RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gXYDpu/RM_3138998.WedJan101930152024 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: 1704943815 Database = /dev/shm/rModeler.gXYDpu/GCF_008822105.2_bTaeGut2.pat.W.v2 - Sequences = 205 - Bases = 1068988106 - N50 = 78982076 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 141770238-151896526 | [ 1 ] 131643951-141770238 | [ ] 121517664-131643951 | [ ] 111391377-121517664 | [ 2 ] 101265090-111391377 | [ ] 91138802-101265089 | [ ] 81012515-91138802 | [ ] 70886228-81012515 | [ 2 ] 60759941-70886228 | [ 2 ] 50633654-60759941 | [ ] 40507366-50633653 | [ ] 30381079-40507366 | [ 3 ] 20254792-30381079 |* [ 5 ] 10128505-20254792 |** [ 8 ] 2218-10128505 |************************************************** [ 182 ] Storage Throughput = good ( 870.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41199082 bp ( 40032569 non ambiguous ) - Num Contigs Represented = 60 - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:56 (hh:mm:ss) Elapsed Time Round Time: 00:19:49 (hh:mm:ss) Elapsed Time : 133 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3168 repeats masked totaling 708284 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10296103 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10035981 bp After Masking: 9156501 bp Masked: 8.76 % -- Input Database Coverage: 10296103 bp out of 1068988106 bp ( 0.96 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:07:01 (hh:mm:ss) Elapsed Time, 930 HSPs Collected Number of families returned by RECON: 334 Round Time: 00:08:07 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8863 repeats masked totaling 2063292 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30942896 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30036505 bp After Masking: 27406314 bp Masked: 8.76 % -- Input Database Coverage: 41238999 bp out of 1068988106 bp ( 3.86 % ) Sampling Time: 00:03:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 303031 Comparison Time: 00:35:49 (hh:mm:ss) Elapsed Time, 6679 HSPs Collected Number of families returned by RECON: 1815 Round Time: 00:39:37 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26182 repeats masked totaling 5815595 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91523898 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 90018410 bp After Masking: 82581503 bp Masked: 8.26 % -- Input Database Coverage: 132762897 bp out of 1068988106 bp ( 12.42 % ) Sampling Time: 00:08:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2643850 Comparison Time: 04:09:21 (hh:mm:ss) Elapsed Time, 46863 HSPs Collected Number of families returned by RECON: 11237 Round Time: 04:21:40 (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 : 00:09:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 87307 repeats masked totaling 21477560 bp(s). - TE Masking time 00:03:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275368194 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 270016455 bp After Masking: 243806377 bp Masked: 9.71 % -- Input Database Coverage: 408131091 bp out of 1068988106 bp ( 38.18 % ) Sampling Time: 00:27:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23836060 Comparison Time: 31:02:07 (hh:mm:ss) Elapsed Time, 243901 HSPs Collected Number of families returned by RECON: 75406 Round Time: 32:25:19 (hh:mm:ss) Elapsed Time : 278 families discovered. RepeatScout/RECON discovery complete: 503 families found Classification Time: 00:37:17 (hh:mm:ss) Elapsed Time Program Time: 38:31:49 (hh:mm:ss) Elapsed Time