RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.oxn7C6/RM_383456.MonJan90307112023 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: 1673262430 Database = /dev/shm/rModeler.oxn7C6/GCF_003369695.1_UOA_Brahman_1 - Sequences = 1250 - Bases = 2680953056 - N50 = 106190332 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146480579-156943404 | [ 1 ] 136017755-146480579 | [ 1 ] 125554931-136017755 | [ 1 ] 115092106-125554930 | [ 4 ] 104629282-115092106 | [ 3 ] 94166458-104629282 | [ 2 ] 83703634-94166458 | [ 2 ] 73240809-83703633 | [ 3 ] 62777985-73240809 | [ 4 ] 52315161-62777985 | [ 4 ] 41852337-52315161 | [ 5 ] 31389512-41852336 | [ ] 20926688-31389512 | [ ] 10463864-20926688 | [ ] 1040-10463864 |************************************************** [ 1220 ] Storage Throughput = excellent ( 1608.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40054167 bp ( 40010977 non ambiguous ) - Num Contigs Represented = 59 - Sequence extraction : 00:01:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:31 (hh:mm:ss) Elapsed Time Round Time: 00:17:31 (hh:mm:ss) Elapsed Time : 231 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14640 repeats masked totaling 3242264 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10008967 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10008467 bp After Masking: 6711628 bp Masked: 32.94 % -- Input Database Coverage: 10008967 bp out of 2680953056 bp ( 0.37 % ) Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:40 (hh:mm:ss) Elapsed Time, 5498 HSPs Collected Number of families returned by RECON: 688 Round Time: 00:06:45 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48733 repeats masked totaling 10555897 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30045120 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 30002430 bp After Masking: 19210684 bp Masked: 35.97 % -- Input Database Coverage: 40054087 bp out of 2680953056 bp ( 1.49 % ) Sampling Time: 00:02:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:23:45 (hh:mm:ss) Elapsed Time, 22614 HSPs Collected Number of families returned by RECON: 2211 Round Time: 00:27:18 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 155824 repeats masked totaling 34693705 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90052501 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 90009877 bp After Masking: 54742969 bp Masked: 39.18 % -- Input Database Coverage: 130106588 bp out of 2680953056 bp ( 4.85 % ) Sampling Time: 00:07:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:53:45 (hh:mm:ss) Elapsed Time, 75871 HSPs Collected Number of families returned by RECON: 7724 Round Time: 02:03:14 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 502123 repeats masked totaling 110479909 bp(s). - TE Masking time 00:03:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270261138 bp Num Contigs Represented = 192 Non ambiguous bp: Initial: 270003724 bp After Masking: 157960505 bp Masked: 41.50 % -- Input Database Coverage: 400367726 bp out of 2680953056 bp ( 14.93 % ) Sampling Time: 00:25:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 12:39:15 (hh:mm:ss) Elapsed Time, 174343 HSPs Collected Number of families returned by RECON: 31790 Round Time: 13:18:05 (hh:mm:ss) Elapsed Time : 314 families discovered. RepeatScout/RECON discovery complete: 808 families found Classification Time: 00:21:00 (hh:mm:ss) Elapsed Time Program Time: 16:33:53 (hh:mm:ss) Elapsed Time