RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VP1AtP/RM_3954935.SunMar102239032024 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: 1710135543 Database = /dev/shm/rModeler.VP1AtP/GCA_027563665.1_DD_ASM_mAP_20210503 - Sequences = 93 - Bases = 2126460045 Storage Throughput = excellent ( 1194.95 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40126268 bp ( 40022535 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:02:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:22 (hh:mm:ss) Elapsed Time Round Time: 00:23:41 (hh:mm:ss) Elapsed Time : 345 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14544 repeats masked totaling 3227597 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10057422 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10031454 bp After Masking: 6552597 bp Masked: 34.68 % -- Input Database Coverage: 10057422 bp out of 2126460045 bp ( 0.47 % ) Sampling Time: 00:02:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:08:29 (hh:mm:ss) Elapsed Time, 3891 HSPs Collected Number of families returned by RECON: 698 Round Time: 00:10:59 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43539 repeats masked totaling 9627331 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30108923 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30031158 bp After Masking: 19829525 bp Masked: 33.97 % -- Input Database Coverage: 40166345 bp out of 2126460045 bp ( 1.89 % ) Sampling Time: 00:04:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:25:03 (hh:mm:ss) Elapsed Time, 23564 HSPs Collected Number of families returned by RECON: 2433 Round Time: 00:30:37 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136907 repeats masked totaling 31021033 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90273021 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 90003341 bp After Masking: 56930836 bp Masked: 36.75 % -- Input Database Coverage: 130439366 bp out of 2126460045 bp ( 6.13 % ) Sampling Time: 00:14:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2548153 Comparison Time: 02:41:34 (hh:mm:ss) Elapsed Time, 122692 HSPs Collected Number of families returned by RECON: 8588 Round Time: 03:01:29 (hh:mm:ss) Elapsed Time : 222 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 459360 repeats masked totaling 102590733 bp(s). - TE Masking time 00:07:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270911604 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 270037514 bp After Masking: 161338458 bp Masked: 40.25 % -- Input Database Coverage: 401350970 bp out of 2126460045 bp ( 18.87 % ) Sampling Time: 00:51:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22994371 Comparison Time: 20:35:18 (hh:mm:ss) Elapsed Time, 281609 HSPs Collected Number of families returned by RECON: 31080 Round Time: 21:44:49 (hh:mm:ss) Elapsed Time : 440 families discovered. RepeatScout/RECON discovery complete: 1069 families found Classification Time: 00:37:48 (hh:mm:ss) Elapsed Time Program Time: 26:29:23 (hh:mm:ss) Elapsed Time