RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QRf1YM/RM_30901.SunJul71411302024 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: 1720386688 Database = /dev/shm/rModeler.QRf1YM/GCF_022702325.1_ASM2270232v1 - Sequences = 21 - Bases = 51946279 Storage Throughput = excellent ( 1044.65 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40004091 bp ( 40004091 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:40 (hh:mm:ss) Elapsed Time Round Time: 01:24:11 (hh:mm:ss) Elapsed Time : 184 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4182 repeats masked totaling 2473342 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003216 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10003216 bp After Masking: 7217130 bp Masked: 27.85 % -- Input Database Coverage: 10003216 bp out of 51946279 bp ( 19.26 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:04 (hh:mm:ss) Elapsed Time, 36970 HSPs Collected Number of families returned by RECON: 488 Round Time: 00:48:17 (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 : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13297 repeats masked totaling 11517868 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30000853 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 30000853 bp After Masking: 17679985 bp Masked: 41.07 % -- Input Database Coverage: 40004069 bp out of 51946279 bp ( 77.01 % ) Sampling Time: 00:02:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:20:30 (hh:mm:ss) Elapsed Time, 34205 HSPs Collected Number of families returned by RECON: 2188 Round Time: 00:24:00 (hh:mm:ss) Elapsed Time : 32 families discovered. - Increasing sample size to include end piece now = 101943063 RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 101943063 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5629 repeats masked totaling 4689835 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11941991 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 11941991 bp After Masking: 6908660 bp Masked: 42.15 % -- Input Database Coverage: 51946060 bp out of 51946279 bp ( 100.00 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 45753 Comparison Time: 00:04:58 (hh:mm:ss) Elapsed Time, 1126 HSPs Collected Number of families returned by RECON: 490 Round Time: 00:06:07 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatScout/RECON discovery complete: 227 families found Classification Time: 00:19:06 (hh:mm:ss) Elapsed Time Program Time: 03:01:41 (hh:mm:ss) Elapsed Time