RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.mP1g0F/RM_658174.WedDec40028262024 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: 1733300906 Database = /scratch/tmp/rModeler.mP1g0F/GCA_964270935.1_mLagAcu1.hap2.1 - Sequences = 879 - Bases = 2422718875 - N50 = 108887159 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 178773039-191542471 | [ 1 ] 166003608-178773039 | [ 2 ] 153234176-166003607 | [ ] 140464745-153234176 | [ 1 ] 127695314-140464745 | [ 1 ] 114925882-127695313 | [ 1 ] 102156451-114925882 | [ 5 ] 89387019-102156450 | [ 3 ] 76617588-89387019 | [ 4 ] 63848157-76617588 | [ ] 51078725-63848156 | [ 2 ] 38309294-51078725 | [ ] 25539862-38309293 | [ 1 ] 12770431-25539862 | [ ] 1000-12770431 |************************************************** [ 858 ] Storage Throughput = excellent ( 1496.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033999 bp ( 40030799 non ambiguous ) - Num Contigs Represented = 79 - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:17 (hh:mm:ss) Elapsed Time Round Time: 00:14:32 (hh:mm:ss) Elapsed Time : 206 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9762 repeats masked totaling 2698562 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039562 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10039362 bp After Masking: 7212919 bp Masked: 28.15 % -- Input Database Coverage: 10039562 bp out of 2422718875 bp ( 0.41 % ) Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:02 (hh:mm:ss) Elapsed Time, 21813 HSPs Collected Number of families returned by RECON: 980 Round Time: 00:03:57 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36484 repeats masked totaling 9661579 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034357 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30031357 bp After Masking: 19671355 bp Masked: 34.50 % -- Input Database Coverage: 40073919 bp out of 2422718875 bp ( 1.65 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:12:55 (hh:mm:ss) Elapsed Time, 39162 HSPs Collected Number of families returned by RECON: 2239 Round Time: 00:15:23 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 117304 repeats masked totaling 32140076 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034926 bp Num Contigs Represented = 168 Non ambiguous bp: Initial: 90026526 bp After Masking: 56382777 bp Masked: 37.37 % -- Input Database Coverage: 130108845 bp out of 2422718875 bp ( 5.37 % ) Sampling Time: 00:06:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 01:14:20 (hh:mm:ss) Elapsed Time, 197178 HSPs Collected Number of families returned by RECON: 8263 Round Time: 01:24:23 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 386742 repeats masked totaling 105148431 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270045412 bp Num Contigs Represented = 369 Non ambiguous bp: Initial: 270022212 bp After Masking: 160231576 bp Masked: 40.66 % -- Input Database Coverage: 400154257 bp out of 2422718875 bp ( 16.52 % ) Sampling Time: 00:16:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 08:25:05 (hh:mm:ss) Elapsed Time, 1947023 HSPs Collected Number of families returned by RECON: 31621 Round Time: 08:51:59 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatScout/RECON discovery complete: 799 families found Classification Time: 00:17:23 (hh:mm:ss) Elapsed Time Program Time: 11:07:37 (hh:mm:ss) Elapsed Time