RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.sUrZez/RM_23384.ThuJul111031012024 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: 1720719056 Database = /dev/shm/rModeler.sUrZez/GCF_002260705.1_Sdu_1.0 - Sequences = 34656 - Bases = 677686174 - N50 = 5864697 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 23258456-24919768 | [ 3 ] 21597145-23258456 | [ ] 19935834-21597145 | [ 2 ] 18274523-19935834 | [ 1 ] 16613212-18274523 | [ ] 14951900-16613211 | [ 2 ] 13290589-14951900 | [ 2 ] 11629278-13290589 | [ 1 ] 9967967-11629278 | [ 1 ] 8306656-9967967 | [ 7 ] 6645344-8306655 | [ 5 ] 4984033-6645344 | [ 10 ] 3322722-4984033 | [ 14 ] 1661411-3322722 | [ 46 ] 100-1661411 |************************************************** [ 34562 ] Storage Throughput = excellent ( 1035.57 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40279946 bp ( 40004280 non ambiguous ) - Num Contigs Represented = 2323 - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:16 (hh:mm:ss) Elapsed Time Round Time: 00:28:17 (hh:mm:ss) Elapsed Time : 391 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6391 repeats masked totaling 640722 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10081302 bp Num Contigs Represented = 671 Non ambiguous bp: Initial: 10021740 bp After Masking: 9130777 bp Masked: 8.89 % -- Input Database Coverage: 10081302 bp out of 677686174 bp ( 1.49 % ) Sampling Time: 00:00:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 326836 Comparison Time: 00:29:58 (hh:mm:ss) Elapsed Time, 10807 HSPs Collected Number of families returned by RECON: 1522 Round Time: 00:31:46 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23220 repeats masked totaling 2769722 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30238867 bp Num Contigs Represented = 1745 Non ambiguous bp: Initial: 30022738 bp After Masking: 26358188 bp Masked: 12.21 % -- Input Database Coverage: 40320169 bp out of 677686174 bp ( 5.95 % ) Sampling Time: 00:02:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2673828 Comparison Time: 00:50:01 (hh:mm:ss) Elapsed Time, 46848 HSPs Collected Number of families returned by RECON: 5902 Round Time: 00:54:58 (hh:mm:ss) Elapsed Time : 120 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80827 repeats masked totaling 10266264 bp(s). - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90785221 bp Num Contigs Represented = 4824 Non ambiguous bp: Initial: 90014087 bp After Masking: 77023899 bp Masked: 14.43 % -- Input Database Coverage: 131105390 bp out of 677686174 bp ( 19.35 % ) Sampling Time: 00:07:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23348361 Comparison Time: 05:15:51 (hh:mm:ss) Elapsed Time, 256329 HSPs Collected Number of families returned by RECON: 22522 Round Time: 05:42:08 (hh:mm:ss) Elapsed Time : 439 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 313226 repeats masked totaling 43041530 bp(s). - TE Masking time 00:09:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272215330 bp Num Contigs Represented = 14072 Non ambiguous bp: Initial: 270002310 bp After Masking: 219039197 bp Masked: 18.88 % -- Input Database Coverage: 403320720 bp out of 677686174 bp ( 59.51 % ) Sampling Time: 00:26:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 210668601 Comparison Time: 39:04:52 (hh:mm:ss) Elapsed Time, 806627 HSPs Collected Number of families returned by RECON: 88017 Round Time: 42:45:39 (hh:mm:ss) Elapsed Time : 1213 families discovered. RepeatScout/RECON discovery complete: 2184 families found Classification Time: 01:27:15 (hh:mm:ss) Elapsed Time Program Time: 51:50:03 (hh:mm:ss) Elapsed Time