RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.dyJCOc/RM_3216.FriJan120335282024 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: 1705059327 Database = /dev/shm/rModeler.dyJCOc/GCA_026018925.1_mTupTan1 - Sequences = 1198 - Bases = 2948294157 - N50 = 113526151 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 250191616-268061703 | [ 1 ] 232321529-250191615 | [ ] 214451443-232321529 | [ 2 ] 196581356-214451442 | [ 1 ] 178711269-196581355 | [ ] 160841183-178711269 | [ 2 ] 142971096-160841182 | [ ] 125101009-142971095 | [ ] 107230923-125101009 | [ 3 ] 89360836-107230922 | [ 3 ] 71490749-89360835 | [ 1 ] 53620663-71490749 | [ 5 ] 35750576-53620662 | [ 6 ] 17880489-35750575 | [ 4 ] 10403-17880489 |************************************************** [ 1170 ] Storage Throughput = excellent ( 1120.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40011573 bp ( 40009350 non ambiguous ) - Num Contigs Represented = 89 - Sequence extraction : 00:02:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:27 (hh:mm:ss) Elapsed Time Round Time: 00:28:44 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16355 repeats masked totaling 3050093 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001931 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10001231 bp After Masking: 5972664 bp Masked: 40.28 % -- Input Database Coverage: 10001931 bp out of 2948294157 bp ( 0.34 % ) Sampling Time: 00:01:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:34 (hh:mm:ss) Elapsed Time, 6574 HSPs Collected Number of families returned by RECON: 743 Round Time: 00:07:48 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53585 repeats masked totaling 9837743 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30009562 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 30008039 bp After Masking: 18230527 bp Masked: 39.25 % -- Input Database Coverage: 40011493 bp out of 2948294157 bp ( 1.36 % ) Sampling Time: 00:04:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:28:39 (hh:mm:ss) Elapsed Time, 21370 HSPs Collected Number of families returned by RECON: 2252 Round Time: 00:34:17 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 163498 repeats masked totaling 30504847 bp(s). - TE Masking time 00:01:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041962 bp Num Contigs Represented = 187 Non ambiguous bp: Initial: 90039062 bp After Masking: 51357516 bp Masked: 42.96 % -- Input Database Coverage: 130053455 bp out of 2948294157 bp ( 4.41 % ) Sampling Time: 00:15:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 03:07:07 (hh:mm:ss) Elapsed Time, 78740 HSPs Collected Number of families returned by RECON: 6976 Round Time: 03:25:57 (hh:mm:ss) Elapsed Time : 167 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 530096 repeats masked totaling 99683043 bp(s). - TE Masking time 00:07:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270013262 bp Num Contigs Represented = 352 Non ambiguous bp: Initial: 270000838 bp After Masking: 147293401 bp Masked: 45.45 % -- Input Database Coverage: 400066717 bp out of 2948294157 bp ( 13.57 % ) Sampling Time: 00:46:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23130201 Comparison Time: 26:11:35 (hh:mm:ss) Elapsed Time, 212536 HSPs Collected Number of families returned by RECON: 27190 Round Time: 27:22:20 (hh:mm:ss) Elapsed Time : 413 families discovered. RepeatScout/RECON discovery complete: 861 families found Classification Time: 00:37:08 (hh:mm:ss) Elapsed Time Program Time: 32:36:14 (hh:mm:ss) Elapsed Time