RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.q3SQDg/RM_30516.ThuDec51806132024 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: 1733450772 Database = /scratch/tmp/rModeler.q3SQDg/GCA_037038625.1_fFunDia1.hap2 - Sequences = 196 - Bases = 1329922595 - N50 = 57407506 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 61000500-65356870 |* [ 5 ] 56644130-61000499 |* [ 6 ] 52287760-56644129 |** [ 7 ] 47931391-52287760 | [ 1 ] 43575021-47931390 |* [ 4 ] 39218651-43575020 | [ ] 34862281-39218650 | [ 1 ] 30505912-34862281 | [ ] 26149542-30505911 | [ ] 21793172-26149541 | [ ] 17436802-21793171 | [ ] 13080433-17436802 | [ ] 8724063-13080432 | [ ] 4367693-8724062 | [ ] 11324-4367693 |************************************************** [ 172 ] Storage Throughput = fair ( 640.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40151708 bp ( 40016599 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:45 (hh:mm:ss) Elapsed Time Round Time: 00:34:20 (hh:mm:ss) Elapsed Time : 883 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14876 repeats masked totaling 3706346 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10121547 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10000008 bp After Masking: 6020532 bp Masked: 39.79 % -- Input Database Coverage: 10121547 bp out of 1329922595 bp ( 0.76 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:02 (hh:mm:ss) Elapsed Time, 8154 HSPs Collected Number of families returned by RECON: 1478 Round Time: 00:06:35 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44652 repeats masked totaling 11083260 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030081 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30016511 bp After Masking: 17990164 bp Masked: 40.07 % -- Input Database Coverage: 40151628 bp out of 1329922595 bp ( 3.02 % ) Sampling Time: 00:03:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:25:54 (hh:mm:ss) Elapsed Time, 62996 HSPs Collected Number of families returned by RECON: 4829 Round Time: 00:32:14 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 150629 repeats masked totaling 36841336 bp(s). - TE Masking time 00:03:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90491516 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 90025492 bp After Masking: 50664194 bp Masked: 43.72 % -- Input Database Coverage: 130643144 bp out of 1329922595 bp ( 9.82 % ) Sampling Time: 00:10:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 02:47:52 (hh:mm:ss) Elapsed Time, 332392 HSPs Collected Number of families returned by RECON: 12446 Round Time: 03:14:53 (hh:mm:ss) Elapsed Time : 569 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 536250 repeats masked totaling 129371110 bp(s). - TE Masking time 00:18:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271418224 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 270015996 bp After Masking: 132414701 bp Masked: 50.96 % -- Input Database Coverage: 402061368 bp out of 1329922595 bp ( 30.23 % ) Sampling Time: 00:41:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23116600 Comparison Time: 19:28:17 (hh:mm:ss) Elapsed Time, 671173 HSPs Collected Number of families returned by RECON: 34369 Round Time: 21:41:52 (hh:mm:ss) Elapsed Time : 1104 families discovered. RepeatScout/RECON discovery complete: 2703 families found Classification Time: 02:24:14 (hh:mm:ss) Elapsed Time Program Time: 28:34:08 (hh:mm:ss) Elapsed Time