RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NaFTRk/RM_3674238.SatNov252138212023 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: 1700977100 Database = /dev/shm/rModeler.NaFTRk/GCF_963082965.1_fCarCar2.1 - Sequences = 277 - Bases = 1684296438 - N50 = 32783810 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 50338285-53933806 | [ 2 ] 46742765-50338285 | [ ] 43147244-46742764 | [ 2 ] 39551724-43147244 | [ 3 ] 35956204-39551724 | [ 2 ] 32360683-35956203 |*** [ 15 ] 28765163-32360683 |*** [ 16 ] 25169642-28765162 |* [ 7 ] 21574122-25169642 | [ 3 ] 17978602-21574122 | [ ] 14383081-17978601 | [ ] 10787561-14383081 | [ ] 7192040-10787560 | [ ] 3596520-7192040 | [ ] 1000-3596520 |************************************************** [ 227 ] Storage Throughput = excellent ( 1100.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027008 bp ( 40023408 non ambiguous ) - Num Contigs Represented = 68 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:43 (hh:mm:ss) Elapsed Time Round Time: 00:26:40 (hh:mm:ss) Elapsed Time : 846 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11456 repeats masked totaling 2864712 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10016091 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 10014891 bp After Masking: 6645462 bp Masked: 33.64 % -- Input Database Coverage: 10016091 bp out of 1684296438 bp ( 0.59 % ) Sampling Time: 00:02:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:04 (hh:mm:ss) Elapsed Time, 6659 HSPs Collected Number of families returned by RECON: 1508 Round Time: 00:09:22 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35106 repeats masked totaling 9077679 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010837 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30008437 bp After Masking: 19723961 bp Masked: 34.27 % -- Input Database Coverage: 40026928 bp out of 1684296438 bp ( 2.38 % ) Sampling Time: 00:04:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:31:57 (hh:mm:ss) Elapsed Time, 56412 HSPs Collected Number of families returned by RECON: 5562 Round Time: 00:38:09 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 113024 repeats masked totaling 28858818 bp(s). - TE Masking time 00:03:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90011325 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 90001945 bp After Masking: 57231350 bp Masked: 36.41 % -- Input Database Coverage: 130038253 bp out of 1684296438 bp ( 7.72 % ) Sampling Time: 00:15:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 03:17:27 (hh:mm:ss) Elapsed Time, 410480 HSPs Collected Number of families returned by RECON: 16898 Round Time: 03:51:11 (hh:mm:ss) Elapsed Time : 669 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 423419 repeats masked totaling 106440157 bp(s). - TE Masking time 00:17:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270057397 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 270027597 bp After Masking: 152636195 bp Masked: 43.47 % -- Input Database Coverage: 400095650 bp out of 1684296438 bp ( 23.75 % ) Sampling Time: 00:52:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 23:09:20 (hh:mm:ss) Elapsed Time, 1020655 HSPs Collected Number of families returned by RECON: 52306 Round Time: 25:10:57 (hh:mm:ss) Elapsed Time : 1357 families discovered. RepeatScout/RECON discovery complete: 2958 families found Classification Time: 02:29:18 (hh:mm:ss) Elapsed Time Program Time: 32:45:37 (hh:mm:ss) Elapsed Time