RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bQu55l/RM_2271486.SunJun302117232024 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: 1719807443 Database = /dev/shm/rModeler.bQu55l/GCF_902827175.1_fGymAcu1.1 - Sequences = 2618 - Bases = 996888495 - N50 = 1960469 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 12264371-13140105 | [ 1 ] 11388638-12264371 | [ ] 10512905-11388638 | [ 1 ] 9637171-10512904 | [ 1 ] 8761438-9637171 | [ 3 ] 7885705-8761438 | [ ] 7009971-7885704 | [ 4 ] 6134238-7009971 | [ 3 ] 5258505-6134238 | [ 8 ] 4382771-5258504 | [ 15 ] 3507038-4382771 | [ 20 ] 2631305-3507038 | [ 34 ] 1755571-2631304 |* [ 55 ] 879838-1755571 |** [ 108 ] 4105-879838 |************************************************** [ 2365 ] Storage Throughput = excellent ( 1013.30 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033484 bp ( 40025792 non ambiguous ) - Num Contigs Represented = 546 - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:18 (hh:mm:ss) Elapsed Time Round Time: 00:23:26 (hh:mm:ss) Elapsed Time : 972 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12933 repeats masked totaling 3935542 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10035919 bp Num Contigs Represented = 213 Non ambiguous bp: Initial: 10034327 bp After Masking: 5505615 bp Masked: 45.13 % -- Input Database Coverage: 10035919 bp out of 996888495 bp ( 1.01 % ) Sampling Time: 00:01:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34716 Comparison Time: 00:04:47 (hh:mm:ss) Elapsed Time, 9897 HSPs Collected Number of families returned by RECON: 947 Round Time: 00:06:31 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37842 repeats masked totaling 11289968 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037485 bp Num Contigs Represented = 450 Non ambiguous bp: Initial: 30031385 bp After Masking: 17040840 bp Masked: 43.26 % -- Input Database Coverage: 40073404 bp out of 996888495 bp ( 4.02 % ) Sampling Time: 00:04:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 312445 Comparison Time: 00:22:14 (hh:mm:ss) Elapsed Time, 29862 HSPs Collected Number of families returned by RECON: 3175 Round Time: 00:26:52 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121079 repeats masked totaling 34632625 bp(s). - TE Masking time 00:03:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90049716 bp Num Contigs Represented = 918 Non ambiguous bp: Initial: 90033389 bp After Masking: 50438879 bp Masked: 43.98 % -- Input Database Coverage: 130123120 bp out of 996888495 bp ( 13.05 % ) Sampling Time: 00:12:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2854855 Comparison Time: 02:16:23 (hh:mm:ss) Elapsed Time, 247169 HSPs Collected Number of families returned by RECON: 10071 Round Time: 02:36:22 (hh:mm:ss) Elapsed Time : 454 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 415201 repeats masked totaling 119629772 bp(s). - TE Masking time 00:14:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270051262 bp Num Contigs Represented = 1533 Non ambiguous bp: Initial: 270000259 bp After Masking: 136087588 bp Masked: 49.60 % -- Input Database Coverage: 400174382 bp out of 996888495 bp ( 40.14 % ) Sampling Time: 00:43:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25052581 Comparison Time: 15:37:28 (hh:mm:ss) Elapsed Time, 601321 HSPs Collected Number of families returned by RECON: 33163 Round Time: 17:09:55 (hh:mm:ss) Elapsed Time : 982 families discovered. RepeatScout/RECON discovery complete: 2469 families found Classification Time: 02:44:27 (hh:mm:ss) Elapsed Time Program Time: 23:27:33 (hh:mm:ss) Elapsed Time