RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.pKVOlm/RM_8775.SunJul211823532024 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: 1721611430 Database = /dev/shm/rModeler.pKVOlm/GCF_018320785.1_ASM1832078v1 - Sequences = 46 - Bases = 1173472134 Storage Throughput = excellent ( 1080.54 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40024865 bp ( 40023665 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:28 (hh:mm:ss) Elapsed Time Round Time: 00:30:33 (hh:mm:ss) Elapsed Time : 875 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18409 repeats masked totaling 3183844 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022482 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10021782 bp After Masking: 6448660 bp Masked: 35.65 % -- Input Database Coverage: 10022482 bp out of 1173472134 bp ( 0.85 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:16:03 (hh:mm:ss) Elapsed Time, 18285 HSPs Collected Number of families returned by RECON: 1770 Round Time: 00:19:18 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56199 repeats masked totaling 9904616 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002303 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30001803 bp After Masking: 19045047 bp Masked: 36.52 % -- Input Database Coverage: 40024785 bp out of 1173472134 bp ( 3.41 % ) Sampling Time: 00:04:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:55:12 (hh:mm:ss) Elapsed Time, 74839 HSPs Collected Number of families returned by RECON: 5318 Round Time: 01:03:59 (hh:mm:ss) Elapsed Time : 201 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 193551 repeats masked totaling 33941201 bp(s). - TE Masking time 00:03:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018477 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 90016877 bp After Masking: 52634384 bp Masked: 41.53 % -- Input Database Coverage: 130043262 bp out of 1173472134 bp ( 11.08 % ) Sampling Time: 00:15:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 04:11:01 (hh:mm:ss) Elapsed Time, 273163 HSPs Collected Number of families returned by RECON: 13033 Round Time: 04:41:35 (hh:mm:ss) Elapsed Time : 583 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 660999 repeats masked totaling 115778831 bp(s). - TE Masking time 00:14:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023488 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 270016988 bp After Masking: 143993503 bp Masked: 46.67 % -- Input Database Coverage: 400066750 bp out of 1173472134 bp ( 34.09 % ) Sampling Time: 00:49:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 42:22:03 (hh:mm:ss) Elapsed Time, 538470 HSPs Collected Number of families returned by RECON: 40605 Round Time: 45:09:50 (hh:mm:ss) Elapsed Time : 1169 families discovered. RepeatScout/RECON discovery complete: 2848 families found Classification Time: 01:32:49 (hh:mm:ss) Elapsed Time Program Time: 53:18:04 (hh:mm:ss) Elapsed Time