RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bUPpqX/RM_134760.SunJan10033332023 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: 1672562012 Database = /dev/shm/rModeler.bUPpqX/GCF_900964775.1_fSclFor1.1 - Sequences = 72 - Bases = 784563014 Storage Throughput = excellent ( 1133.39 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017040 bp ( 40015837 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:17 (hh:mm:ss) Elapsed Time Round Time: 00:20:22 (hh:mm:ss) Elapsed Time : 286 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11084 repeats masked totaling 1955311 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008069 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10007556 bp After Masking: 7927575 bp Masked: 20.78 % -- Input Database Coverage: 10008069 bp out of 784563014 bp ( 1.28 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:44 (hh:mm:ss) Elapsed Time, 3910 HSPs Collected Number of families returned by RECON: 709 Round Time: 00:06:37 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35507 repeats masked totaling 6167036 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008959 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30008269 bp After Masking: 23519284 bp Masked: 21.62 % -- Input Database Coverage: 40017028 bp out of 784563014 bp ( 5.10 % ) Sampling Time: 00:01:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:28:18 (hh:mm:ss) Elapsed Time, 27590 HSPs Collected Number of families returned by RECON: 2773 Round Time: 00:30:57 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 111993 repeats masked totaling 19801389 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039569 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90035572 bp After Masking: 69274935 bp Masked: 23.06 % -- Input Database Coverage: 130056597 bp out of 784563014 bp ( 16.58 % ) Sampling Time: 00:05:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 03:01:08 (hh:mm:ss) Elapsed Time, 97750 HSPs Collected Number of families returned by RECON: 10260 Round Time: 03:10:39 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 382929 repeats masked totaling 66194456 bp(s). - TE Masking time 00:05:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270027624 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 270003157 bp After Masking: 200637298 bp Masked: 25.69 % -- Input Database Coverage: 400084221 bp out of 784563014 bp ( 50.99 % ) Sampling Time: 00:18:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22872466 Comparison Time: 25:09:22 (hh:mm:ss) Elapsed Time, 348631 HSPs Collected Number of families returned by RECON: 47610 Round Time: 26:17:42 (hh:mm:ss) Elapsed Time : 505 families discovered. RepeatScout/RECON discovery complete: 1078 families found Classification Time: 00:55:52 (hh:mm:ss) Elapsed Time Program Time: 31:22:09 (hh:mm:ss) Elapsed Time