RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.QkF1Ns/RM_1103756.ThuNov141359562024 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: 1731621595 Database = /scratch/tmp/rModeler.QkF1Ns/GCA_964211835.1_bAnsAns1.hap1.1 - Sequences = 819 - Bases = 1313455045 - N50 = 88459368 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201485353-215877093 | [ 1 ] 187093613-201485352 | [ ] 172701874-187093613 | [ ] 158310134-172701873 | [ 1 ] 143918395-158310134 | [ ] 129526655-143918394 | [ ] 115134916-129526655 | [ 1 ] 100743176-115134915 | [ ] 86351437-100743176 | [ 1 ] 71959697-86351436 | [ 1 ] 57567958-71959697 | [ 1 ] 43176218-57567957 | [ ] 28784479-43176218 | [ 4 ] 14392739-28784478 | [ 11 ] 1000-14392739 |************************************************** [ 798 ] Storage Throughput = excellent ( 1456.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036253 bp ( 40030253 non ambiguous ) - Num Contigs Represented = 98 - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:06 (hh:mm:ss) Elapsed Time Round Time: 00:12:43 (hh:mm:ss) Elapsed Time : 77 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1946 repeats masked totaling 809352 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012471 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10010871 bp After Masking: 8354561 bp Masked: 16.55 % -- Input Database Coverage: 10012471 bp out of 1313455045 bp ( 0.76 % ) Sampling Time: 00:01:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:19 (hh:mm:ss) Elapsed Time, 2662 HSPs Collected Number of families returned by RECON: 189 Round Time: 00:04:20 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6390 repeats masked totaling 2813874 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023702 bp Num Contigs Represented = 88 Non ambiguous bp: Initial: 30019302 bp After Masking: 24353473 bp Masked: 18.87 % -- Input Database Coverage: 40036173 bp out of 1313455045 bp ( 3.05 % ) Sampling Time: 00:03:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:16:15 (hh:mm:ss) Elapsed Time, 6062 HSPs Collected Number of families returned by RECON: 1161 Round Time: 00:19:46 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19015 repeats masked totaling 8029274 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040996 bp Num Contigs Represented = 199 Non ambiguous bp: Initial: 90030996 bp After Masking: 74404948 bp Masked: 17.36 % -- Input Database Coverage: 130077169 bp out of 1313455045 bp ( 9.90 % ) Sampling Time: 00:08:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 01:50:24 (hh:mm:ss) Elapsed Time, 146266 HSPs Collected Number of families returned by RECON: 7535 Round Time: 02:04:43 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 72427 repeats masked totaling 29871500 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270049015 bp Num Contigs Represented = 365 Non ambiguous bp: Initial: 270008815 bp After Masking: 218979915 bp Masked: 18.90 % -- Input Database Coverage: 400126184 bp out of 1313455045 bp ( 30.46 % ) Sampling Time: 00:28:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23321035 Comparison Time: 12:11:34 (hh:mm:ss) Elapsed Time, 824279 HSPs Collected Number of families returned by RECON: 47683 Round Time: 13:06:41 (hh:mm:ss) Elapsed Time : 210 families discovered. RepeatScout/RECON discovery complete: 362 families found Classification Time: 00:18:20 (hh:mm:ss) Elapsed Time Program Time: 16:06:33 (hh:mm:ss) Elapsed Time