RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.MnVdM3/RM_3536107.MonJun241444042024 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: 1719265444 Database = /dev/shm/rModeler.MnVdM3/GCF_963692335.1_fOsmEpe2.1 - Sequences = 1007 - Bases = 508721272 - N50 = 18663607 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 25582896-27410175 | [ 1 ] 23755618-25582896 | [ 3 ] 21928340-23755618 | [ 3 ] 20101061-21928339 | [ 1 ] 18273783-20101061 | [ 6 ] 16446505-18273783 | [ 1 ] 14619226-16446504 | [ 4 ] 12791948-14619226 | [ 3 ] 10964670-12791948 | [ 2 ] 9137391-10964669 | [ 3 ] 7310113-9137391 | [ 1 ] 5482835-7310113 | [ ] 3655556-5482834 | [ ] 1828278-3655556 | [ ] 1000-1828278 |************************************************** [ 979 ] Storage Throughput = excellent ( 1301.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40053637 bp ( 40006837 non ambiguous ) - Num Contigs Represented = 122 - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:15 (hh:mm:ss) Elapsed Time Round Time: 00:21:09 (hh:mm:ss) Elapsed Time : 416 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6185 repeats masked totaling 1706985 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014848 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10004848 bp After Masking: 7363115 bp Masked: 26.40 % -- Input Database Coverage: 10014848 bp out of 508721272 bp ( 1.97 % ) Sampling Time: 00:01:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34453 Comparison Time: 00:06:40 (hh:mm:ss) Elapsed Time, 12924 HSPs Collected Number of families returned by RECON: 1177 Round Time: 00:08:53 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17343 repeats masked totaling 4937918 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038709 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 30001909 bp After Masking: 21932580 bp Masked: 26.90 % -- Input Database Coverage: 40053557 bp out of 508721272 bp ( 7.87 % ) Sampling Time: 00:05:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 311655 Comparison Time: 00:32:24 (hh:mm:ss) Elapsed Time, 50207 HSPs Collected Number of families returned by RECON: 5347 Round Time: 00:39:41 (hh:mm:ss) Elapsed Time : 47 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58417 repeats masked totaling 15362181 bp(s). - TE Masking time 00:01:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90118584 bp Num Contigs Represented = 207 Non ambiguous bp: Initial: 90032064 bp After Masking: 65808454 bp Masked: 26.91 % -- Input Database Coverage: 130172141 bp out of 508721272 bp ( 25.59 % ) Sampling Time: 00:14:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2767128 Comparison Time: 03:31:22 (hh:mm:ss) Elapsed Time, 302438 HSPs Collected Number of families returned by RECON: 19260 Round Time: 04:05:52 (hh:mm:ss) Elapsed Time : 290 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:39:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 215645 repeats masked totaling 55311107 bp(s). - TE Masking time 00:08:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270265926 bp Num Contigs Represented = 565 Non ambiguous bp: Initial: 270008224 bp After Masking: 187743208 bp Masked: 30.47 % -- Input Database Coverage: 400438067 bp out of 508721272 bp ( 78.71 % ) Sampling Time: 00:50:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24918270 Comparison Time: 26:54:21 (hh:mm:ss) Elapsed Time, 1391325 HSPs Collected Number of families returned by RECON: 77687 Round Time: 29:40:19 (hh:mm:ss) Elapsed Time : 806 families discovered. RepeatScout/RECON discovery complete: 1568 families found Classification Time: 01:43:31 (hh:mm:ss) Elapsed Time Program Time: 36:39:25 (hh:mm:ss) Elapsed Time