RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.JyOfgX/RM_2701466.TueApr222310592025 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: 1745388658 Database = /dev/shm/rModeler.JyOfgX/GCA_964212035.2_mMyoNat1.hap1.2 - Sequences = 212 - Bases = 2138592721 - N50 = 110615897 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 215824789-231240774 | [ 3 ] 200408804-215824788 | [ ] 184992819-200408803 | [ ] 169576834-184992818 | [ ] 154160849-169576833 | [ 1 ] 138744864-154160848 | [ ] 123328879-138744863 | [ ] 107912894-123328878 | [ 2 ] 92496909-107912893 | [ 3 ] 77080924-92496908 |* [ 4 ] 61664939-77080923 | [ 2 ] 46248954-61664938 | [ 3 ] 30832969-46248953 | [ 2 ] 15416984-30832968 | [ 3 ] 1000-15416984 |************************************************** [ 189 ] Storage Throughput = excellent ( 1844.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018197 bp ( 40016997 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:08 (hh:mm:ss) Elapsed Time Round Time: 00:12:44 (hh:mm:ss) Elapsed Time : 364 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:20 (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... 15073 repeats masked totaling 2790488 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025194 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10024994 bp After Masking: 6984554 bp Masked: 30.33 % -- Input Database Coverage: 10025194 bp out of 2138592721 bp ( 0.47 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 11214 HSPs Collected Number of families returned by RECON: 819 Round Time: 00:03:44 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47970 repeats masked totaling 8941985 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30032923 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30031923 bp After Masking: 19573522 bp Masked: 34.82 % -- Input Database Coverage: 40058117 bp out of 2138592721 bp ( 1.87 % ) Sampling Time: 00:01:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:16:39 (hh:mm:ss) Elapsed Time, 24639 HSPs Collected Number of families returned by RECON: 2307 Round Time: 00:18:57 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:54 (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... 154039 repeats masked totaling 29004033 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90007334 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 90004644 bp After Masking: 57454638 bp Masked: 36.16 % -- Input Database Coverage: 130065451 bp out of 2138592721 bp ( 6.08 % ) Sampling Time: 00:05:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:16:58 (hh:mm:ss) Elapsed Time, 123192 HSPs Collected Number of families returned by RECON: 7845 Round Time: 01:24:12 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:08:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 499075 repeats masked totaling 94137487 bp(s). - TE Masking time 00:02:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014380 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 270009780 bp After Masking: 164303255 bp Masked: 39.15 % -- Input Database Coverage: 400079831 bp out of 2138592721 bp ( 18.71 % ) Sampling Time: 00:18:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 08:37:27 (hh:mm:ss) Elapsed Time, 465012 HSPs Collected Number of families returned by RECON: 31902 Round Time: 09:06:24 (hh:mm:ss) Elapsed Time : 534 families discovered. RepeatScout/RECON discovery complete: 1185 families found Classification Time: 00:25:44 (hh:mm:ss) Elapsed Time Program Time: 11:31:45 (hh:mm:ss) Elapsed Time