RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wckWec/RM_99888.ThuJan50853022023 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: 1672937581 Database = /dev/shm/rModeler.wckWec/GCF_009829145.1_bChiLan1.pri - Sequences = 93 - Bases = 1089631598 Storage Throughput = excellent ( 1051.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40212149 bp ( 40006603 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:17 (hh:mm:ss) Elapsed Time Round Time: 00:21:46 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2162 repeats masked totaling 626596 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10068031 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10027184 bp After Masking: 9316902 bp Masked: 7.08 % -- Input Database Coverage: 10068031 bp out of 1089631598 bp ( 0.92 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:43 (hh:mm:ss) Elapsed Time, 713 HSPs Collected Number of families returned by RECON: 294 Round Time: 00:07:44 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6532 repeats masked totaling 1934368 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30183962 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 30019263 bp After Masking: 27741830 bp Masked: 7.59 % -- Input Database Coverage: 40251993 bp out of 1089631598 bp ( 3.69 % ) Sampling Time: 00:02:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:35:43 (hh:mm:ss) Elapsed Time, 4876 HSPs Collected Number of families returned by RECON: 1573 Round Time: 00:39:13 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20839 repeats masked totaling 6072550 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90339715 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90029062 bp After Masking: 82905752 bp Masked: 7.91 % -- Input Database Coverage: 130591708 bp out of 1089631598 bp ( 11.98 % ) Sampling Time: 00:09:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 04:15:17 (hh:mm:ss) Elapsed Time, 49516 HSPs Collected Number of families returned by RECON: 9713 Round Time: 04:27:40 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71860 repeats masked totaling 20879688 bp(s). - TE Masking time 00:02:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270597398 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270006480 bp After Masking: 246539837 bp Masked: 8.69 % -- Input Database Coverage: 401189106 bp out of 1089631598 bp ( 36.82 % ) Sampling Time: 00:26:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 33:05:23 (hh:mm:ss) Elapsed Time, 193450 HSPs Collected Number of families returned by RECON: 67863 Round Time: 34:22:06 (hh:mm:ss) Elapsed Time : 229 families discovered. RepeatScout/RECON discovery complete: 385 families found Classification Time: 00:25:21 (hh:mm:ss) Elapsed Time Program Time: 40:23:50 (hh:mm:ss) Elapsed Time