RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.zt7gSw/RM_4023879.TueApr221224572025 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: 1745349896 Database = /data/tmp/rModeler.zt7gSw/GCA_047301625.1_ASM4730162v1 - Sequences = 43 - Bases = 865958939 Storage Throughput = good ( 878.95 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031758 bp ( 40031558 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:03 (hh:mm:ss) Elapsed Time Round Time: 00:27:03 (hh:mm:ss) Elapsed Time : 472 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13859 repeats masked totaling 2053072 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10025883 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10025883 bp After Masking: 7417083 bp Masked: 26.02 % -- Input Database Coverage: 10025883 bp out of 865958939 bp ( 1.16 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:57 (hh:mm:ss) Elapsed Time, 22707 HSPs Collected Number of families returned by RECON: 1568 Round Time: 00:08:10 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46232 repeats masked totaling 6341471 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005795 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30005595 bp After Masking: 22502327 bp Masked: 25.01 % -- Input Database Coverage: 40031678 bp out of 865958939 bp ( 4.62 % ) Sampling Time: 00:03:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:28:25 (hh:mm:ss) Elapsed Time, 66683 HSPs Collected Number of families returned by RECON: 5361 Round Time: 00:38:00 (hh:mm:ss) Elapsed Time : 141 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 156130 repeats masked totaling 21905534 bp(s). - TE Masking time 00:01:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018053 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90017953 bp After Masking: 64656540 bp Masked: 28.17 % -- Input Database Coverage: 130049731 bp out of 865958939 bp ( 15.02 % ) Sampling Time: 00:11:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 03:19:21 (hh:mm:ss) Elapsed Time, 249195 HSPs Collected Number of families returned by RECON: 17011 Round Time: 05:23:30 (hh:mm:ss) Elapsed Time : 440 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 541703 repeats masked totaling 77908685 bp(s). - TE Masking time 00:07:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270009636 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 270009236 bp After Masking: 181410339 bp Masked: 32.81 % -- Input Database Coverage: 400059367 bp out of 865958939 bp ( 46.20 % ) Sampling Time: 00:28:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 22:42:03 (hh:mm:ss) Elapsed Time, 760401 HSPs Collected Number of families returned by RECON: 58782 Round Time: 27:04:39 (hh:mm:ss) Elapsed Time : 968 families discovered. RepeatScout/RECON discovery complete: 2043 families found Classification Time: 01:23:55 (hh:mm:ss) Elapsed Time Program Time: 35:05:17 (hh:mm:ss) Elapsed Time