RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SyEEs2/RM_620491.WedApr231836012025 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: 1745458560 Database = /dev/shm/rModeler.SyEEs2/GCA_048301445.1_SynTyp1_v1.hap1 - Sequences = 152 - Bases = 368300239 - N50 = 16212348 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 26429220-28315844 | [ 1 ] 24542596-26429219 | [ 1 ] 22655973-24542596 | [ ] 20769349-22655972 | [ 2 ] 18882725-20769348 | [ 1 ] 16996102-18882725 | [ 2 ] 15109478-16996101 |* [ 3 ] 13222854-15109477 | [ 2 ] 11336231-13222854 |* [ 4 ] 9449607-11336230 | [ 2 ] 7562983-9449606 |* [ 3 ] 5676360-7562983 | [ 1 ] 3789736-5676359 | [ ] 1903112-3789735 | [ ] 16489-1903112 |************************************************** [ 130 ] Storage Throughput = excellent ( 1631.51 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010985 bp ( 40010185 non ambiguous ) - Num Contigs Represented = 84 - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:20 (hh:mm:ss) Elapsed Time Round Time: 00:12:49 (hh:mm:ss) Elapsed Time : 290 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5484 repeats masked totaling 1641475 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10019382 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10019182 bp After Masking: 6993629 bp Masked: 30.20 % -- Input Database Coverage: 10019382 bp out of 368300239 bp ( 2.72 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:32 (hh:mm:ss) Elapsed Time, 6257 HSPs Collected Number of families returned by RECON: 895 Round Time: 00:03:20 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18182 repeats masked totaling 5113648 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031603 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 30031003 bp After Masking: 21594567 bp Masked: 28.09 % -- Input Database Coverage: 40050985 bp out of 368300239 bp ( 10.87 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:11:09 (hh:mm:ss) Elapsed Time, 24373 HSPs Collected Number of families returned by RECON: 3625 Round Time: 00:13:24 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58357 repeats masked totaling 15376987 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013158 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 90012058 bp After Masking: 64219418 bp Masked: 28.65 % -- Input Database Coverage: 130064143 bp out of 368300239 bp ( 35.31 % ) Sampling Time: 00:05:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 01:06:44 (hh:mm:ss) Elapsed Time, 250702 HSPs Collected Number of families returned by RECON: 15087 Round Time: 01:15:28 (hh:mm:ss) Elapsed Time : 305 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 199741 repeats masked totaling 50906620 bp(s). - TE Masking time 00:02:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 238235878 bp Num Contigs Represented = 149 Non ambiguous bp: Initial: 238229978 bp After Masking: 160151358 bp Masked: 32.77 % -- Input Database Coverage: 368300021 bp out of 368300239 bp ( 100.00 % ) Sampling Time: 00:14:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 18027010 Comparison Time: 06:09:26 (hh:mm:ss) Elapsed Time, 691461 HSPs Collected Number of families returned by RECON: 49337 Round Time: 06:46:51 (hh:mm:ss) Elapsed Time : 644 families discovered. RepeatScout/RECON discovery complete: 1299 families found Classification Time: 00:33:10 (hh:mm:ss) Elapsed Time Program Time: 09:05:02 (hh:mm:ss) Elapsed Time