RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.q9yxNe/RM_342085.WedJan40441512023 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: 1672836111 Database = /dev/shm/rModeler.q9yxNe/GCF_003957565.2_bTaeGut1.4.pri - Sequences = 199 - Bases = 1056271262 - N50 = 75396176 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 141542913-151653088 | [ 1 ] 131432739-141542913 | [ ] 121322564-131432738 | [ ] 111212390-121322564 | [ 2 ] 101102216-111212390 | [ ] 90992041-101102215 | [ ] 80881867-90992041 | [ ] 70771692-80881866 | [ 3 ] 60661518-70771692 | [ 1 ] 50551344-60661518 | [ ] 40441169-50551343 | [ ] 30330995-40441169 | [ 3 ] 20220820-30330994 |* [ 5 ] 10110646-20220820 |* [ 7 ] 472-10110646 |************************************************** [ 177 ] Storage Throughput = excellent ( 1449.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40076495 bp ( 40028569 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:18 (hh:mm:ss) Elapsed Time Round Time: 00:16:09 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2861 repeats masked totaling 717929 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10051613 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10026400 bp After Masking: 9074985 bp Masked: 9.49 % -- Input Database Coverage: 10051613 bp out of 1056271262 bp ( 0.95 % ) Sampling Time: 00:00:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:18 (hh:mm:ss) Elapsed Time, 1146 HSPs Collected Number of families returned by RECON: 322 Round Time: 00:07:18 (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 : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7475 repeats masked totaling 1832915 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024802 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30002089 bp After Masking: 27440573 bp Masked: 8.54 % -- Input Database Coverage: 40076415 bp out of 1056271262 bp ( 3.79 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:27:44 (hh:mm:ss) Elapsed Time, 6381 HSPs Collected Number of families returned by RECON: 1739 Round Time: 00:30:59 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23549 repeats masked totaling 5649599 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90226332 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 90014100 bp After Masking: 82240491 bp Masked: 8.64 % -- Input Database Coverage: 130302747 bp out of 1056271262 bp ( 12.34 % ) Sampling Time: 00:07:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:46:37 (hh:mm:ss) Elapsed Time, 44977 HSPs Collected Number of families returned by RECON: 11209 Round Time: 02:56:20 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80445 repeats masked totaling 20867011 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271087740 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 270005626 bp After Masking: 242245055 bp Masked: 10.28 % -- Input Database Coverage: 401390487 bp out of 1056271262 bp ( 38.00 % ) Sampling Time: 00:27:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23109801 Comparison Time: 21:08:32 (hh:mm:ss) Elapsed Time, 254906 HSPs Collected Number of families returned by RECON: 73636 Round Time: 22:33:03 (hh:mm:ss) Elapsed Time : 273 families discovered. RepeatScout/RECON discovery complete: 478 families found Classification Time: 00:24:03 (hh:mm:ss) Elapsed Time Program Time: 26:47:52 (hh:mm:ss) Elapsed Time