RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ODKGos/RM_56172.SunMar300237062025 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: 1743327426 Database = /dev/shm/rModeler.ODKGos/GCA_048565345.1_aManAur1.hap1 - Sequences = 3088 - Bases = 3336112499 - N50 = 380747897 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 471526222-505206504 | [ 1 ] 437845940-471526221 | [ ] 404165658-437845939 | [ 1 ] 370485377-404165658 | [ 1 ] 336805095-370485376 | [ 1 ] 303124813-336805094 | [ 1 ] 269444531-303124812 | [ ] 235764250-269444531 | [ ] 202083968-235764249 | [ ] 168403686-202083967 | [ 2 ] 134723404-168403685 | [ 3 ] 101043123-134723404 | [ 3 ] 67362841-101043122 | [ ] 33682559-67362840 | [ ] 2278-33682559 |************************************************** [ 3075 ] Storage Throughput = excellent ( 1923.68 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010559 bp ( 40000359 non ambiguous ) - Num Contigs Represented = 84 - Sequence extraction : 00:03:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:29 (hh:mm:ss) Elapsed Time Round Time: 00:14:50 (hh:mm:ss) Elapsed Time : 731 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19793 repeats masked totaling 4111845 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027405 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10024605 bp After Masking: 4516953 bp Masked: 54.94 % -- Input Database Coverage: 10027405 bp out of 3336112499 bp ( 0.30 % ) Sampling Time: 00:01:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:02:54 (hh:mm:ss) Elapsed Time, 9872 HSPs Collected Number of families returned by RECON: 1395 Round Time: 00:04:54 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:17 (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... 61286 repeats masked totaling 12650001 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023085 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30015685 bp After Masking: 13232841 bp Masked: 55.91 % -- Input Database Coverage: 40050490 bp out of 3336112499 bp ( 1.20 % ) Sampling Time: 00:06:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 293761 Comparison Time: 00:11:34 (hh:mm:ss) Elapsed Time, 60880 HSPs Collected Number of families returned by RECON: 4687 Round Time: 00:18:51 (hh:mm:ss) Elapsed Time : 147 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 201534 repeats masked totaling 40843663 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041067 bp Num Contigs Represented = 180 Non ambiguous bp: Initial: 90015867 bp After Masking: 36506305 bp Masked: 59.44 % -- Input Database Coverage: 130091557 bp out of 3336112499 bp ( 3.90 % ) Sampling Time: 00:19:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2627778 Comparison Time: 00:55:52 (hh:mm:ss) Elapsed Time, 268735 HSPs Collected Number of families returned by RECON: 11990 Round Time: 01:19:48 (hh:mm:ss) Elapsed Time : 507 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 679850 repeats masked totaling 137406903 bp(s). - TE Masking time 00:03:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270084462 bp Num Contigs Represented = 429 Non ambiguous bp: Initial: 270016430 bp After Masking: 96274320 bp Masked: 64.35 % -- Input Database Coverage: 400176019 bp out of 3336112499 bp ( 12.00 % ) Sampling Time: 00:59:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23615628 Comparison Time: 05:25:32 (hh:mm:ss) Elapsed Time, 910860 HSPs Collected Number of families returned by RECON: 31212 Round Time: 06:44:53 (hh:mm:ss) Elapsed Time : 1353 families discovered. RepeatScout/RECON discovery complete: 2757 families found Classification Time: 00:47:35 (hh:mm:ss) Elapsed Time Program Time: 09:30:51 (hh:mm:ss) Elapsed Time