RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.R8xxav/RM_62651.SunJan10152082023 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: 1672566728 Database = /dev/shm/rModeler.R8xxav/GCF_914725855.1_fThuAlb1.1 - Sequences = 68 - Bases = 792101331 Storage Throughput = excellent ( 1342.51 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027316 bp ( 40026716 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:38 (hh:mm:ss) Elapsed Time Round Time: 00:22:39 (hh:mm:ss) Elapsed Time : 584 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9401 repeats masked totaling 1406069 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004922 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10004522 bp After Masking: 8345296 bp Masked: 16.58 % -- Input Database Coverage: 10004922 bp out of 792101331 bp ( 1.26 % ) Sampling Time: 00:01:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 7481 HSPs Collected Number of families returned by RECON: 1778 Round Time: 00:07:42 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:35 (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... 30125 repeats masked totaling 4392778 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022314 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30022114 bp After Masking: 24956483 bp Masked: 16.87 % -- Input Database Coverage: 40027236 bp out of 792101331 bp ( 5.05 % ) Sampling Time: 00:03:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:32:18 (hh:mm:ss) Elapsed Time, 61430 HSPs Collected Number of families returned by RECON: 6578 Round Time: 00:37:53 (hh:mm:ss) Elapsed Time : 137 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100460 repeats masked totaling 15369310 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041347 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90037747 bp After Masking: 72601038 bp Masked: 19.37 % -- Input Database Coverage: 130068583 bp out of 792101331 bp ( 16.42 % ) Sampling Time: 00:09:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:26:23 (hh:mm:ss) Elapsed Time, 342598 HSPs Collected Number of families returned by RECON: 21821 Round Time: 03:53:59 (hh:mm:ss) Elapsed Time : 617 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 392760 repeats masked totaling 64100602 bp(s). - TE Masking time 00:11:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028690 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 270020890 bp After Masking: 199125060 bp Masked: 26.26 % -- Input Database Coverage: 400097273 bp out of 792101331 bp ( 50.51 % ) Sampling Time: 00:39:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 26:50:59 (hh:mm:ss) Elapsed Time, 1139605 HSPs Collected Number of families returned by RECON: 75953 Round Time: 29:33:45 (hh:mm:ss) Elapsed Time : 1480 families discovered. RepeatScout/RECON discovery complete: 2831 families found Classification Time: 02:08:04 (hh:mm:ss) Elapsed Time Program Time: 36:44:02 (hh:mm:ss) Elapsed Time