RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.H3DlBW/RM_3043.TueDec51723512023 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: 1701825829 Database = /dev/shm/rModeler.H3DlBW/GCA_948146105.1_fSynAcu2.1 - Sequences = 251 - Bases = 359216277 - N50 = 15567408 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 26941534-28865858 | [ 1 ] 25017210-26941533 | [ 1 ] 23092886-25017209 | [ ] 21168562-23092885 | [ 1 ] 19244238-21168561 | [ 1 ] 17319914-19244237 | [ 3 ] 15395590-17319913 | [ 1 ] 13471267-15395590 | [ 4 ] 11546943-13471266 | [ 3 ] 9622619-11546942 | [ 4 ] 7698295-9622618 | [ 2 ] 5773971-7698294 | [ 1 ] 3849647-5773970 | [ ] 1925323-3849646 | [ ] 1000-1925323 |************************************************** [ 229 ] Storage Throughput = excellent ( 1111.83 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030080 bp ( 40028280 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:26 (hh:mm:ss) Elapsed Time Round Time: 00:32:27 (hh:mm:ss) Elapsed Time : 332 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6442 repeats masked totaling 1726516 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030017 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10029817 bp After Masking: 7495488 bp Masked: 25.27 % -- Input Database Coverage: 10030017 bp out of 359216277 bp ( 2.79 % ) Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 127253 HSPs Collected Number of families returned by RECON: 962 Round Time: 00:07:11 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19331 repeats masked totaling 5173225 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040063 bp Num Contigs Represented = 71 Non ambiguous bp: Initial: 30038463 bp After Masking: 22369286 bp Masked: 25.53 % -- Input Database Coverage: 40070080 bp out of 359216277 bp ( 11.15 % ) Sampling Time: 00:02:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:29:14 (hh:mm:ss) Elapsed Time, 55270 HSPs Collected Number of families returned by RECON: 4152 Round Time: 00:34:31 (hh:mm:ss) Elapsed Time : 64 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64367 repeats masked totaling 16380531 bp(s). - TE Masking time 00:01:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012779 bp Num Contigs Represented = 127 Non ambiguous bp: Initial: 90007979 bp After Masking: 66629709 bp Masked: 25.97 % -- Input Database Coverage: 130082859 bp out of 359216277 bp ( 36.21 % ) Sampling Time: 00:07:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2598060 Comparison Time: 03:58:41 (hh:mm:ss) Elapsed Time, 315759 HSPs Collected Number of families returned by RECON: 16398 Round Time: 04:19:08 (hh:mm:ss) Elapsed Time : 318 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 204286 repeats masked totaling 49603952 bp(s). - TE Masking time 00:07:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 229133130 bp Num Contigs Represented = 196 Non ambiguous bp: Initial: 229120730 bp After Masking: 162203149 bp Masked: 29.21 % -- Input Database Coverage: 359215989 bp out of 359216277 bp ( 100.00 % ) Sampling Time: 00:21:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 16834503 Comparison Time: 20:52:36 (hh:mm:ss) Elapsed Time, 1125453 HSPs Collected Number of families returned by RECON: 50739 Round Time: 22:22:47 (hh:mm:ss) Elapsed Time : 732 families discovered. RepeatScout/RECON discovery complete: 1460 families found Classification Time: 01:09:30 (hh:mm:ss) Elapsed Time Program Time: 29:05:34 (hh:mm:ss) Elapsed Time