RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.D8k5kO/RM_15566.WedJul30424372024 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: 1720005877 Database = /dev/shm/rModeler.D8k5kO/GCA_902713435.1_fAciRut3.1_paternal_haplotype - Sequences = 224 - Bases = 1663879616 - N50 = 49934420 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 98024846-105025451 | [ 2 ] 91024242-98024846 | [ 1 ] 84023638-91024242 | [ 2 ] 77023034-84023638 | [ 1 ] 70022430-77023034 | [ ] 63021825-70022429 | [ 1 ] 56021221-63021825 | [ 2 ] 49020617-56021221 | [ 1 ] 42020013-49020617 | [ 2 ] 35019409-42020013 | [ 2 ] 28018804-35019408 |** [ 8 ] 21018200-28018804 |* [ 6 ] 14017596-21018200 |* [ 4 ] 7016992-14017596 |** [ 10 ] 16388-7016992 |************************************************** [ 182 ] Storage Throughput = excellent ( 1061.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003693 bp ( 40001585 non ambiguous ) - Num Contigs Represented = 80 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:33 (hh:mm:ss) Elapsed Time Round Time: 00:35:11 (hh:mm:ss) Elapsed Time : 949 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11946 repeats masked totaling 2692091 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002022 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 10000714 bp After Masking: 6753296 bp Masked: 32.47 % -- Input Database Coverage: 10002022 bp out of 1663879616 bp ( 0.60 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:26 (hh:mm:ss) Elapsed Time, 9302 HSPs Collected Number of families returned by RECON: 1944 Round Time: 00:07:02 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36750 repeats masked totaling 7980115 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001591 bp Num Contigs Represented = 75 Non ambiguous bp: Initial: 30000791 bp After Masking: 20422930 bp Masked: 31.93 % -- Input Database Coverage: 40003613 bp out of 1663879616 bp ( 2.40 % ) Sampling Time: 00:04:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:30:48 (hh:mm:ss) Elapsed Time, 61214 HSPs Collected Number of families returned by RECON: 5984 Round Time: 00:37:27 (hh:mm:ss) Elapsed Time : 155 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 123054 repeats masked totaling 25840051 bp(s). - TE Masking time 00:03:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032650 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 90027009 bp After Masking: 59120586 bp Masked: 34.33 % -- Input Database Coverage: 130036263 bp out of 1663879616 bp ( 7.82 % ) Sampling Time: 00:12:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:38:51 (hh:mm:ss) Elapsed Time, 392932 HSPs Collected Number of families returned by RECON: 18550 Round Time: 04:10:31 (hh:mm:ss) Elapsed Time : 703 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 463635 repeats masked totaling 96151785 bp(s). - TE Masking time 00:19:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270016477 bp Num Contigs Represented = 140 Non ambiguous bp: Initial: 270003335 bp After Masking: 158800240 bp Masked: 41.19 % -- Input Database Coverage: 400052740 bp out of 1663879616 bp ( 24.04 % ) Sampling Time: 00:50:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 26:30:22 (hh:mm:ss) Elapsed Time, 999453 HSPs Collected Number of families returned by RECON: 55454 Round Time: 29:19:02 (hh:mm:ss) Elapsed Time : 1512 families discovered. RepeatScout/RECON discovery complete: 3334 families found Classification Time: 02:35:54 (hh:mm:ss) Elapsed Time Program Time: 37:25:07 (hh:mm:ss) Elapsed Time