RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.MFnvdA/RM_316238.SatJan111742202025 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: 1736646138 Database = /data/tmp/rModeler.MFnvdA/GCF_043380555.1_NfurGRZ-RIMD1 - Sequences = 304 - Bases = 1479202486 - N50 = 81344259 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 108022340-115738151 | [ 1 ] 100306530-108022340 | [ 1 ] 92590720-100306530 | [ 1 ] 84874910-92590720 | [ 1 ] 77159100-84874910 | [ 4 ] 69443290-77159100 | [ 4 ] 61727480-69443290 | [ 4 ] 54011670-61727480 | [ 1 ] 46295860-54011670 | [ 1 ] 38580050-46295860 | [ ] 30864240-38580050 | [ ] 23148430-30864240 | [ 1 ] 15432620-23148430 | [ ] 7716810-15432620 | [ ] 1000-7716810 |************************************************** [ 285 ] Storage Throughput = excellent ( 1772.82 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023635 bp ( 40022035 non ambiguous ) - Num Contigs Represented = 47 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:11 (hh:mm:ss) Elapsed Time Round Time: 00:20:40 (hh:mm:ss) Elapsed Time : 690 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10970 repeats masked totaling 3661414 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038537 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10037737 bp After Masking: 3884026 bp Masked: 61.31 % -- Input Database Coverage: 10038537 bp out of 1479202486 bp ( 0.68 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:08 (hh:mm:ss) Elapsed Time, 5893 HSPs Collected Number of families returned by RECON: 849 Round Time: 00:04:15 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32383 repeats masked totaling 10453318 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025018 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30024218 bp After Masking: 11569525 bp Masked: 61.47 % -- Input Database Coverage: 40063555 bp out of 1479202486 bp ( 2.71 % ) Sampling Time: 00:05:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:07:59 (hh:mm:ss) Elapsed Time, 30268 HSPs Collected Number of families returned by RECON: 2434 Round Time: 00:14:22 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 101921 repeats masked totaling 32638778 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018458 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 90013058 bp After Masking: 33373431 bp Masked: 62.92 % -- Input Database Coverage: 130082013 bp out of 1479202486 bp ( 8.79 % ) Sampling Time: 00:16:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 00:43:40 (hh:mm:ss) Elapsed Time, 164928 HSPs Collected Number of families returned by RECON: 7156 Round Time: 01:03:58 (hh:mm:ss) Elapsed Time : 356 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:55:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 340935 repeats masked totaling 107300366 bp(s). - TE Masking time 00:04:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270013428 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 270002128 bp After Masking: 88480599 bp Masked: 67.23 % -- Input Database Coverage: 400095441 bp out of 1479202486 bp ( 27.05 % ) Sampling Time: 01:04:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 03:47:36 (hh:mm:ss) Elapsed Time, 721117 HSPs Collected Number of families returned by RECON: 21525 Round Time: 05:04:17 (hh:mm:ss) Elapsed Time : 775 families discovered. RepeatScout/RECON discovery complete: 1909 families found Classification Time: 00:46:07 (hh:mm:ss) Elapsed Time Program Time: 07:33:39 (hh:mm:ss) Elapsed Time