RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.j0bTVm/RM_15488.WedJun260028142024 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: 1719386893 Database = /dev/shm/rModeler.j0bTVm/GCF_028878055.2_NHGRI_mSymSyn1-v2.0_pri - Sequences = 27 - Bases = 3262904224 Storage Throughput = excellent ( 1092.70 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003566 bp ( 40003566 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:28:59 (hh:mm:ss) Elapsed Time Round Time: 00:54:24 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13291 repeats masked totaling 3121440 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002433 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10002433 bp After Masking: 5838302 bp Masked: 41.63 % -- Input Database Coverage: 10002433 bp out of 3262904224 bp ( 0.31 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:58 (hh:mm:ss) Elapsed Time, 4863 HSPs Collected Number of families returned by RECON: 817 Round Time: 00:06:42 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40606 repeats masked totaling 9573352 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30001053 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30001053 bp After Masking: 16869046 bp Masked: 43.77 % -- Input Database Coverage: 40003486 bp out of 3262904224 bp ( 1.23 % ) Sampling Time: 00:04:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:24:47 (hh:mm:ss) Elapsed Time, 23508 HSPs Collected Number of families returned by RECON: 2073 Round Time: 00:30:10 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125359 repeats masked totaling 29877638 bp(s). - TE Masking time 00:02:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90043068 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90003062 bp After Masking: 48450118 bp Masked: 46.17 % -- Input Database Coverage: 130046554 bp out of 3262904224 bp ( 3.99 % ) Sampling Time: 00:13:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2532375 Comparison Time: 02:41:52 (hh:mm:ss) Elapsed Time, 99813 HSPs Collected Number of families returned by RECON: 7244 Round Time: 03:04:27 (hh:mm:ss) Elapsed Time : 167 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 429443 repeats masked totaling 99873762 bp(s). - TE Masking time 00:08:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270096960 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 270016947 bp After Masking: 137219605 bp Masked: 49.18 % -- Input Database Coverage: 400143514 bp out of 3262904224 bp ( 12.26 % ) Sampling Time: 00:42:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 20:14:56 (hh:mm:ss) Elapsed Time, 272971 HSPs Collected Number of families returned by RECON: 26026 Round Time: 21:19:04 (hh:mm:ss) Elapsed Time : 409 families discovered. RepeatScout/RECON discovery complete: 905 families found Classification Time: 00:48:21 (hh:mm:ss) Elapsed Time Program Time: 26:43:08 (hh:mm:ss) Elapsed Time