RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SqO7vR/RM_221514.SatDec311118362022 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: 1672514314 Database = /dev/shm/rModeler.SqO7vR/GCA_014839995.1_fXenCan1.pri - Sequences = 410 - Bases = 736214936 - N50 = 29948867 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 34028216-36457923 | [ 2 ] 31598509-34028215 | [ 5 ] 29168803-31598509 | [ 4 ] 26739096-29168802 | [ 7 ] 24309389-26739095 | [ 4 ] 21879683-24309389 | [ 2 ] 19449976-21879682 | [ ] 17020269-19449975 | [ ] 14590563-17020269 | [ ] 12160856-14590562 | [ ] 9731149-12160855 | [ ] 7301443-9731149 | [ ] 4871736-7301442 | [ 1 ] 2442029-4871735 | [ ] 12323-2442029 |************************************************** [ 385 ] Storage Throughput = excellent ( 1672.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40393282 bp ( 40007937 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:37 (hh:mm:ss) Elapsed Time Round Time: 00:16:07 (hh:mm:ss) Elapsed Time : 401 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7302 repeats masked totaling 1467273 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10094414 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10027637 bp After Masking: 7993356 bp Masked: 20.29 % -- Input Database Coverage: 10094414 bp out of 736214936 bp ( 1.37 % ) Sampling Time: 00:01:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:05:50 (hh:mm:ss) Elapsed Time, 7745 HSPs Collected Number of families returned by RECON: 1379 Round Time: 00:07:09 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24464 repeats masked totaling 5130010 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30338868 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30020200 bp After Masking: 23264086 bp Masked: 22.51 % -- Input Database Coverage: 40433282 bp out of 736214936 bp ( 5.49 % ) Sampling Time: 00:03:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:25:41 (hh:mm:ss) Elapsed Time, 43320 HSPs Collected Number of families returned by RECON: 4368 Round Time: 00:29:56 (hh:mm:ss) Elapsed Time : 119 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86309 repeats masked totaling 17086818 bp(s). - TE Masking time 00:01:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91288616 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 90037483 bp After Masking: 68388100 bp Masked: 24.04 % -- Input Database Coverage: 131721898 bp out of 736214936 bp ( 17.89 % ) Sampling Time: 00:09:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2650753 Comparison Time: 02:36:32 (hh:mm:ss) Elapsed Time, 192158 HSPs Collected Number of families returned by RECON: 14651 Round Time: 02:52:17 (hh:mm:ss) Elapsed Time : 365 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 315081 repeats masked totaling 64176558 bp(s). - TE Masking time 00:05:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272733557 bp Num Contigs Represented = 208 Non ambiguous bp: Initial: 270015102 bp After Masking: 191926887 bp Masked: 28.92 % -- Input Database Coverage: 404455455 bp out of 736214936 bp ( 54.94 % ) Sampling Time: 00:31:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23650003 Comparison Time: 16:45:11 (hh:mm:ss) Elapsed Time, 620648 HSPs Collected Number of families returned by RECON: 55584 Round Time: 18:02:01 (hh:mm:ss) Elapsed Time : 1007 families discovered. RepeatScout/RECON discovery complete: 1912 families found Classification Time: 01:11:21 (hh:mm:ss) Elapsed Time Program Time: 22:58:51 (hh:mm:ss) Elapsed Time