RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.hSO6oI/RM_3136469.SatFeb222347432025 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: 1740296861 Database = /dev/shm/rModeler.hSO6oI/GCA_964638665.1_fPorCra3.hap2.1 - Sequences = 1407 - Bases = 1511638839 - N50 = 54146670 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 123140274-131935937 | [ 1 ] 114344612-123140274 | [ 1 ] 105548949-114344611 | [ ] 96753287-105548949 | [ 1 ] 87957624-96753286 | [ ] 79161962-87957624 | [ ] 70366299-79161961 | [ 1 ] 61570637-70366299 | [ 1 ] 52774974-61570636 | [ 5 ] 43979312-52774974 | [ 1 ] 35183649-43979311 | [ 5 ] 26387987-35183649 | [ 5 ] 17592324-26387986 | [ 8 ] 8796662-17592324 | [ 2 ] 1000-8796662 |************************************************** [ 1376 ] Storage Throughput = excellent ( 1848.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024399 bp ( 40011799 non ambiguous ) - Num Contigs Represented = 128 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:00 (hh:mm:ss) Elapsed Time Round Time: 00:15:34 (hh:mm:ss) Elapsed Time : 1508 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18170 repeats masked totaling 3526922 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005470 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 10001070 bp After Masking: 5042012 bp Masked: 49.59 % -- Input Database Coverage: 10005470 bp out of 1511638839 bp ( 0.66 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 5939 HSPs Collected Number of families returned by RECON: 1754 Round Time: 00:04:09 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53586 repeats masked totaling 10337266 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018849 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 30010649 bp After Masking: 15014150 bp Masked: 49.97 % -- Input Database Coverage: 40024319 bp out of 1511638839 bp ( 2.65 % ) Sampling Time: 00:03:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:11:04 (hh:mm:ss) Elapsed Time, 54833 HSPs Collected Number of families returned by RECON: 5897 Round Time: 00:15:44 (hh:mm:ss) Elapsed Time : 112 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 168278 repeats masked totaling 31166450 bp(s). - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90054935 bp Num Contigs Represented = 197 Non ambiguous bp: Initial: 90021095 bp After Masking: 44811855 bp Masked: 50.22 % -- Input Database Coverage: 130079254 bp out of 1511638839 bp ( 8.61 % ) Sampling Time: 00:11:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2636956 Comparison Time: 00:57:01 (hh:mm:ss) Elapsed Time, 429733 HSPs Collected Number of families returned by RECON: 17102 Round Time: 01:15:28 (hh:mm:ss) Elapsed Time : 824 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 599105 repeats masked totaling 113171790 bp(s). - TE Masking time 00:06:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270122601 bp Num Contigs Represented = 457 Non ambiguous bp: Initial: 270020367 bp After Masking: 115447576 bp Masked: 57.24 % -- Input Database Coverage: 400201855 bp out of 1511638839 bp ( 26.47 % ) Sampling Time: 00:35:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23918986 Comparison Time: 05:47:24 (hh:mm:ss) Elapsed Time, 1291267 HSPs Collected Number of families returned by RECON: 45652 Round Time: 07:11:42 (hh:mm:ss) Elapsed Time : 2026 families discovered. RepeatScout/RECON discovery complete: 4470 families found Classification Time: 01:25:30 (hh:mm:ss) Elapsed Time Program Time: 10:28:07 (hh:mm:ss) Elapsed Time