RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.4aA616/RM_1507891.MonJan131454522025 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: 1736808890 Database = /data/tmp/rModeler.4aA616/GCA_964270355.1_Elg.assembly.v.1.0 - Sequences = 1737 - Bases = 2545527011 - N50 = 44645339 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 97866395-104856839 | [ 1 ] 90875951-97866395 | [ 1 ] 83885507-90875951 | [ ] 76895063-83885507 | [ ] 69904619-76895063 | [ 1 ] 62914175-69904619 | [ 2 ] 55923731-62914175 | [ 5 ] 48933287-55923731 | [ 5 ] 41942843-48933287 | [ 9 ] 34952399-41942843 | [ 7 ] 27961955-34952399 | [ 5 ] 20971511-27961955 | [ 6 ] 13981067-20971511 | [ 13 ] 6990623-13981067 | [ 16 ] 179-6990623 |************************************************** [ 1666 ] Storage Throughput = excellent ( 1269.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022859 bp ( 40022859 non ambiguous ) - Num Contigs Represented = 147 - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:01 (hh:mm:ss) Elapsed Time Round Time: 00:15:20 (hh:mm:ss) Elapsed Time : 228 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13052 repeats masked totaling 2792613 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001771 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 10001771 bp After Masking: 7165786 bp Masked: 28.35 % -- Input Database Coverage: 10001771 bp out of 2545527011 bp ( 0.39 % ) Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:02:40 (hh:mm:ss) Elapsed Time, 18403 HSPs Collected Number of families returned by RECON: 824 Round Time: 00:03:06 (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 : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42574 repeats masked totaling 9545978 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021063 bp Num Contigs Represented = 129 Non ambiguous bp: Initial: 30021063 bp After Masking: 20254465 bp Masked: 32.53 % -- Input Database Coverage: 40022834 bp out of 2545527011 bp ( 1.57 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 294528 Comparison Time: 00:14:46 (hh:mm:ss) Elapsed Time, 87691 HSPs Collected Number of families returned by RECON: 2174 Round Time: 00:16:10 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 136066 repeats masked totaling 30766654 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90021457 bp Num Contigs Represented = 198 Non ambiguous bp: Initial: 90021457 bp After Masking: 58767233 bp Masked: 34.72 % -- Input Database Coverage: 130044291 bp out of 2545527011 bp ( 5.11 % ) Sampling Time: 00:02:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2616328 Comparison Time: 01:44:00 (hh:mm:ss) Elapsed Time, 2078535 HSPs Collected Number of families returned by RECON: 8039 Round Time: 01:48:55 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 449519 repeats masked totaling 100413312 bp(s). - TE Masking time 00:03:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270016791 bp Num Contigs Represented = 352 Non ambiguous bp: Initial: 270016791 bp After Masking: 168248393 bp Masked: 37.69 % -- Input Database Coverage: 400061082 bp out of 2545527011 bp ( 15.72 % ) Sampling Time: 00:10:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23485231 Comparison Time: 10:52:58 (hh:mm:ss) Elapsed Time, 16067163 HSPs Collected Number of families returned by RECON: 33197 Round Time: 11:14:35 (hh:mm:ss) Elapsed Time : 336 families discovered. RepeatScout/RECON discovery complete: 823 families found Classification Time: 00:13:23 (hh:mm:ss) Elapsed Time Program Time: 13:51:29 (hh:mm:ss) Elapsed Time