RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.tc7jur/RM_6318.FriDec10942352023 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: 1701452548 Database = /dev/shm/rModeler.tc7jur/GCA_030020305.1_mLoxAfr1.hap1 - Sequences = 1084 - Bases = 3575747632 - N50 = 123319788 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 608888783-652380084 | [ 1 ] 565397482-608888783 | [ ] 521906181-565397482 | [ ] 478414880-521906181 | [ ] 434923579-478414880 | [ ] 391432278-434923579 | [ ] 347940977-391432278 | [ ] 304449676-347940977 | [ ] 260958375-304449676 | [ ] 217467074-260958375 | [ 1 ] 173975773-217467074 | [ ] 130484472-173975773 | [ 4 ] 86993171-130484472 | [ 8 ] 43501870-86993171 | [ 11 ] 10569-43501870 |************************************************** [ 1059 ] Storage Throughput = excellent ( 1213.88 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017030 bp ( 40017030 non ambiguous ) - Num Contigs Represented = 123 - Sequence extraction : 00:04:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:40 (hh:mm:ss) Elapsed Time Round Time: 00:45:59 (hh:mm:ss) Elapsed Time : 321 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16761 repeats masked totaling 4773310 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003796 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10003796 bp After Masking: 4960033 bp Masked: 50.42 % -- Input Database Coverage: 10003796 bp out of 3575747632 bp ( 0.28 % ) Sampling Time: 00:02:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:45:29 (hh:mm:ss) Elapsed Time, 58157 HSPs Collected Number of families returned by RECON: 662 Round Time: 00:49:22 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 51820 repeats masked totaling 13863151 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013231 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 30013231 bp After Masking: 14991669 bp Masked: 50.05 % -- Input Database Coverage: 40017027 bp out of 3575747632 bp ( 1.12 % ) Sampling Time: 00:10:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 01:21:05 (hh:mm:ss) Elapsed Time, 418391 HSPs Collected Number of families returned by RECON: 1852 Round Time: 01:33:46 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 165821 repeats masked totaling 44485283 bp(s). - TE Masking time 00:02:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90062166 bp Num Contigs Represented = 199 Non ambiguous bp: Initial: 90009443 bp After Masking: 42735899 bp Masked: 52.52 % -- Input Database Coverage: 130079193 bp out of 3575747632 bp ( 3.64 % ) Sampling Time: 00:23:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 03:39:58 (hh:mm:ss) Elapsed Time, 3120838 HSPs Collected Number of families returned by RECON: 6243 Round Time: 04:15:48 (hh:mm:ss) Elapsed Time : 161 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:28:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 522573 repeats masked totaling 139923324 bp(s). - TE Masking time 00:09:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270419102 bp Num Contigs Represented = 379 Non ambiguous bp: Initial: 270006096 bp After Masking: 121415707 bp Masked: 55.03 % -- Input Database Coverage: 400498295 bp out of 3575747632 bp ( 11.20 % ) Sampling Time: 01:14:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23096206 Comparison Time: 26:06:44 (hh:mm:ss) Elapsed Time, 30527275 HSPs Collected Number of families returned by RECON: 22698 Round Time: 27:55:00 (hh:mm:ss) Elapsed Time : 426 families discovered. RepeatScout/RECON discovery complete: 969 families found Classification Time: 00:48:12 (hh:mm:ss) Elapsed Time Program Time: 36:08:07 (hh:mm:ss) Elapsed Time