RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BiPSMg/RM_131783.ThuJan120825142023 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: 1673540714 Database = /dev/shm/rModeler.BiPSMg/GCF_902655055.1_mLutLut1.2 - Sequences = 44 - Bases = 2438458878 Storage Throughput = excellent ( 1313.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043237 bp ( 40039737 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:03:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:47 (hh:mm:ss) Elapsed Time Round Time: 00:32:47 (hh:mm:ss) Elapsed Time : 159 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9750 repeats masked totaling 2346710 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000657 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10000157 bp After Masking: 7596544 bp Masked: 24.04 % -- Input Database Coverage: 10000657 bp out of 2438458878 bp ( 0.41 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:40 (hh:mm:ss) Elapsed Time, 5986 HSPs Collected Number of families returned by RECON: 893 Round Time: 00:08:20 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33585 repeats masked totaling 8097346 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30042579 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30039579 bp After Masking: 21796221 bp Masked: 27.44 % -- Input Database Coverage: 40043236 bp out of 2438458878 bp ( 1.64 % ) Sampling Time: 00:03:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:29:33 (hh:mm:ss) Elapsed Time, 24755 HSPs Collected Number of families returned by RECON: 2539 Round Time: 00:34:31 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109316 repeats masked totaling 26115411 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90005118 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90000585 bp After Masking: 63371511 bp Masked: 29.59 % -- Input Database Coverage: 130048354 bp out of 2438458878 bp ( 5.33 % ) Sampling Time: 00:11:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2530125 Comparison Time: 02:57:03 (hh:mm:ss) Elapsed Time, 73012 HSPs Collected Number of families returned by RECON: 9972 Round Time: 03:13:01 (hh:mm:ss) Elapsed Time : 155 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:27:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 383982 repeats masked totaling 86666207 bp(s). - TE Masking time 00:04:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022616 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 270012286 bp After Masking: 181958352 bp Masked: 32.61 % -- Input Database Coverage: 400070970 bp out of 2438458878 bp ( 16.41 % ) Sampling Time: 00:43:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 25:04:57 (hh:mm:ss) Elapsed Time, 201593 HSPs Collected Number of families returned by RECON: 40486 Round Time: 26:19:21 (hh:mm:ss) Elapsed Time : 350 families discovered. RepeatScout/RECON discovery complete: 739 families found Classification Time: 00:25:41 (hh:mm:ss) Elapsed Time Program Time: 31:13:41 (hh:mm:ss) Elapsed Time