RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.GSXX3s/RM_1426974.MonApr141420142025 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: 1744665613 Database = /data/tmp/rModeler.GSXX3s/GCA_043880425.1_ASM4388042v1 - Sequences = 1486 - Bases = 2323192134 - N50 = 186824502 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 240606734-257792783 | [ 1 ] 223420685-240606734 | [ 1 ] 206234636-223420685 | [ 1 ] 189048587-206234636 | [ 1 ] 171862538-189048587 | [ 2 ] 154676489-171862538 | [ 1 ] 137490440-154676489 | [ ] 120304391-137490440 | [ 2 ] 103118342-120304391 | [ 1 ] 85932293-103118342 | [ 3 ] 68746244-85932293 | [ 1 ] 51560195-68746244 | [ ] 34374146-51560195 | [ ] 17188097-34374146 | [ ] 2048-17188097 |************************************************** [ 1472 ] Storage Throughput = excellent ( 1570.18 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035301 bp ( 40033581 non ambiguous ) - Num Contigs Represented = 93 - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:41 (hh:mm:ss) Elapsed Time Round Time: 00:17:46 (hh:mm:ss) Elapsed Time : 168 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 00:01:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7498 repeats masked totaling 2297814 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10037387 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10037387 bp After Masking: 7207673 bp Masked: 28.19 % -- Input Database Coverage: 10037387 bp out of 2323192134 bp ( 0.43 % ) Sampling Time: 00:01:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:19 (hh:mm:ss) Elapsed Time, 5558 HSPs Collected Number of families returned by RECON: 791 Round Time: 00:05:23 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26948 repeats masked totaling 6914701 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037834 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 30036114 bp After Masking: 20913926 bp Masked: 30.37 % -- Input Database Coverage: 40075221 bp out of 2323192134 bp ( 1.73 % ) Sampling Time: 00:06:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:19:31 (hh:mm:ss) Elapsed Time, 619324 HSPs Collected Number of families returned by RECON: 2203 Round Time: 00:26:18 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 87612 repeats masked totaling 22746253 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039667 bp Num Contigs Represented = 183 Non ambiguous bp: Initial: 90037667 bp After Masking: 61192433 bp Masked: 32.04 % -- Input Database Coverage: 130114888 bp out of 2323192134 bp ( 5.60 % ) Sampling Time: 00:17:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2593503 Comparison Time: 02:03:02 (hh:mm:ss) Elapsed Time, 3527282 HSPs Collected Number of families returned by RECON: 8578 Round Time: 02:22:33 (hh:mm:ss) Elapsed Time : 156 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 298685 repeats masked totaling 76074236 bp(s). - TE Masking time 00:02:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270015446 bp Num Contigs Represented = 441 Non ambiguous bp: Initial: 270007558 bp After Masking: 175201915 bp Masked: 35.11 % -- Input Database Coverage: 400130334 bp out of 2323192134 bp ( 17.22 % ) Sampling Time: 01:01:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23232336 Comparison Time: 17:38:27 (hh:mm:ss) Elapsed Time, 62755767 HSPs Collected Number of families returned by RECON: 35805 Round Time: 19:16:00 (hh:mm:ss) Elapsed Time : 357 families discovered. RepeatScout/RECON discovery complete: 761 families found Classification Time: 00:17:50 (hh:mm:ss) Elapsed Time Program Time: 22:45:50 (hh:mm:ss) Elapsed Time