RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ss3lAh/RM_59016.WedJan41627412023 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: 1672878461 Database = /dev/shm/rModeler.ss3lAh/GCF_019393635.1_mDroGli1.pri - Sequences = 17 - Bases = 3303199800 Storage Throughput = excellent ( 1319.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039920 bp ( 40039520 non ambiguous ) - Num Contigs Represented = 7 - Sequence extraction : 00:17:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:43 (hh:mm:ss) Elapsed Time Round Time: 00:45:40 (hh:mm:ss) Elapsed Time : 343 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26197 repeats masked totaling 3966133 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039920 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 10039820 bp After Masking: 5957595 bp Masked: 40.66 % -- Input Database Coverage: 10039920 bp out of 3303199800 bp ( 0.30 % ) Sampling Time: 00:05:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:08 (hh:mm:ss) Elapsed Time, 21730 HSPs Collected Number of families returned by RECON: 1184 Round Time: 00:13:22 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:11:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 88168 repeats masked totaling 13604185 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039920 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 30039620 bp After Masking: 16051176 bp Masked: 46.57 % -- Input Database Coverage: 40079840 bp out of 3303199800 bp ( 1.21 % ) Sampling Time: 00:13:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:30:07 (hh:mm:ss) Elapsed Time, 22522 HSPs Collected Number of families returned by RECON: 2804 Round Time: 00:44:53 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:34:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 279220 repeats masked totaling 43812933 bp(s). - TE Masking time 00:02:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90079920 bp Num Contigs Represented = 8 Non ambiguous bp: Initial: 90039023 bp After Masking: 45081464 bp Masked: 49.93 % -- Input Database Coverage: 130159760 bp out of 3303199800 bp ( 3.94 % ) Sampling Time: 00:41:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:52:03 (hh:mm:ss) Elapsed Time, 86069 HSPs Collected Number of families returned by RECON: 9660 Round Time: 03:38:48 (hh:mm:ss) Elapsed Time : 199 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:51:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 888885 repeats masked totaling 138258311 bp(s). - TE Masking time 00:08:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270439920 bp Num Contigs Represented = 7 Non ambiguous bp: Initial: 270024495 bp After Masking: 128374387 bp Masked: 52.46 % -- Input Database Coverage: 400599680 bp out of 3303199800 bp ( 12.13 % ) Sampling Time: 02:13:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22852180 Comparison Time: 17:42:15 (hh:mm:ss) Elapsed Time, 243495 HSPs Collected Number of families returned by RECON: 35212 Round Time: 20:35:45 (hh:mm:ss) Elapsed Time : 514 families discovered. RepeatScout/RECON discovery complete: 1160 families found Classification Time: 00:40:33 (hh:mm:ss) Elapsed Time Program Time: 26:39:01 (hh:mm:ss) Elapsed Time