RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.ut7Qhs/RM_1169271.TueNov121200432024 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: 1731441643 Database = /scratch/tmp/rModeler.ut7Qhs/GCA_964270905.1_mLagAcu1.hap1.1 - Sequences = 899 - Bases = 2676209414 - N50 = 116187269 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 190377748-203976112 | [ 2 ] 176779385-190377748 | [ ] 163181021-176779384 | [ 1 ] 149582658-163181021 | [ 1 ] 135984294-149582657 | [ 1 ] 122385931-135984294 | [ 1 ] 108787567-122385930 | [ 4 ] 95189204-108787567 | [ 2 ] 81590840-95189203 | [ 6 ] 67992477-81590840 | [ 1 ] 54394113-67992476 | [ 2 ] 40795750-54394113 | [ ] 27197386-40795749 | [ 1 ] 13599023-27197386 | [ 1 ] 660-13599023 |************************************************** [ 876 ] Storage Throughput = excellent ( 1576.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009261 bp ( 40004884 non ambiguous ) - Num Contigs Represented = 96 - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:42 (hh:mm:ss) Elapsed Time Round Time: 00:15:00 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9291 repeats masked totaling 2764031 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009456 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10008656 bp After Masking: 7091972 bp Masked: 29.14 % -- Input Database Coverage: 10009456 bp out of 2676209414 bp ( 0.37 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:20 (hh:mm:ss) Elapsed Time, 229824 HSPs Collected Number of families returned by RECON: 835 Round Time: 00:06:47 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33371 repeats masked totaling 10862322 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039770 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 30036193 bp After Masking: 18409244 bp Masked: 38.71 % -- Input Database Coverage: 40049226 bp out of 2676209414 bp ( 1.50 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:12:15 (hh:mm:ss) Elapsed Time, 33827 HSPs Collected Number of families returned by RECON: 2071 Round Time: 00:14:36 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 107262 repeats masked totaling 33403847 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90008406 bp Num Contigs Represented = 177 Non ambiguous bp: Initial: 90002551 bp After Masking: 54229716 bp Masked: 39.75 % -- Input Database Coverage: 130057632 bp out of 2676209414 bp ( 4.86 % ) Sampling Time: 00:05:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 01:13:02 (hh:mm:ss) Elapsed Time, 150476 HSPs Collected Number of families returned by RECON: 7681 Round Time: 01:24:08 (hh:mm:ss) Elapsed Time : 158 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 361396 repeats masked totaling 107098389 bp(s). - TE Masking time 00:01:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270042518 bp Num Contigs Represented = 342 Non ambiguous bp: Initial: 270023573 bp After Masking: 156346646 bp Masked: 42.10 % -- Input Database Coverage: 400100150 bp out of 2676209414 bp ( 14.95 % ) Sampling Time: 00:17:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 08:30:46 (hh:mm:ss) Elapsed Time, 1218476 HSPs Collected Number of families returned by RECON: 30326 Round Time: 08:57:36 (hh:mm:ss) Elapsed Time : 345 families discovered. RepeatScout/RECON discovery complete: 780 families found Classification Time: 00:16:54 (hh:mm:ss) Elapsed Time Program Time: 11:15:01 (hh:mm:ss) Elapsed Time