RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.rUNuRO/RM_25514.SunNov171333392024 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: 1731879218 Database = /scratch/tmp/rModeler.rUNuRO/GCA_038501925.1_aXenPet1.paternal.cur - Sequences = 888 - Bases = 2883796191 - N50 = 160355179 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 224943307-241009896 | [ 1 ] 208876719-224943307 | [ 1 ] 192810130-208876718 | [ 1 ] 176743542-192810130 | [ ] 160676954-176743542 | [ 3 ] 144610365-160676953 | [ 5 ] 128543777-144610365 | [ 4 ] 112477188-128543776 | [ 2 ] 96410600-112477188 | [ 1 ] 80344012-96410600 | [ ] 64277423-80344011 | [ ] 48210835-64277423 | [ ] 32144246-48210834 | [ ] 16077658-32144246 | [ ] 11070-16077658 |************************************************** [ 870 ] Storage Throughput = fair ( 635.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021698 bp ( 40020498 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:13 (hh:mm:ss) Elapsed Time Round Time: 00:30:54 (hh:mm:ss) Elapsed Time : 661 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18276 repeats masked totaling 3665793 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039286 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10038686 bp After Masking: 5894107 bp Masked: 41.29 % -- Input Database Coverage: 10039286 bp out of 2883796191 bp ( 0.35 % ) Sampling Time: 00:01:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:03 (hh:mm:ss) Elapsed Time, 11893 HSPs Collected Number of families returned by RECON: 1203 Round Time: 00:07:24 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54919 repeats masked totaling 11081706 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022351 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30021751 bp After Masking: 17198638 bp Masked: 42.71 % -- Input Database Coverage: 40061637 bp out of 2883796191 bp ( 1.39 % ) Sampling Time: 00:06:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:25:31 (hh:mm:ss) Elapsed Time, 47324 HSPs Collected Number of families returned by RECON: 4116 Round Time: 00:33:48 (hh:mm:ss) Elapsed Time : 106 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 178443 repeats masked totaling 35949071 bp(s). - TE Masking time 00:02:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005503 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 90003103 bp After Masking: 49459928 bp Masked: 45.05 % -- Input Database Coverage: 130067140 bp out of 2883796191 bp ( 4.51 % ) Sampling Time: 00:17:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 02:51:13 (hh:mm:ss) Elapsed Time, 215763 HSPs Collected Number of families returned by RECON: 13508 Round Time: 03:25:50 (hh:mm:ss) Elapsed Time : 398 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 589314 repeats masked totaling 118987644 bp(s). - TE Masking time 00:10:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038338 bp Num Contigs Represented = 170 Non ambiguous bp: Initial: 270030552 bp After Masking: 136493460 bp Masked: 49.45 % -- Input Database Coverage: 400105478 bp out of 2883796191 bp ( 13.87 % ) Sampling Time: 00:57:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 20:38:27 (hh:mm:ss) Elapsed Time, 726358 HSPs Collected Number of families returned by RECON: 45214 Round Time: 23:13:28 (hh:mm:ss) Elapsed Time : 1075 families discovered. RepeatScout/RECON discovery complete: 2257 families found Classification Time: 01:35:58 (hh:mm:ss) Elapsed Time Program Time: 29:27:22 (hh:mm:ss) Elapsed Time