RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.SZ7bif/RM_308643.MonNov181614502024 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: 1731975288 Database = /scratch/tmp/rModeler.SZ7bif/GCF_028878055.3_NHGRI_mSymSyn1-v2.1_pri - Sequences = 27 - Bases = 3262904224 Storage Throughput = excellent ( 1463.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40003894 bp ( 40003894 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:32 (hh:mm:ss) Elapsed Time Round Time: 00:19:41 (hh:mm:ss) Elapsed Time : 231 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11593 repeats masked totaling 3072228 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000274 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000274 bp After Masking: 5832951 bp Masked: 41.67 % -- Input Database Coverage: 10000274 bp out of 3262904224 bp ( 0.31 % ) Sampling Time: 00:00:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:35 (hh:mm:ss) Elapsed Time, 4482 HSPs Collected Number of families returned by RECON: 721 Round Time: 00:03:21 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38227 repeats masked totaling 9583231 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003540 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30003540 bp After Masking: 16250160 bp Masked: 45.84 % -- Input Database Coverage: 40003814 bp out of 3262904224 bp ( 1.23 % ) Sampling Time: 00:02:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:11:34 (hh:mm:ss) Elapsed Time, 30521 HSPs Collected Number of families returned by RECON: 1896 Round Time: 00:15:49 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125167 repeats masked totaling 31042238 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90123227 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90003209 bp After Masking: 46977700 bp Masked: 47.80 % -- Input Database Coverage: 130127041 bp out of 3262904224 bp ( 3.99 % ) Sampling Time: 00:06:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 00:54:27 (hh:mm:ss) Elapsed Time, 98450 HSPs Collected Number of families returned by RECON: 6424 Round Time: 01:02:40 (hh:mm:ss) Elapsed Time : 170 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 405417 repeats masked totaling 100824086 bp(s). - TE Masking time 00:03:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270043076 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270003070 bp After Masking: 135687403 bp Masked: 49.75 % -- Input Database Coverage: 400170117 bp out of 3262904224 bp ( 12.26 % ) Sampling Time: 00:17:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22798128 Comparison Time: 06:18:58 (hh:mm:ss) Elapsed Time, 302415 HSPs Collected Number of families returned by RECON: 25309 Round Time: 06:46:11 (hh:mm:ss) Elapsed Time : 365 families discovered. RepeatScout/RECON discovery complete: 834 families found Classification Time: 00:21:53 (hh:mm:ss) Elapsed Time Program Time: 08:49:35 (hh:mm:ss) Elapsed Time