RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gpO6rc/RM_7539.SatJul271113042024 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: 1722103982 Database = /dev/shm/rModeler.gpO6rc/GCF_019924925.1_HZGC01 - Sequences = 31 - Bases = 893215104 Storage Throughput = good ( 996.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030599 bp ( 40026599 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:06 (hh:mm:ss) Elapsed Time Round Time: 00:29:49 (hh:mm:ss) Elapsed Time : 1264 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19075 repeats masked totaling 3478496 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001508 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000508 bp After Masking: 6263131 bp Masked: 37.37 % -- Input Database Coverage: 10001508 bp out of 893215104 bp ( 1.12 % ) Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:54 (hh:mm:ss) Elapsed Time, 25458 HSPs Collected Number of families returned by RECON: 1822 Round Time: 00:09:05 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59750 repeats masked totaling 10757612 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029011 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30026011 bp After Masking: 18520719 bp Masked: 38.32 % -- Input Database Coverage: 40030519 bp out of 893215104 bp ( 4.48 % ) Sampling Time: 00:03:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:36:13 (hh:mm:ss) Elapsed Time, 73123 HSPs Collected Number of families returned by RECON: 5732 Round Time: 00:43:44 (hh:mm:ss) Elapsed Time : 142 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 189643 repeats masked totaling 34048129 bp(s). - TE Masking time 00:04:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90037126 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90021091 bp After Masking: 53899333 bp Masked: 40.13 % -- Input Database Coverage: 130067645 bp out of 893215104 bp ( 14.56 % ) Sampling Time: 00:11:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 04:41:15 (hh:mm:ss) Elapsed Time, 625382 HSPs Collected Number of families returned by RECON: 16398 Round Time: 05:15:43 (hh:mm:ss) Elapsed Time : 722 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 658533 repeats masked totaling 119005988 bp(s). - TE Masking time 00:22:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270086478 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 270031873 bp After Masking: 144565727 bp Masked: 46.46 % -- Input Database Coverage: 400154123 bp out of 893215104 bp ( 44.80 % ) Sampling Time: 00:45:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 28:16:18 (hh:mm:ss) Elapsed Time, 1813524 HSPs Collected Number of families returned by RECON: 47303 Round Time: 30:37:13 (hh:mm:ss) Elapsed Time : 1467 families discovered. RepeatScout/RECON discovery complete: 3615 families found Classification Time: 02:14:09 (hh:mm:ss) Elapsed Time Program Time: 39:29:43 (hh:mm:ss) Elapsed Time