RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.VyyCCm/RM_3682157.TueNov191558212024 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: 1732060700 Database = /scratch/tmp/rModeler.VyyCCm/GCA_040894005.1_aEngPut4.maternal - Sequences = 936 - Bases = 2158203323 - N50 = 228224547 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 285887154-306306954 | [ 1 ] 265467354-285887153 | [ 1 ] 245047555-265467354 | [ ] 224627755-245047554 | [ 2 ] 204207956-224627755 | [ 1 ] 183788156-204207955 | [ 2 ] 163368357-183788156 | [ ] 142948557-163368356 | [ ] 122528758-142948557 | [ 1 ] 102108958-122528757 | [ 2 ] 81689159-102108958 | [ 1 ] 61269359-81689158 | [ ] 40849560-61269359 | [ ] 20429760-40849559 | [ ] 9961-20429760 |************************************************** [ 925 ] Storage Throughput = excellent ( 1600.82 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40021749 bp ( 40019349 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:50 (hh:mm:ss) Elapsed Time Round Time: 00:15:27 (hh:mm:ss) Elapsed Time : 702 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16146 repeats masked totaling 3511587 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020593 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10019593 bp After Masking: 4671528 bp Masked: 53.38 % -- Input Database Coverage: 10020593 bp out of 2158203323 bp ( 0.46 % ) Sampling Time: 00:02:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:37 (hh:mm:ss) Elapsed Time, 25862 HSPs Collected Number of families returned by RECON: 1224 Round Time: 00:05:15 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48038 repeats masked totaling 10345095 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30041076 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30039676 bp After Masking: 13892792 bp Masked: 53.75 % -- Input Database Coverage: 40061669 bp out of 2158203323 bp ( 1.86 % ) Sampling Time: 00:06:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:10:09 (hh:mm:ss) Elapsed Time, 59238 HSPs Collected Number of families returned by RECON: 4177 Round Time: 00:17:50 (hh:mm:ss) Elapsed Time : 125 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157475 repeats masked totaling 34485258 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017428 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 90014028 bp After Masking: 39475113 bp Masked: 56.15 % -- Input Database Coverage: 130079097 bp out of 2158203323 bp ( 6.03 % ) Sampling Time: 00:18:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 00:48:59 (hh:mm:ss) Elapsed Time, 379762 HSPs Collected Number of families returned by RECON: 11379 Round Time: 01:11:51 (hh:mm:ss) Elapsed Time : 450 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:39:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 536806 repeats masked totaling 118001442 bp(s). - TE Masking time 00:02:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044305 bp Num Contigs Represented = 266 Non ambiguous bp: Initial: 270035332 bp After Masking: 102810671 bp Masked: 61.93 % -- Input Database Coverage: 400123402 bp out of 2158203323 bp ( 18.54 % ) Sampling Time: 00:56:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23164221 Comparison Time: 05:30:24 (hh:mm:ss) Elapsed Time, 854208 HSPs Collected Number of families returned by RECON: 31186 Round Time: 06:47:39 (hh:mm:ss) Elapsed Time : 1093 families discovered. RepeatScout/RECON discovery complete: 2381 families found Classification Time: 00:42:04 (hh:mm:ss) Elapsed Time Program Time: 09:20:06 (hh:mm:ss) Elapsed Time