RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.a62l4u/RM_36652.WedDec282239112022 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: 1672295950 Database = /dev/shm/rModeler.a62l4u/GCF_009769545.1_fCycLum1.pri - Sequences = 48 - Bases = 572885595 Storage Throughput = excellent ( 1242.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40718948 bp ( 40031879 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:21 (hh:mm:ss) Elapsed Time Round Time: 00:20:12 (hh:mm:ss) Elapsed Time : 269 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 00:02:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3618 repeats masked totaling 650599 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10121585 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10030027 bp After Masking: 8431266 bp Masked: 15.94 % -- Input Database Coverage: 10121585 bp out of 572885595 bp ( 1.77 % ) Sampling Time: 00:02:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:55 (hh:mm:ss) Elapsed Time, 6465 HSPs Collected Number of families returned by RECON: 1298 Round Time: 00:08:33 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12812 repeats masked totaling 2314284 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30597283 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30001772 bp After Masking: 24784994 bp Masked: 17.39 % -- Input Database Coverage: 40718868 bp out of 572885595 bp ( 7.11 % ) Sampling Time: 00:08:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:30:30 (hh:mm:ss) Elapsed Time, 39661 HSPs Collected Number of families returned by RECON: 5214 Round Time: 00:39:55 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49176 repeats masked totaling 8459416 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91774230 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90031336 bp After Masking: 72029560 bp Masked: 20.00 % -- Input Database Coverage: 132493098 bp out of 572885595 bp ( 23.13 % ) Sampling Time: 00:23:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2639253 Comparison Time: 03:29:44 (hh:mm:ss) Elapsed Time, 219147 HSPs Collected Number of families returned by RECON: 18960 Round Time: 04:05:16 (hh:mm:ss) Elapsed Time : 332 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:10:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 196491 repeats masked totaling 34401317 bp(s). - TE Masking time 00:06:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 275257452 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 270005400 bp After Masking: 207409779 bp Masked: 23.18 % -- Input Database Coverage: 407750550 bp out of 572885595 bp ( 71.17 % ) Sampling Time: 01:20:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23787753 Comparison Time: 27:13:42 (hh:mm:ss) Elapsed Time, 799190 HSPs Collected Number of families returned by RECON: 73408 Round Time: 30:03:09 (hh:mm:ss) Elapsed Time : 915 families discovered. RepeatScout/RECON discovery complete: 1614 families found Classification Time: 01:07:23 (hh:mm:ss) Elapsed Time Program Time: 36:24:28 (hh:mm:ss) Elapsed Time