RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9UFkx2/RM_2318156.SatJul60417002024 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: 1720264619 Database = /dev/shm/rModeler.9UFkx2/GCF_034236695.1_Oner_Uvic_2.0 - Sequences = 11378 - Bases = 2645636310 - N50 = 94065161 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 102357519-109668754 | [ 8 ] 95046285-102357519 | [ 3 ] 87735051-95046285 | [ 2 ] 80423816-87735050 | [ 3 ] 73112582-80423816 | [ 1 ] 65801348-73112582 | [ 2 ] 58490114-65801348 | [ 4 ] 51178879-58490113 | [ 4 ] 43867645-51178879 | [ 1 ] 36556411-43867645 | [ ] 29245177-36556411 | [ 1 ] 21933942-29245176 | [ ] 14622708-21933942 | [ ] 7311474-14622708 | [ ] 240-7311474 |************************************************** [ 11349 ] Storage Throughput = excellent ( 1111.12 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40051394 bp ( 40025363 non ambiguous ) - Num Contigs Represented = 260 - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:59 (hh:mm:ss) Elapsed Time Round Time: 00:23:38 (hh:mm:ss) Elapsed Time : 802 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12741 repeats masked totaling 3362068 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10047848 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 10037217 bp After Masking: 3994600 bp Masked: 60.20 % -- Input Database Coverage: 10047848 bp out of 2645636310 bp ( 0.38 % ) Sampling Time: 00:07:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 38226 Comparison Time: 00:04:55 (hh:mm:ss) Elapsed Time, 6213 HSPs Collected Number of families returned by RECON: 1077 Round Time: 00:12:45 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 37456 repeats masked totaling 10239307 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046799 bp Num Contigs Represented = 212 Non ambiguous bp: Initial: 30031399 bp After Masking: 11407248 bp Masked: 62.02 % -- Input Database Coverage: 40094647 bp out of 2645636310 bp ( 1.52 % ) Sampling Time: 00:28:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 361675 Comparison Time: 00:19:47 (hh:mm:ss) Elapsed Time, 32899 HSPs Collected Number of families returned by RECON: 3285 Round Time: 00:49:07 (hh:mm:ss) Elapsed Time : 89 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:26:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 112690 repeats masked totaling 29664209 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90054889 bp Num Contigs Represented = 522 Non ambiguous bp: Initial: 90002943 bp After Masking: 33045059 bp Masked: 63.28 % -- Input Database Coverage: 130149536 bp out of 2645636310 bp ( 4.92 % ) Sampling Time: 01:31:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3146286 Comparison Time: 01:41:06 (hh:mm:ss) Elapsed Time, 215876 HSPs Collected Number of families returned by RECON: 9349 Round Time: 03:18:30 (hh:mm:ss) Elapsed Time : 430 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 04:52:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 389535 repeats masked totaling 102156162 bp(s). - TE Masking time 00:06:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270199751 bp Num Contigs Represented = 1521 Non ambiguous bp: Initial: 270026021 bp After Masking: 85832586 bp Masked: 68.21 % -- Input Database Coverage: 400349287 bp out of 2645636310 bp ( 15.13 % ) Sampling Time: 05:09:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 28731990 Comparison Time: 10:24:48 (hh:mm:ss) Elapsed Time, 540530 HSPs Collected Number of families returned by RECON: 29904 Round Time: 16:00:24 (hh:mm:ss) Elapsed Time : 876 families discovered. RepeatScout/RECON discovery complete: 2204 families found Classification Time: 01:14:36 (hh:mm:ss) Elapsed Time Program Time: 21:59:01 (hh:mm:ss) Elapsed Time