RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.xoq3J3/RM_1203063.MonMay151958312023 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: 1684205910 Database = /dev/shm/rModeler.xoq3J3/GCF_027172205.1_rPodRaf1.pri - Sequences = 27 - Bases = 1513131503 Storage Throughput = good ( 979.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003422 bp ( 40003422 non ambiguous ) - Num Contigs Represented = 20 - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:33 (hh:mm:ss) Elapsed Time Round Time: 00:26:46 (hh:mm:ss) Elapsed Time : 554 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18565 repeats masked totaling 3278454 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000757 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10000757 bp After Masking: 6549627 bp Masked: 34.51 % -- Input Database Coverage: 10000757 bp out of 1513131503 bp ( 0.66 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:01 (hh:mm:ss) Elapsed Time, 10151 HSPs Collected Number of families returned by RECON: 1300 Round Time: 00:07:31 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55486 repeats masked totaling 9982115 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002658 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 30002658 bp After Masking: 18777691 bp Masked: 37.41 % -- Input Database Coverage: 40003415 bp out of 1513131503 bp ( 2.64 % ) Sampling Time: 00:03:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:28:22 (hh:mm:ss) Elapsed Time, 50540 HSPs Collected Number of families returned by RECON: 4181 Round Time: 00:33:43 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 183159 repeats masked totaling 32486201 bp(s). - TE Masking time 00:01:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027957 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 90027957 bp After Masking: 54812198 bp Masked: 39.12 % -- Input Database Coverage: 130031372 bp out of 1513131503 bp ( 8.59 % ) Sampling Time: 00:09:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:46:00 (hh:mm:ss) Elapsed Time, 257683 HSPs Collected Number of families returned by RECON: 13738 Round Time: 03:06:28 (hh:mm:ss) Elapsed Time : 423 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 609834 repeats masked totaling 107255764 bp(s). - TE Masking time 00:07:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270007404 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 270002448 bp After Masking: 154590651 bp Masked: 42.74 % -- Input Database Coverage: 400038776 bp out of 1513131503 bp ( 26.44 % ) Sampling Time: 00:32:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 19:13:02 (hh:mm:ss) Elapsed Time, 550908 HSPs Collected Number of families returned by RECON: 48115 Round Time: 20:56:16 (hh:mm:ss) Elapsed Time : 1090 families discovered. RepeatScout/RECON discovery complete: 2219 families found Classification Time: 01:15:24 (hh:mm:ss) Elapsed Time Program Time: 26:26:08 (hh:mm:ss) Elapsed Time