RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5diqWL/RM_128133.SatJan71550582023 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: 1673135457 Database = /dev/shm/rModeler.5diqWL/GCF_021462225.1_DD_fGirMul_XY1 - Sequences = 72 - Bases = 1150004004 Storage Throughput = excellent ( 1123.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40135246 bp ( 40020030 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:58 (hh:mm:ss) Elapsed Time Round Time: 00:19:48 (hh:mm:ss) Elapsed Time : 560 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12097 repeats masked totaling 3731849 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10050494 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10037498 bp After Masking: 6213610 bp Masked: 38.10 % -- Input Database Coverage: 10050494 bp out of 1150004004 bp ( 0.87 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:32 (hh:mm:ss) Elapsed Time, 10936 HSPs Collected Number of families returned by RECON: 1500 Round Time: 00:06:48 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38341 repeats masked totaling 11659476 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30124608 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30022388 bp After Masking: 17974168 bp Masked: 40.13 % -- Input Database Coverage: 40175102 bp out of 1150004004 bp ( 3.49 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:25:33 (hh:mm:ss) Elapsed Time, 63441 HSPs Collected Number of families returned by RECON: 4518 Round Time: 00:30:46 (hh:mm:ss) Elapsed Time : 107 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 130684 repeats masked totaling 38573786 bp(s). - TE Masking time 00:02:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90402712 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90015694 bp After Masking: 50321719 bp Masked: 44.10 % -- Input Database Coverage: 130577814 bp out of 1150004004 bp ( 11.35 % ) Sampling Time: 00:09:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 02:37:34 (hh:mm:ss) Elapsed Time, 237999 HSPs Collected Number of families returned by RECON: 10967 Round Time: 02:57:07 (hh:mm:ss) Elapsed Time : 375 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 450160 repeats masked totaling 129754962 bp(s). - TE Masking time 00:10:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271263768 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 270012467 bp After Masking: 136897115 bp Masked: 49.30 % -- Input Database Coverage: 401841582 bp out of 1150004004 bp ( 34.94 % ) Sampling Time: 00:34:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23062236 Comparison Time: 17:53:22 (hh:mm:ss) Elapsed Time, 568851 HSPs Collected Number of families returned by RECON: 33694 Round Time: 19:20:50 (hh:mm:ss) Elapsed Time : 925 families discovered. RepeatScout/RECON discovery complete: 1983 families found Classification Time: 01:54:43 (hh:mm:ss) Elapsed Time Program Time: 25:10:02 (hh:mm:ss) Elapsed Time