RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.KkTwxe/RM_2973794.FriDec62002202024 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: 1733544140 Database = /scratch/tmp/rModeler.KkTwxe/GCA_964188415.1_fProPar1.1_alternate_haplotype - Sequences = 23 - Bases = 1013731500 Storage Throughput = excellent ( 1448.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045770 bp ( 40005914 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:09 (hh:mm:ss) Elapsed Time Round Time: 00:13:34 (hh:mm:ss) Elapsed Time : 1205 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 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23807 repeats masked totaling 3266941 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041383 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10030583 bp After Masking: 5515827 bp Masked: 45.01 % -- Input Database Coverage: 10041383 bp out of 1013731500 bp ( 0.99 % ) Sampling Time: 00:01:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 11199 HSPs Collected Number of families returned by RECON: 1852 Round Time: 00:04:21 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 71327 repeats masked totaling 9652777 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30044307 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30015051 bp After Masking: 16035944 bp Masked: 46.57 % -- Input Database Coverage: 40085690 bp out of 1013731500 bp ( 3.95 % ) Sampling Time: 00:03:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:12:00 (hh:mm:ss) Elapsed Time, 63040 HSPs Collected Number of families returned by RECON: 6135 Round Time: 00:16:57 (hh:mm:ss) Elapsed Time : 131 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 224038 repeats masked totaling 29104562 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90117091 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 90030211 bp After Masking: 48933862 bp Masked: 45.65 % -- Input Database Coverage: 130202781 bp out of 1013731500 bp ( 12.84 % ) Sampling Time: 00:08:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:04:59 (hh:mm:ss) Elapsed Time, 414199 HSPs Collected Number of families returned by RECON: 19839 Round Time: 01:23:19 (hh:mm:ss) Elapsed Time : 821 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 775555 repeats masked totaling 104652862 bp(s). - TE Masking time 00:05:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270287715 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 270022793 bp After Masking: 131201694 bp Masked: 51.41 % -- Input Database Coverage: 400490496 bp out of 1013731500 bp ( 39.51 % ) Sampling Time: 00:31:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 06:48:41 (hh:mm:ss) Elapsed Time, 1340221 HSPs Collected Number of families returned by RECON: 57612 Round Time: 08:10:43 (hh:mm:ss) Elapsed Time : 1845 families discovered. RepeatScout/RECON discovery complete: 4026 families found Classification Time: 01:03:22 (hh:mm:ss) Elapsed Time Program Time: 11:12:16 (hh:mm:ss) Elapsed Time