RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yT5wYe/RM_2539695.TueMay160904272023 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: 1684253066 Database = /dev/shm/rModeler.yT5wYe/GCF_027358585.1_fPanHyp1.pri - Sequences = 58 - Bases = 764974446 Storage Throughput = good ( 978.16 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40352824 bp ( 40033632 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:35 (hh:mm:ss) Elapsed Time Round Time: 00:22:47 (hh:mm:ss) Elapsed Time : 542 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13526 repeats masked totaling 1885486 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10145625 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 10027601 bp After Masking: 7505097 bp Masked: 25.16 % -- Input Database Coverage: 10145625 bp out of 764974446 bp ( 1.33 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:07:29 (hh:mm:ss) Elapsed Time, 20850 HSPs Collected Number of families returned by RECON: 1778 Round Time: 00:09:54 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43403 repeats masked totaling 6186245 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30207119 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30005951 bp After Masking: 21963677 bp Masked: 26.80 % -- Input Database Coverage: 40352744 bp out of 764974446 bp ( 5.28 % ) Sampling Time: 00:06:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:36:29 (hh:mm:ss) Elapsed Time, 83873 HSPs Collected Number of families returned by RECON: 6692 Round Time: 00:46:05 (hh:mm:ss) Elapsed Time : 166 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149271 repeats masked totaling 22132501 bp(s). - TE Masking time 00:01:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90573881 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90027113 bp After Masking: 62949936 bp Masked: 30.08 % -- Input Database Coverage: 130926625 bp out of 764974446 bp ( 17.12 % ) Sampling Time: 00:18:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 03:46:44 (hh:mm:ss) Elapsed Time, 309390 HSPs Collected Number of families returned by RECON: 20006 Round Time: 04:19:29 (hh:mm:ss) Elapsed Time : 485 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 529526 repeats masked totaling 81531043 bp(s). - TE Masking time 00:10:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271480509 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 270006122 bp After Masking: 174176209 bp Masked: 35.49 % -- Input Database Coverage: 402407134 bp out of 764974446 bp ( 52.60 % ) Sampling Time: 00:51:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23116600 Comparison Time: 27:40:53 (hh:mm:ss) Elapsed Time, 938332 HSPs Collected Number of families returned by RECON: 64954 Round Time: 30:06:59 (hh:mm:ss) Elapsed Time : 1186 families discovered. RepeatScout/RECON discovery complete: 2407 families found Classification Time: 01:42:09 (hh:mm:ss) Elapsed Time Program Time: 37:27:23 (hh:mm:ss) Elapsed Time