RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.rO8KPD/RM_399697.SunNov170449412024 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: 1731847779 Database = /scratch/tmp/rModeler.rO8KPD/GCF_036013445.1_bCalNic1.hap1 - Sequences = 806 - Bases = 1285834579 - N50 = 110148392 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202003808-216431472 | [ 1 ] 187576145-202003808 | [ ] 173148481-187576144 | [ ] 158720818-173148481 | [ 1 ] 144293155-158720818 | [ ] 129865491-144293154 | [ ] 115437828-129865491 | [ 1 ] 101010164-115437827 | [ 1 ] 86582501-101010164 | [ ] 72154838-86582501 | [ 1 ] 57727174-72154837 | [ 1 ] 43299511-57727174 | [ ] 28871847-43299510 | [ 3 ] 14444184-28871847 | [ 8 ] 16521-14444184 |************************************************** [ 789 ] Storage Throughput = excellent ( 1465.05 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40001014 bp ( 40000114 non ambiguous ) - Num Contigs Represented = 123 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:20 (hh:mm:ss) Elapsed Time Round Time: 00:10:54 (hh:mm:ss) Elapsed Time : 92 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2355 repeats masked totaling 928302 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011849 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 10011649 bp After Masking: 8151722 bp Masked: 18.58 % -- Input Database Coverage: 10011849 bp out of 1285834579 bp ( 0.78 % ) Sampling Time: 00:03:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:56 (hh:mm:ss) Elapsed Time, 690 HSPs Collected Number of families returned by RECON: 205 Round Time: 00:06:17 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6853 repeats masked totaling 2587862 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023485 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 30022785 bp After Masking: 25170789 bp Masked: 16.16 % -- Input Database Coverage: 40035334 bp out of 1285834579 bp ( 3.11 % ) Sampling Time: 00:08:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:13:19 (hh:mm:ss) Elapsed Time, 7832 HSPs Collected Number of families returned by RECON: 1219 Round Time: 00:21:42 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22943 repeats masked totaling 8144141 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90024548 bp Num Contigs Represented = 221 Non ambiguous bp: Initial: 90024048 bp After Masking: 74317751 bp Masked: 17.45 % -- Input Database Coverage: 130059882 bp out of 1285834579 bp ( 10.11 % ) Sampling Time: 00:27:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 01:25:21 (hh:mm:ss) Elapsed Time, 94247 HSPs Collected Number of families returned by RECON: 7200 Round Time: 01:54:26 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:07:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76847 repeats masked totaling 27126682 bp(s). - TE Masking time 00:01:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270005025 bp Num Contigs Represented = 423 Non ambiguous bp: Initial: 270000242 bp After Masking: 221384651 bp Masked: 18.01 % -- Input Database Coverage: 400064907 bp out of 1285834579 bp ( 31.11 % ) Sampling Time: 01:16:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23314206 Comparison Time: 10:25:10 (hh:mm:ss) Elapsed Time, 871390 HSPs Collected Number of families returned by RECON: 47586 Round Time: 11:55:59 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatScout/RECON discovery complete: 399 families found Classification Time: 00:14:53 (hh:mm:ss) Elapsed Time Program Time: 14:44:11 (hh:mm:ss) Elapsed Time