RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.5D0VQW/RM_1148188.TueNov121153082024 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: 1731441188 Database = /scratch/tmp/rModeler.5D0VQW/GCF_963924715.1_fThuThy2.1 - Sequences = 119 - Bases = 799047066 - N50 = 35057343 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 39207654-42008130 |* [ 3 ] 36407179-39207654 | [ 1 ] 33606704-36407179 |**** [ 8 ] 30806228-33606703 |** [ 4 ] 28005753-30806228 |** [ 4 ] 25205278-28005753 |* [ 3 ] 22404802-25205277 | [ ] 19604327-22404802 | [ 1 ] 16803852-19604327 | [ ] 14003376-16803851 | [ ] 11202901-14003376 | [ ] 8402426-11202901 | [ ] 5601950-8402425 | [ ] 2801475-5601950 | [ ] 1000-2801475 |************************************************** [ 95 ] Storage Throughput = excellent ( 1581.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035621 bp ( 40032621 non ambiguous ) - Num Contigs Represented = 32 - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:03 (hh:mm:ss) Elapsed Time Round Time: 00:09:17 (hh:mm:ss) Elapsed Time : 562 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9562 repeats masked totaling 1418008 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001472 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000472 bp After Masking: 8335501 bp Masked: 16.65 % -- Input Database Coverage: 10001472 bp out of 799047066 bp ( 1.25 % ) Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 7302 HSPs Collected Number of families returned by RECON: 1753 Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29630 repeats masked totaling 4512776 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034069 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30032069 bp After Masking: 24477362 bp Masked: 18.50 % -- Input Database Coverage: 40035541 bp out of 799047066 bp ( 5.01 % ) Sampling Time: 00:01:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:14:49 (hh:mm:ss) Elapsed Time, 58588 HSPs Collected Number of families returned by RECON: 6390 Round Time: 00:18:32 (hh:mm:ss) Elapsed Time : 137 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102991 repeats masked totaling 15824356 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030461 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90018578 bp After Masking: 71415393 bp Masked: 20.67 % -- Input Database Coverage: 130066002 bp out of 799047066 bp ( 16.28 % ) Sampling Time: 00:04:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:34:14 (hh:mm:ss) Elapsed Time, 349352 HSPs Collected Number of families returned by RECON: 21830 Round Time: 01:46:51 (hh:mm:ss) Elapsed Time : 631 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 389427 repeats masked totaling 63593769 bp(s). - TE Masking time 00:04:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037208 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 270005075 bp After Masking: 197744216 bp Masked: 26.76 % -- Input Database Coverage: 400103210 bp out of 799047066 bp ( 50.07 % ) Sampling Time: 00:14:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 10:54:19 (hh:mm:ss) Elapsed Time, 976535 HSPs Collected Number of families returned by RECON: 73432 Round Time: 12:05:55 (hh:mm:ss) Elapsed Time : 1469 families discovered. RepeatScout/RECON discovery complete: 2817 families found Classification Time: 01:00:50 (hh:mm:ss) Elapsed Time Program Time: 15:25:04 (hh:mm:ss) Elapsed Time