RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.bbeY7R/RM_3933098.SunFeb232316192025 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: 1740381377 Database = /dev/shm/rModeler.bbeY7R/GCA_965152195.1_rNatDep2.hap2 - Sequences = 61 - Bases = 2130756730 Storage Throughput = excellent ( 1700.91 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037027 bp ( 40036327 non ambiguous ) - Num Contigs Represented = 31 - Sequence extraction : 00:01:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:27 (hh:mm:ss) Elapsed Time Round Time: 00:11:16 (hh:mm:ss) Elapsed Time : 557 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13596 repeats masked totaling 2779164 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033914 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10033914 bp After Masking: 7186199 bp Masked: 28.38 % -- Input Database Coverage: 10033914 bp out of 2130756730 bp ( 0.47 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 17559 HSPs Collected Number of families returned by RECON: 1870 Round Time: 00:03:51 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44845 repeats masked totaling 8932740 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003033 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30002333 bp After Masking: 20847817 bp Masked: 30.51 % -- Input Database Coverage: 40036947 bp out of 2130756730 bp ( 1.88 % ) Sampling Time: 00:10:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:26 (hh:mm:ss) Elapsed Time, 95436 HSPs Collected Number of families returned by RECON: 5819 Round Time: 00:23:42 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155243 repeats masked totaling 31317189 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90010588 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 90009288 bp After Masking: 58244373 bp Masked: 35.29 % -- Input Database Coverage: 130047535 bp out of 2130756730 bp ( 6.10 % ) Sampling Time: 00:05:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 01:05:43 (hh:mm:ss) Elapsed Time, 263197 HSPs Collected Number of families returned by RECON: 14371 Round Time: 01:18:05 (hh:mm:ss) Elapsed Time : 463 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 536082 repeats masked totaling 111318069 bp(s). - TE Masking time 00:03:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028231 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 270022331 bp After Masking: 157251973 bp Masked: 41.76 % -- Input Database Coverage: 400075766 bp out of 2130756730 bp ( 18.78 % ) Sampling Time: 00:18:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22791376 Comparison Time: 07:06:43 (hh:mm:ss) Elapsed Time, 605492 HSPs Collected Number of families returned by RECON: 46103 Round Time: 07:55:23 (hh:mm:ss) Elapsed Time : 1040 families discovered. RepeatScout/RECON discovery complete: 2234 families found Classification Time: 00:43:19 (hh:mm:ss) Elapsed Time Program Time: 10:35:36 (hh:mm:ss) Elapsed Time