambiguous bp: Initial: 10004342 bp After Masking: 3773242 bp Masked: 62.28 % -- Input Database Coverage: 10005142 bp out of 4915935452 bp ( 0.20 % ) Sampling Time: 00:02:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:34 (hh:mm:ss) Elapsed Time, 25351 HSPs Collected Number of families returned by RECON: 1227 Round Time: 00:06:07 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67372 repeats masked totaling 16115125 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030937 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30026035 bp After Masking: 10772533 bp Masked: 64.12 % -- Input Database Coverage: 40036079 bp out of 4915935452 bp ( 0.81 % ) Sampling Time: 00:06:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:11:18 (hh:mm:ss) Elapsed Time, 62746 HSPs Collected Number of families returned by RECON: 4267 Round Time: 00:19:03 (hh:mm:ss) Elapsed Time : 120 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:10:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 209860 repeats masked totaling 49924193 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026121 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90014721 bp After Masking: 29943726 bp Masked: 66.73 % -- Input Database Coverage: 130062200 bp out of 4915935452 bp ( 2.65 % ) Sampling Time: 00:20:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 00:51:59 (hh:mm:ss) Elapsed Time, 298075 HSPs Collected Number of families returned by RECON: 11290 Round Time: 01:17:32 (hh:mm:ss) Elapsed Time : 556 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:31:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 696401 repeats masked totaling 162842031 bp(s). - TE Masking time 00:05:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039178 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 270004550 bp After Masking: 76670851 bp Masked: 71.60 % -- Input Database Coverage: 400101378 bp out of 4915935452 bp ( 8.14 % ) Sampling Time: 01:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22899528 Comparison Time: 05:12:35 (hh:mm:ss) Elapsed Time, 815570 HSPs Collected Number of families returned by RECON: 28754 Round Time: 06:36:02 (hh:mm:ss) Elapsed Time : 1294 families discovered. RepeatScout/RECON discovery complete: 3161 families found Classification Time: 00:49:10 (hh:mm:ss) Elapsed Time Program Time: 09:29:18 (hh:mm:ss) Elapsed Time