RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7VBDj4/RM_773479.SatJul192053192025 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: 1752983598 Database = /dev/shm/rModeler.7VBDj4/GCA_048593335.1_ASM4859333v1 - Sequences = 8 - Bases = 3349423305 Storage Throughput = excellent ( 1121.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40000074 bp ( 40000074 non ambiguous ) - Num Contigs Represented = 8 - Sequence extraction : 00:10:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:31 (hh:mm:ss) Elapsed Time Round Time: 00:40:48 (hh:mm:ss) Elapsed Time : 319 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21107 repeats masked totaling 3860759 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000039 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 10000039 bp After Masking: 6036088 bp Masked: 39.64 % -- Input Database Coverage: 10000039 bp out of 3349423305 bp ( 0.30 % ) Sampling Time: 00:03:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:45 (hh:mm:ss) Elapsed Time, 13689 HSPs Collected Number of families returned by RECON: 1272 Round Time: 00:08:29 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:07:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67217 repeats masked totaling 13049250 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000034 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 30000034 bp After Masking: 16537436 bp Masked: 44.88 % -- Input Database Coverage: 40000073 bp out of 3349423305 bp ( 1.19 % ) Sampling Time: 00:10:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:24:05 (hh:mm:ss) Elapsed Time, 30061 HSPs Collected Number of families returned by RECON: 3146 Round Time: 00:35:47 (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 : 00:22:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 212833 repeats masked totaling 42438778 bp(s). - TE Masking time 00:02:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90000383 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 90000383 bp After Masking: 46540811 bp Masked: 48.29 % -- Input Database Coverage: 130000456 bp out of 3349423305 bp ( 3.88 % ) Sampling Time: 00:27:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 02:43:25 (hh:mm:ss) Elapsed Time, 97168 HSPs Collected Number of families returned by RECON: 9791 Round Time: 03:15:51 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:06:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 700309 repeats masked totaling 134654933 bp(s). - TE Masking time 00:08:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270001100 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 270001085 bp After Masking: 132118301 bp Masked: 51.07 % -- Input Database Coverage: 400001556 bp out of 3349423305 bp ( 11.94 % ) Sampling Time: 01:28:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22777875 Comparison Time: 20:30:02 (hh:mm:ss) Elapsed Time, 230955 HSPs Collected Number of families returned by RECON: 36057 Round Time: 22:34:49 (hh:mm:ss) Elapsed Time : 463 families discovered. RepeatScout/RECON discovery complete: 1080 families found Classification Time: 00:34:55 (hh:mm:ss) Elapsed Time Program Time: 27:50:39 (hh:mm:ss) Elapsed Time