RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.SZ2CZX/RM_3273185.MonNov180818252024 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: 1731946705 Database = /scratch/tmp/rModeler.SZ2CZX/GCA_029215775.1_rAnnSte1.0.hap1 - Sequences = 134 - Bases = 1890507581 - N50 = 367647868 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 396120441-424413838 | [ 1 ] 367827045-396120441 | [ ] 339533649-367827045 | [ 1 ] 311240253-339533649 | [ ] 282946857-311240253 | [ ] 254653460-282946856 | [ 1 ] 226360064-254653460 | [ 1 ] 198066668-226360064 | [ 1 ] 169773272-198066668 | [ 1 ] 141479876-169773272 | [ ] 113186479-141479875 | [ 1 ] 84893083-113186479 | [ ] 56599687-84893083 | [ 1 ] 28306291-56599687 | [ ] 12895-28306291 |************************************************** [ 126 ] Storage Throughput = excellent ( 1168.53 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027448 bp ( 40027448 non ambiguous ) - Num Contigs Represented = 19 - Sequence extraction : 00:02:51 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:17 (hh:mm:ss) Elapsed Time Round Time: 00:12:25 (hh:mm:ss) Elapsed Time : 647 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21363 repeats masked totaling 3665199 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003588 bp Num Contigs Represented = 10 Non ambiguous bp: Initial: 10003588 bp After Masking: 6210861 bp Masked: 37.91 % -- Input Database Coverage: 10003588 bp out of 1890507581 bp ( 0.53 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 14302 HSPs Collected Number of families returned by RECON: 1601 Round Time: 00:04:12 (hh:mm:ss) Elapsed Time : 42 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67112 repeats masked totaling 11462128 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023780 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 30023780 bp After Masking: 17916970 bp Masked: 40.32 % -- Input Database Coverage: 40027368 bp out of 1890507581 bp ( 2.12 % ) Sampling Time: 00:03:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:13:19 (hh:mm:ss) Elapsed Time, 52907 HSPs Collected Number of families returned by RECON: 4666 Round Time: 00:17:41 (hh:mm:ss) Elapsed Time : 136 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 214258 repeats masked totaling 37080627 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036442 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90036342 bp After Masking: 51102806 bp Masked: 43.24 % -- Input Database Coverage: 130063810 bp out of 1890507581 bp ( 6.88 % ) Sampling Time: 00:10:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:15:41 (hh:mm:ss) Elapsed Time, 226447 HSPs Collected Number of families returned by RECON: 14208 Round Time: 01:36:24 (hh:mm:ss) Elapsed Time : 510 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 733343 repeats masked totaling 126067862 bp(s). - TE Masking time 00:04:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270016152 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 270015852 bp After Masking: 138602417 bp Masked: 48.67 % -- Input Database Coverage: 400079962 bp out of 1890507581 bp ( 21.16 % ) Sampling Time: 00:32:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 07:26:29 (hh:mm:ss) Elapsed Time, 646592 HSPs Collected Number of families returned by RECON: 42936 Round Time: 08:25:37 (hh:mm:ss) Elapsed Time : 1070 families discovered. RepeatScout/RECON discovery complete: 2405 families found Classification Time: 00:38:20 (hh:mm:ss) Elapsed Time Program Time: 11:14:39 (hh:mm:ss) Elapsed Time