RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.XoYyvD/RM_93460.SunMar102332282024 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: 1710138747 Database = /dev/shm/rModeler.XoYyvD/GCA_030820635.1_KIZ_Lrid_1.0 - Sequences = 297 - Bases = 1243762172 - N50 = 128275377 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 203262020-217777156 | [ 1 ] 188746884-203262019 | [ ] 174231748-188746883 | [ ] 159716613-174231748 | [ 1 ] 145201477-159716612 | [ ] 130686341-145201476 | [ ] 116171205-130686340 | [ 1 ] 101656070-116171205 | [ ] 87140934-101656069 | [ 1 ] 72625798-87140933 | [ 2 ] 58110662-72625797 | [ 1 ] 43595527-58110662 | [ 3 ] 29080391-43595526 | [ ] 14565255-29080390 | [ 5 ] 50120-14565255 |************************************************** [ 282 ] Storage Throughput = excellent ( 1095.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009688 bp ( 40009188 non ambiguous ) - Num Contigs Represented = 72 - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:14 (hh:mm:ss) Elapsed Time Round Time: 00:27:29 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3180 repeats masked totaling 820366 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022007 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10021907 bp After Masking: 9024314 bp Masked: 9.95 % -- Input Database Coverage: 10022007 bp out of 1243762172 bp ( 0.81 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:51 (hh:mm:ss) Elapsed Time, 52939 HSPs Collected Number of families returned by RECON: 244 Round Time: 00:08:21 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9959 repeats masked totaling 2513475 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027524 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30027124 bp After Masking: 26797503 bp Masked: 10.76 % -- Input Database Coverage: 40049531 bp out of 1243762172 bp ( 3.22 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:30:41 (hh:mm:ss) Elapsed Time, 6311 HSPs Collected Number of families returned by RECON: 1285 Round Time: 00:34:35 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27526 repeats masked totaling 7085378 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012536 bp Num Contigs Represented = 113 Non ambiguous bp: Initial: 90011536 bp After Masking: 80731359 bp Masked: 10.31 % -- Input Database Coverage: 130062067 bp out of 1243762172 bp ( 10.46 % ) Sampling Time: 00:09:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 03:46:03 (hh:mm:ss) Elapsed Time, 58780 HSPs Collected Number of families returned by RECON: 7795 Round Time: 03:57:56 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86298 repeats masked totaling 23827708 bp(s). - TE Masking time 00:02:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034872 bp Num Contigs Represented = 172 Non ambiguous bp: Initial: 270031672 bp After Masking: 240788321 bp Masked: 10.83 % -- Input Database Coverage: 400096939 bp out of 1243762172 bp ( 32.17 % ) Sampling Time: 00:32:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 32:10:57 (hh:mm:ss) Elapsed Time, 516188 HSPs Collected Number of families returned by RECON: 51335 Round Time: 33:17:42 (hh:mm:ss) Elapsed Time : 241 families discovered. RepeatScout/RECON discovery complete: 355 families found Classification Time: 00:28:57 (hh:mm:ss) Elapsed Time Program Time: 38:55:00 (hh:mm:ss) Elapsed Time