RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VjQ9bm/RM_2622967.TueJul91935152024 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: 1720578914 Database = /dev/shm/rModeler.VjQ9bm/GCF_030014155.1_HZAU_Pvac_v1 - Sequences = 78 - Bases = 692121426 Storage Throughput = excellent ( 1188.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40046358 bp ( 40037695 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:35 (hh:mm:ss) Elapsed Time Round Time: 00:23:07 (hh:mm:ss) Elapsed Time : 448 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8332 repeats masked totaling 1712454 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005054 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10003554 bp After Masking: 7465960 bp Masked: 25.37 % -- Input Database Coverage: 10005054 bp out of 692121426 bp ( 1.45 % ) Sampling Time: 00:02:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:00 (hh:mm:ss) Elapsed Time, 6504 HSPs Collected Number of families returned by RECON: 1201 Round Time: 00:08:53 (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 : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27517 repeats masked totaling 5459169 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041295 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30034132 bp After Masking: 21890962 bp Masked: 27.11 % -- Input Database Coverage: 40046349 bp out of 692121426 bp ( 5.79 % ) Sampling Time: 00:08:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:30:01 (hh:mm:ss) Elapsed Time, 34357 HSPs Collected Number of families returned by RECON: 4271 Round Time: 00:39:13 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 87250 repeats masked totaling 16766771 bp(s). - TE Masking time 00:01:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041162 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90021444 bp After Masking: 65335495 bp Masked: 27.42 % -- Input Database Coverage: 130087511 bp out of 692121426 bp ( 18.80 % ) Sampling Time: 00:25:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 03:27:03 (hh:mm:ss) Elapsed Time, 172099 HSPs Collected Number of families returned by RECON: 16202 Round Time: 04:03:00 (hh:mm:ss) Elapsed Time : 352 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 323469 repeats masked totaling 61619997 bp(s). - TE Masking time 00:08:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270067591 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 270010533 bp After Masking: 185202303 bp Masked: 31.41 % -- Input Database Coverage: 400155102 bp out of 692121426 bp ( 57.82 % ) Sampling Time: 01:13:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 24:45:20 (hh:mm:ss) Elapsed Time, 665798 HSPs Collected Number of families returned by RECON: 58520 Round Time: 27:08:17 (hh:mm:ss) Elapsed Time : 962 families discovered. RepeatScout/RECON discovery complete: 1841 families found Classification Time: 01:30:25 (hh:mm:ss) Elapsed Time Program Time: 33:52:55 (hh:mm:ss) Elapsed Time