RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7fCSdr/RM_146063.ThuDec292033362022 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: 1672374815 Database = /dev/shm/rModeler.7fCSdr/GCF_009819705.1_fHipHip1.pri - Sequences = 57 - Bases = 596792615 Storage Throughput = excellent ( 1037.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40280372 bp ( 40019321 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:23 (hh:mm:ss) Elapsed Time Round Time: 00:24:03 (hh:mm:ss) Elapsed Time : 371 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 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8125 repeats masked totaling 1039250 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10117454 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10037681 bp After Masking: 8739271 bp Masked: 12.94 % -- Input Database Coverage: 10117454 bp out of 596792615 bp ( 1.70 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:11 (hh:mm:ss) Elapsed Time, 6351 HSPs Collected Number of families returned by RECON: 1277 Round Time: 00:07:24 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 25233 repeats masked totaling 3195464 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30202886 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30021608 bp After Masking: 25923769 bp Masked: 13.65 % -- Input Database Coverage: 40320340 bp out of 596792615 bp ( 6.76 % ) Sampling Time: 00:03:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:32:27 (hh:mm:ss) Elapsed Time, 38829 HSPs Collected Number of families returned by RECON: 5004 Round Time: 00:37:41 (hh:mm:ss) Elapsed Time : 95 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 85133 repeats masked totaling 10659703 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90614800 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90026146 bp After Masking: 76417910 bp Masked: 15.12 % -- Input Database Coverage: 130935140 bp out of 596792615 bp ( 21.94 % ) Sampling Time: 00:11:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 03:39:37 (hh:mm:ss) Elapsed Time, 212931 HSPs Collected Number of families returned by RECON: 19389 Round Time: 04:06:23 (hh:mm:ss) Elapsed Time : 356 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 310107 repeats masked totaling 41732943 bp(s). - TE Masking time 00:06:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271551949 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 270006181 bp After Masking: 220132436 bp Masked: 18.47 % -- Input Database Coverage: 402487089 bp out of 596792615 bp ( 67.44 % ) Sampling Time: 00:35:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23137003 Comparison Time: 26:25:03 (hh:mm:ss) Elapsed Time, 699617 HSPs Collected Number of families returned by RECON: 77648 Round Time: 30:21:31 (hh:mm:ss) Elapsed Time : 994 families discovered. RepeatScout/RECON discovery complete: 1833 families found Classification Time: 01:28:39 (hh:mm:ss) Elapsed Time Program Time: 37:05:41 (hh:mm:ss) Elapsed Time