RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.pG3sxg/RM_2809575.SatNov160812172024 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: 1731773537 Database = /scratch/tmp/rModeler.pG3sxg/GCA_964264875.1_mNycLei1.hap1.1 - Sequences = 1281 - Bases = 2233532335 - N50 = 92232743 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 207245010-222048154 | [ 1 ] 192441866-207245009 | [ 2 ] 177638723-192441866 | [ ] 162835579-177638722 | [ ] 148032436-162835579 | [ ] 133229292-148032435 | [ ] 118426148-133229291 | [ ] 103623005-118426148 | [ 2 ] 88819861-103623004 | [ 3 ] 74016718-88819861 | [ 3 ] 59213574-74016717 | [ 3 ] 44410430-59213573 | [ 4 ] 29607287-44410430 | [ 1 ] 14804143-29607286 | [ 3 ] 1000-14804143 |************************************************** [ 1259 ] Storage Throughput = excellent ( 1535.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047354 bp ( 40039754 non ambiguous ) - Num Contigs Represented = 142 - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:30 (hh:mm:ss) Elapsed Time Round Time: 00:15:36 (hh:mm:ss) Elapsed Time : 378 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14284 repeats masked totaling 3121673 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022230 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 10020430 bp After Masking: 6089496 bp Masked: 39.23 % -- Input Database Coverage: 10022230 bp out of 2233532335 bp ( 0.45 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:03:07 (hh:mm:ss) Elapsed Time, 11491 HSPs Collected Number of families returned by RECON: 680 Round Time: 00:04:46 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45266 repeats masked totaling 9346461 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025122 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 30019322 bp After Masking: 17702250 bp Masked: 41.03 % -- Input Database Coverage: 40047352 bp out of 2233532335 bp ( 1.79 % ) Sampling Time: 00:04:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:13:17 (hh:mm:ss) Elapsed Time, 19130 HSPs Collected Number of families returned by RECON: 1930 Round Time: 00:18:00 (hh:mm:ss) Elapsed Time : 39 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143470 repeats masked totaling 28990273 bp(s). - TE Masking time 00:01:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042071 bp Num Contigs Represented = 261 Non ambiguous bp: Initial: 90028104 bp After Masking: 51695764 bp Masked: 42.58 % -- Input Database Coverage: 130089423 bp out of 2233532335 bp ( 5.82 % ) Sampling Time: 00:13:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:13:39 (hh:mm:ss) Elapsed Time, 99100 HSPs Collected Number of families returned by RECON: 6904 Round Time: 01:29:20 (hh:mm:ss) Elapsed Time : 193 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:28:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 458393 repeats masked totaling 92780201 bp(s). - TE Masking time 00:05:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270064102 bp Num Contigs Represented = 503 Non ambiguous bp: Initial: 270020234 bp After Masking: 150259637 bp Masked: 44.35 % -- Input Database Coverage: 400153525 bp out of 2233532335 bp ( 17.92 % ) Sampling Time: 00:41:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23362030 Comparison Time: 07:59:07 (hh:mm:ss) Elapsed Time, 291508 HSPs Collected Number of families returned by RECON: 28257 Round Time: 08:51:42 (hh:mm:ss) Elapsed Time : 488 families discovered. RepeatScout/RECON discovery complete: 1106 families found Classification Time: 00:35:13 (hh:mm:ss) Elapsed Time Program Time: 11:34:37 (hh:mm:ss) Elapsed Time