RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.c8EuNe/RM_24370.SatNov252138312023 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: 1700977110 Database = /dev/shm/rModeler.c8EuNe/GCA_017639645.1_bFalNau1.mat - Sequences = 551 - Bases = 1156765323 - N50 = 68351649 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 111633065-119606795 | [ 2 ] 103659335-111633064 | [ ] 95685605-103659334 | [ ] 87711875-95685604 | [ ] 79738146-87711875 | [ 1 ] 71764416-79738145 | [ 2 ] 63790686-71764415 | [ 2 ] 55816956-63790685 | [ 2 ] 47843226-55816955 | [ 1 ] 39869497-47843226 | [ ] 31895767-39869496 | [ 4 ] 23922037-31895766 | [ 2 ] 15948307-23922036 | [ 2 ] 7974577-15948306 | [ 3 ] 848-7974577 |************************************************** [ 530 ] Storage Throughput = excellent ( 1171.46 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40399445 bp ( 40033507 non ambiguous ) - Num Contigs Represented = 86 - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:09 (hh:mm:ss) Elapsed Time Round Time: 00:27:38 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1473 repeats masked totaling 541725 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10128572 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10013349 bp After Masking: 9332443 bp Masked: 6.80 % -- Input Database Coverage: 10128572 bp out of 1156765323 bp ( 0.88 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:07:03 (hh:mm:ss) Elapsed Time, 877 HSPs Collected Number of families returned by RECON: 298 Round Time: 00:07:56 (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 : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4342 repeats masked totaling 1461725 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30270793 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 30020078 bp After Masking: 28334242 bp Masked: 5.62 % -- Input Database Coverage: 40399365 bp out of 1156765323 bp ( 3.49 % ) Sampling Time: 00:02:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:41:00 (hh:mm:ss) Elapsed Time, 5512 HSPs Collected Number of families returned by RECON: 1603 Round Time: 00:43:43 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14572 repeats masked totaling 4713592 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90764262 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 90024381 bp After Masking: 84648030 bp Masked: 5.97 % -- Input Database Coverage: 131163627 bp out of 1156765323 bp ( 11.34 % ) Sampling Time: 00:09:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2630071 Comparison Time: 05:52:10 (hh:mm:ss) Elapsed Time, 50397 HSPs Collected Number of families returned by RECON: 9592 Round Time: 06:05:52 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56473 repeats masked totaling 18189586 bp(s). - TE Masking time 00:04:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272529585 bp Num Contigs Represented = 234 Non ambiguous bp: Initial: 270039401 bp After Masking: 249543723 bp Masked: 7.59 % -- Input Database Coverage: 403693212 bp out of 1156765323 bp ( 34.90 % ) Sampling Time: 00:25:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23595015 Comparison Time: 44:39:12 (hh:mm:ss) Elapsed Time, 183604 HSPs Collected Number of families returned by RECON: 62369 Round Time: 46:13:09 (hh:mm:ss) Elapsed Time : 236 families discovered. RepeatScout/RECON discovery complete: 406 families found Classification Time: 00:51:53 (hh:mm:ss) Elapsed Time Program Time: 54:30:11 (hh:mm:ss) Elapsed Time