RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.RbYmld/RM_143293.ThuJan121041262023 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: 1673548885 Database = /dev/shm/rModeler.RbYmld/GCF_009762305.2_mZalCal1.pri.v2 - Sequences = 47 - Bases = 2409685272 Storage Throughput = excellent ( 1293.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40361120 bp ( 40008733 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:03:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:26 (hh:mm:ss) Elapsed Time Round Time: 00:32:03 (hh:mm:ss) Elapsed Time : 167 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:56 (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... 9205 repeats masked totaling 2379181 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040216 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10025991 bp After Masking: 7588227 bp Masked: 24.31 % -- Input Database Coverage: 10040216 bp out of 2409685272 bp ( 0.42 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:28 (hh:mm:ss) Elapsed Time, 5923 HSPs Collected Number of families returned by RECON: 985 Round Time: 00:08:21 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31038 repeats masked totaling 7846001 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30360904 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 30022742 bp After Masking: 21968010 bp Masked: 26.83 % -- Input Database Coverage: 40401120 bp out of 2409685272 bp ( 1.68 % ) Sampling Time: 00:03:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:29:21 (hh:mm:ss) Elapsed Time, 27973 HSPs Collected Number of families returned by RECON: 2551 Round Time: 00:34:28 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 106488 repeats masked totaling 27531864 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90569626 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 90000523 bp After Masking: 61934020 bp Masked: 31.18 % -- Input Database Coverage: 130970746 bp out of 2409685272 bp ( 5.44 % ) Sampling Time: 00:13:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 03:06:31 (hh:mm:ss) Elapsed Time, 73404 HSPs Collected Number of families returned by RECON: 9134 Round Time: 03:25:16 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:29:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 361852 repeats masked totaling 89985802 bp(s). - TE Masking time 00:05:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272226084 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270020962 bp After Masking: 178414847 bp Masked: 33.93 % -- Input Database Coverage: 403196830 bp out of 2409685272 bp ( 16.73 % ) Sampling Time: 00:47:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 24:04:16 (hh:mm:ss) Elapsed Time, 190503 HSPs Collected Number of families returned by RECON: 37621 Round Time: 25:14:08 (hh:mm:ss) Elapsed Time : 364 families discovered. RepeatScout/RECON discovery complete: 790 families found Classification Time: 00:25:40 (hh:mm:ss) Elapsed Time Program Time: 30:19:56 (hh:mm:ss) Elapsed Time