RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.BDYdwY/RM_110439.FriDec60647372024 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: 1733496457 Database = /scratch/tmp/rModeler.BDYdwY/GCA_964194215.1_mRhiHip2.hap2.1 - Sequences = 1079 - Bases = 2240459116 - N50 = 93073186 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 116171426-124469314 | [ 1 ] 107873538-116171425 | [ 3 ] 99575651-107873538 | [ 4 ] 91277763-99575650 | [ 2 ] 82979876-91277763 | [ 2 ] 74681988-82979875 | [ 2 ] 66384100-74681987 | [ 2 ] 58086213-66384100 | [ 3 ] 49788325-58086212 | [ 3 ] 41490438-49788325 | [ 2 ] 33192550-41490437 | [ 1 ] 24894662-33192549 | [ 2 ] 16596775-24894662 | [ 1 ] 8298887-16596774 | [ 1 ] 1000-8298887 |************************************************** [ 1050 ] Storage Throughput = excellent ( 1472.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039566 bp ( 40032766 non ambiguous ) - Num Contigs Represented = 95 - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:14 (hh:mm:ss) Elapsed Time Round Time: 00:17:27 (hh:mm:ss) Elapsed Time : 194 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 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8234 repeats masked totaling 2213853 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020531 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10019731 bp After Masking: 7494200 bp Masked: 25.21 % -- Input Database Coverage: 10020531 bp out of 2240459116 bp ( 0.45 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:52 (hh:mm:ss) Elapsed Time, 4574 HSPs Collected Number of families returned by RECON: 755 Round Time: 00:04:29 (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 : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27332 repeats masked totaling 7687579 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019031 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 30013031 bp After Masking: 21207155 bp Masked: 29.34 % -- Input Database Coverage: 40039562 bp out of 2240459116 bp ( 1.79 % ) Sampling Time: 00:03:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:13:23 (hh:mm:ss) Elapsed Time, 20051 HSPs Collected Number of families returned by RECON: 2352 Round Time: 00:17:38 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 90698 repeats masked totaling 25184058 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026290 bp Num Contigs Represented = 167 Non ambiguous bp: Initial: 90014090 bp After Masking: 61622660 bp Masked: 31.54 % -- Input Database Coverage: 130065852 bp out of 2240459116 bp ( 5.81 % ) Sampling Time: 00:10:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 01:14:38 (hh:mm:ss) Elapsed Time, 87894 HSPs Collected Number of families returned by RECON: 8715 Round Time: 01:26:54 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:29:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 311561 repeats masked totaling 82720484 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270055380 bp Num Contigs Represented = 380 Non ambiguous bp: Initial: 270020853 bp After Masking: 176390994 bp Masked: 34.68 % -- Input Database Coverage: 400121232 bp out of 2240459116 bp ( 17.86 % ) Sampling Time: 00:37:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23280076 Comparison Time: 08:26:12 (hh:mm:ss) Elapsed Time, 193090 HSPs Collected Number of families returned by RECON: 35764 Round Time: 09:14:23 (hh:mm:ss) Elapsed Time : 349 families discovered. RepeatScout/RECON discovery complete: 809 families found Classification Time: 00:17:48 (hh:mm:ss) Elapsed Time Program Time: 11:38:39 (hh:mm:ss) Elapsed Time