RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.wPq27X/RM_3630560.ThuDec50622472024 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: 1733408566 Database = /scratch/tmp/rModeler.wPq27X/GCA_964211785.1_bAnsAns1.hap2.1 - Sequences = 381 - Bases = 1168290161 - N50 = 123554224 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202233844-216679048 | [ 1 ] 187788641-202233844 | [ ] 173343438-187788641 | [ ] 158898235-173343438 | [ 1 ] 144453032-158898235 | [ ] 130007828-144453031 | [ ] 115562625-130007828 | [ 1 ] 101117422-115562625 | [ ] 86672219-101117422 | [ ] 72227016-86672219 | [ 1 ] 57781812-72227015 | [ 1 ] 43336609-57781812 | [ ] 28891406-43336609 | [ 3 ] 14446203-28891406 |* [ 10 ] 1000-14446203 |************************************************** [ 363 ] Storage Throughput = excellent ( 1436.28 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008303 bp ( 40003503 non ambiguous ) - Num Contigs Represented = 86 - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:55 (hh:mm:ss) Elapsed Time Round Time: 00:15:47 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1734 repeats masked totaling 763472 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019856 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10017856 bp After Masking: 8517110 bp Masked: 14.98 % -- Input Database Coverage: 10019856 bp out of 1168290161 bp ( 0.86 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:07 (hh:mm:ss) Elapsed Time, 496 HSPs Collected Number of families returned by RECON: 214 Round Time: 00:04:05 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5624 repeats masked totaling 2403230 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028433 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 30025633 bp After Masking: 25622740 bp Masked: 14.66 % -- Input Database Coverage: 40048289 bp out of 1168290161 bp ( 3.43 % ) Sampling Time: 00:02:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:14:15 (hh:mm:ss) Elapsed Time, 5921 HSPs Collected Number of families returned by RECON: 1244 Round Time: 00:17:10 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17251 repeats masked totaling 7306811 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90048190 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 90035990 bp After Masking: 76925035 bp Masked: 14.56 % -- Input Database Coverage: 130096479 bp out of 1168290161 bp ( 11.14 % ) Sampling Time: 00:07:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 01:30:55 (hh:mm:ss) Elapsed Time, 58257 HSPs Collected Number of families returned by RECON: 7552 Round Time: 01:53:48 (hh:mm:ss) Elapsed Time : 57 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61024 repeats masked totaling 27803230 bp(s). - TE Masking time 00:01:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041060 bp Num Contigs Represented = 246 Non ambiguous bp: Initial: 270006460 bp After Masking: 223825645 bp Masked: 17.10 % -- Input Database Coverage: 400137539 bp out of 1168290161 bp ( 34.25 % ) Sampling Time: 00:23:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23157415 Comparison Time: 11:26:11 (hh:mm:ss) Elapsed Time, 196453 HSPs Collected Number of families returned by RECON: 49919 Round Time: 12:17:59 (hh:mm:ss) Elapsed Time : 198 families discovered. RepeatScout/RECON discovery complete: 336 families found Classification Time: 00:18:26 (hh:mm:ss) Elapsed Time Program Time: 15:07:15 (hh:mm:ss) Elapsed Time