RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6QisGM/RM_4113654.SunJul201134552025 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: 1753036494 Database = /dev/shm/rModeler.6QisGM/GCA_964212025.2_mMyoNat1.hap2.2 - Sequences = 173 - Bases = 1932610702 - N50 = 109636865 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 217190245-232703763 | [ 1 ] 201676727-217190244 | [ 2 ] 186163210-201676727 | [ ] 170649692-186163209 | [ ] 155136175-170649692 | [ ] 139622657-155136174 | [ ] 124109140-139622657 | [ ] 108595622-124109139 | [ 2 ] 93082105-108595622 | [ 3 ] 77568587-93082104 |* [ 4 ] 62055070-77568587 | [ 1 ] 46541552-62055069 |* [ 4 ] 31028035-46541552 | [ 1 ] 15514517-31028034 | [ 3 ] 1000-15514517 |************************************************** [ 152 ] Storage Throughput = excellent ( 1166.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012834 bp ( 40012634 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:02:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:45 (hh:mm:ss) Elapsed Time Round Time: 00:29:32 (hh:mm:ss) Elapsed Time : 358 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14369 repeats masked totaling 2459132 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022339 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10022139 bp After Masking: 7233743 bp Masked: 27.82 % -- Input Database Coverage: 10022339 bp out of 1932610702 bp ( 0.52 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:45 (hh:mm:ss) Elapsed Time, 9241 HSPs Collected Number of families returned by RECON: 797 Round Time: 00:06:13 (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 : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47158 repeats masked totaling 8327066 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030415 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30030415 bp After Masking: 20588199 bp Masked: 31.44 % -- Input Database Coverage: 40052754 bp out of 1932610702 bp ( 2.07 % ) Sampling Time: 00:03:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:26:06 (hh:mm:ss) Elapsed Time, 54117 HSPs Collected Number of families returned by RECON: 2409 Round Time: 00:30:47 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 147107 repeats masked totaling 25740350 bp(s). - TE Masking time 00:01:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016910 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 90015310 bp After Masking: 60598767 bp Masked: 32.68 % -- Input Database Coverage: 130069664 bp out of 1932610702 bp ( 6.73 % ) Sampling Time: 00:11:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:07:52 (hh:mm:ss) Elapsed Time, 145938 HSPs Collected Number of families returned by RECON: 8946 Round Time: 03:23:49 (hh:mm:ss) Elapsed Time : 194 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 485038 repeats masked totaling 86440292 bp(s). - TE Masking time 00:07:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270011674 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 270009474 bp After Masking: 172856402 bp Masked: 35.98 % -- Input Database Coverage: 400081338 bp out of 1932610702 bp ( 20.70 % ) Sampling Time: 00:38:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 24:30:42 (hh:mm:ss) Elapsed Time, 514195 HSPs Collected Number of families returned by RECON: 36143 Round Time: 25:48:41 (hh:mm:ss) Elapsed Time : 510 families discovered. RepeatScout/RECON discovery complete: 1147 families found Classification Time: 00:51:14 (hh:mm:ss) Elapsed Time Program Time: 31:10:16 (hh:mm:ss) Elapsed Time