RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.GFq4eG/RM_3944197.ThuDec50309582024 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: 1733396998 Database = /scratch/tmp/rModeler.GFq4eG/GCA_964212025.1_mMyoNat1.hap2.1 - Sequences = 319 - Bases = 1930603033 - N50 = 101457914 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 215566230-230963676 | [ 1 ] 200168785-215566230 | [ 2 ] 184771340-200168785 | [ ] 169373895-184771340 | [ ] 153976450-169373895 | [ ] 138579005-153976450 | [ ] 123181560-138579005 | [ ] 107784115-123181560 | [ 1 ] 92386670-107784115 | [ 4 ] 76989225-92386670 | [ 4 ] 61591780-76989225 | [ 1 ] 46194335-61591780 | [ 4 ] 30796890-46194335 | [ 1 ] 15399445-30796890 | [ 2 ] 2000-15399445 |************************************************* [ 299 ] Storage Throughput = excellent ( 1531.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012343 bp ( 40006543 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:45 (hh:mm:ss) Elapsed Time Round Time: 00:11:04 (hh:mm:ss) Elapsed Time : 326 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 00:00:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14275 repeats masked totaling 2732558 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027043 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10025443 bp After Masking: 7064161 bp Masked: 29.54 % -- Input Database Coverage: 10027043 bp out of 1930603033 bp ( 0.52 % ) Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 6069 HSPs Collected Number of families returned by RECON: 811 Round Time: 00:03:34 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45271 repeats masked totaling 8540555 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025220 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30021020 bp After Masking: 20392660 bp Masked: 32.07 % -- Input Database Coverage: 40052263 bp out of 1930603033 bp ( 2.07 % ) Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:11:54 (hh:mm:ss) Elapsed Time, 21742 HSPs Collected Number of families returned by RECON: 2396 Round Time: 00:14:10 (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 : 00:02:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143342 repeats masked totaling 26960090 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042328 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 90029204 bp After Masking: 59629361 bp Masked: 33.77 % -- Input Database Coverage: 130094591 bp out of 1930603033 bp ( 6.74 % ) Sampling Time: 00:05:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 01:08:25 (hh:mm:ss) Elapsed Time, 93091 HSPs Collected Number of families returned by RECON: 8438 Round Time: 01:15:54 (hh:mm:ss) Elapsed Time : 207 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 465680 repeats masked totaling 87901017 bp(s). - TE Masking time 00:02:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270079289 bp Num Contigs Represented = 134 Non ambiguous bp: Initial: 270038910 bp After Masking: 172277160 bp Masked: 36.20 % -- Input Database Coverage: 400173880 bp out of 1930603033 bp ( 20.73 % ) Sampling Time: 00:17:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 08:24:56 (hh:mm:ss) Elapsed Time, 299375 HSPs Collected Number of families returned by RECON: 36674 Round Time: 08:56:12 (hh:mm:ss) Elapsed Time : 516 families discovered. RepeatScout/RECON discovery complete: 1129 families found Classification Time: 00:22:48 (hh:mm:ss) Elapsed Time Program Time: 11:03:42 (hh:mm:ss) Elapsed Time