RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tPP4lV/RM_159747.SatJan142129092023 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: 1673760549 Database = /dev/shm/rModeler.tPP4lV/GCA_936440315.1_fBarBab1.1 - Sequences = 92 - Bases = 1584929904 Storage Throughput = excellent ( 1367.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001800 bp ( 40001000 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:01 (hh:mm:ss) Elapsed Time Round Time: 00:24:18 (hh:mm:ss) Elapsed Time : 853 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13941 repeats masked totaling 3040148 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002535 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10002335 bp After Masking: 6775201 bp Masked: 32.26 % -- Input Database Coverage: 10002535 bp out of 1584929904 bp ( 0.63 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:10 (hh:mm:ss) Elapsed Time, 8915 HSPs Collected Number of families returned by RECON: 1630 Round Time: 00:07:29 (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 : 00:00:26 (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... 42957 repeats masked totaling 9112938 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30039265 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 30038665 bp After Masking: 20013576 bp Masked: 33.37 % -- Input Database Coverage: 40041800 bp out of 1584929904 bp ( 2.53 % ) Sampling Time: 00:03:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:48 (hh:mm:ss) Elapsed Time, 54336 HSPs Collected Number of families returned by RECON: 5534 Round Time: 00:33:44 (hh:mm:ss) Elapsed Time : 124 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 138721 repeats masked totaling 28112805 bp(s). - TE Masking time 00:02:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038755 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 90037555 bp After Masking: 59452929 bp Masked: 33.97 % -- Input Database Coverage: 130080555 bp out of 1584929904 bp ( 8.21 % ) Sampling Time: 00:10:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:11:11 (hh:mm:ss) Elapsed Time, 371395 HSPs Collected Number of families returned by RECON: 17046 Round Time: 03:35:24 (hh:mm:ss) Elapsed Time : 622 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 501634 repeats masked totaling 103107086 bp(s). - TE Masking time 00:15:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023952 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 270019752 bp After Masking: 158858698 bp Masked: 41.17 % -- Input Database Coverage: 400104507 bp out of 1584929904 bp ( 25.24 % ) Sampling Time: 00:41:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 22:26:17 (hh:mm:ss) Elapsed Time, 995391 HSPs Collected Number of families returned by RECON: 54140 Round Time: 25:01:37 (hh:mm:ss) Elapsed Time : 1299 families discovered. RepeatScout/RECON discovery complete: 2917 families found Classification Time: 02:24:05 (hh:mm:ss) Elapsed Time Program Time: 32:06:37 (hh:mm:ss) Elapsed Time