RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TOCvAD/RM_15835.TueJan100457002023 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: 1673355420 Database = /dev/shm/rModeler.TOCvAD/GCF_015220715.1_fPygNat1.pri - Sequences = 55 - Bases = 1222050449 Storage Throughput = excellent ( 1048.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40289610 bp ( 40026700 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:32 (hh:mm:ss) Elapsed Time Round Time: 00:26:23 (hh:mm:ss) Elapsed Time : 561 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16567 repeats masked totaling 2673882 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10027371 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10007235 bp After Masking: 6467561 bp Masked: 35.37 % -- Input Database Coverage: 10027371 bp out of 1222050449 bp ( 0.82 % ) Sampling Time: 00:02:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:35 (hh:mm:ss) Elapsed Time, 13230 HSPs Collected Number of families returned by RECON: 1780 Round Time: 00:10:06 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53965 repeats masked totaling 8911890 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30262223 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30019449 bp After Masking: 18855496 bp Masked: 37.19 % -- Input Database Coverage: 40289594 bp out of 1222050449 bp ( 3.30 % ) Sampling Time: 00:06:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:31:07 (hh:mm:ss) Elapsed Time, 72141 HSPs Collected Number of families returned by RECON: 5622 Round Time: 00:40:58 (hh:mm:ss) Elapsed Time : 182 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 184857 repeats masked totaling 30469440 bp(s). - TE Masking time 00:02:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90693264 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 90004110 bp After Masking: 52830851 bp Masked: 41.30 % -- Input Database Coverage: 130982858 bp out of 1222050449 bp ( 10.72 % ) Sampling Time: 00:20:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 03:13:55 (hh:mm:ss) Elapsed Time, 301534 HSPs Collected Number of families returned by RECON: 15740 Round Time: 03:50:30 (hh:mm:ss) Elapsed Time : 535 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 647785 repeats masked totaling 108026756 bp(s). - TE Masking time 00:11:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272490709 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 270034695 bp After Masking: 142672533 bp Masked: 47.17 % -- Input Database Coverage: 403473567 bp out of 1222050449 bp ( 33.02 % ) Sampling Time: 01:04:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23259610 Comparison Time: 22:43:38 (hh:mm:ss) Elapsed Time, 657307 HSPs Collected Number of families returned by RECON: 45874 Round Time: 25:07:54 (hh:mm:ss) Elapsed Time : 1125 families discovered. RepeatScout/RECON discovery complete: 2443 families found Classification Time: 01:38:59 (hh:mm:ss) Elapsed Time Program Time: 31:54:50 (hh:mm:ss) Elapsed Time