RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LmYnvz/RM_18211.ThuJan50759172023 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: 1672934356 Database = /dev/shm/rModeler.LmYnvz/GCF_010993605.1_kPetMar1.pri - Sequences = 1434 - Bases = 1089050413 - N50 = 13147369 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 31969824-34253345 | [ 1 ] 29686304-31969824 | [ ] 27402784-29686304 | [ ] 25119264-27402784 | [ 3 ] 22835744-25119264 | [ ] 20552223-22835743 | [ ] 18268703-20552223 | [ 2 ] 15985183-18268703 | [ 5 ] 13701663-15985183 | [ 14 ] 11418143-13701663 | [ 19 ] 9134622-11418142 | [ 15 ] 6851102-9134622 | [ 6 ] 4567582-6851102 | [ 5 ] 2284062-4567582 | [ 6 ] 542-2284062 |************************************************** [ 1358 ] Storage Throughput = excellent ( 1463.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40407337 bp ( 40022350 non ambiguous ) - Num Contigs Represented = 223 - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:33 (hh:mm:ss) Elapsed Time Round Time: 00:18:52 (hh:mm:ss) Elapsed Time : 541 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21090 repeats masked totaling 3097461 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10201814 bp Num Contigs Represented = 115 Non ambiguous bp: Initial: 10005875 bp After Masking: 4724212 bp Masked: 52.79 % -- Input Database Coverage: 10201814 bp out of 1089050413 bp ( 0.94 % ) Sampling Time: 00:06:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34716 Comparison Time: 00:06:10 (hh:mm:ss) Elapsed Time, 34306 HSPs Collected Number of families returned by RECON: 1004 Round Time: 00:15:57 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 70804 repeats masked totaling 10803210 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30205475 bp Num Contigs Represented = 180 Non ambiguous bp: Initial: 30016427 bp After Masking: 13278518 bp Masked: 55.76 % -- Input Database Coverage: 40407289 bp out of 1089050413 bp ( 3.71 % ) Sampling Time: 00:16:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 298378 Comparison Time: 00:20:50 (hh:mm:ss) Elapsed Time, 30454 HSPs Collected Number of families returned by RECON: 2789 Round Time: 00:38:24 (hh:mm:ss) Elapsed Time : 104 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:49:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 222612 repeats masked totaling 34976579 bp(s). - TE Masking time 00:01:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91027822 bp Num Contigs Represented = 388 Non ambiguous bp: Initial: 90017136 bp After Masking: 37115565 bp Masked: 58.77 % -- Input Database Coverage: 131435111 bp out of 1089050413 bp ( 12.07 % ) Sampling Time: 00:50:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2720278 Comparison Time: 01:41:06 (hh:mm:ss) Elapsed Time, 126444 HSPs Collected Number of families returned by RECON: 8452 Round Time: 02:35:15 (hh:mm:ss) Elapsed Time : 288 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:40:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 711506 repeats masked totaling 111373319 bp(s). - TE Masking time 00:04:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274263214 bp Num Contigs Represented = 715 Non ambiguous bp: Initial: 270006710 bp After Masking: 104865805 bp Masked: 61.16 % -- Input Database Coverage: 405698325 bp out of 1089050413 bp ( 37.25 % ) Sampling Time: 02:46:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24777280 Comparison Time: 10:26:39 (hh:mm:ss) Elapsed Time, 298978 HSPs Collected Number of families returned by RECON: 26982 Round Time: 13:37:21 (hh:mm:ss) Elapsed Time : 650 families discovered. RepeatScout/RECON discovery complete: 1609 families found Classification Time: 00:33:33 (hh:mm:ss) Elapsed Time Program Time: 17:59:22 (hh:mm:ss) Elapsed Time