RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.DpgeIE/RM_3410117.SunJul280429082024 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: 1722166148 Database = /dev/shm/rModeler.DpgeIE/GCF_021292245.1_ASM2129224v1 - Sequences = 15020 - Bases = 829587215 - N50 = 35274882 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 51476625-55153512 | [ 1 ] 47799738-51476625 | [ ] 44122851-47799738 | [ ] 40445964-44122851 | [ ] 36769077-40445964 | [ 4 ] 33092190-36769077 | [ 8 ] 29415303-33092190 | [ 7 ] 25738416-29415303 | [ 1 ] 22061529-25738416 | [ 2 ] 18384642-22061529 | [ ] 14707755-18384642 | [ ] 11030868-14707755 | [ ] 7353981-11030868 | [ ] 3677094-7353981 | [ ] 207-3677094 |************************************************** [ 14997 ] Storage Throughput = excellent ( 1184.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40136824 bp ( 40007172 non ambiguous ) - Num Contigs Represented = 776 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:57 (hh:mm:ss) Elapsed Time Round Time: 00:19:02 (hh:mm:ss) Elapsed Time : 1032 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13938 repeats masked totaling 1942620 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10066013 bp Num Contigs Represented = 207 Non ambiguous bp: Initial: 10035525 bp After Masking: 7879830 bp Masked: 21.48 % -- Input Database Coverage: 10066013 bp out of 829587215 bp ( 1.21 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 88831 Comparison Time: 00:06:49 (hh:mm:ss) Elapsed Time, 8881 HSPs Collected Number of families returned by RECON: 1867 Round Time: 00:08:00 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42757 repeats masked totaling 6199846 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30111678 bp Num Contigs Represented = 593 Non ambiguous bp: Initial: 30012214 bp After Masking: 23193047 bp Masked: 22.72 % -- Input Database Coverage: 40177691 bp out of 829587215 bp ( 4.84 % ) Sampling Time: 00:02:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 822403 Comparison Time: 00:31:42 (hh:mm:ss) Elapsed Time, 60176 HSPs Collected Number of families returned by RECON: 6260 Round Time: 00:36:15 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143023 repeats masked totaling 21793787 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90440228 bp Num Contigs Represented = 1704 Non ambiguous bp: Initial: 90035898 bp After Masking: 66456081 bp Masked: 26.19 % -- Input Database Coverage: 130617919 bp out of 829587215 bp ( 15.74 % ) Sampling Time: 00:07:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 7237110 Comparison Time: 03:12:37 (hh:mm:ss) Elapsed Time, 336045 HSPs Collected Number of families returned by RECON: 19904 Round Time: 03:34:16 (hh:mm:ss) Elapsed Time : 685 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 512533 repeats masked totaling 80591925 bp(s). - TE Masking time 00:10:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270936185 bp Num Contigs Represented = 4835 Non ambiguous bp: Initial: 270007707 bp After Masking: 184526778 bp Masked: 31.66 % -- Input Database Coverage: 401554104 bp out of 829587215 bp ( 48.40 % ) Sampling Time: 00:27:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 63050835 Comparison Time: 21:30:28 (hh:mm:ss) Elapsed Time, 834586 HSPs Collected Number of families returned by RECON: 66141 Round Time: 23:23:36 (hh:mm:ss) Elapsed Time : 1460 families discovered. RepeatScout/RECON discovery complete: 3366 families found Classification Time: 01:36:57 (hh:mm:ss) Elapsed Time Program Time: 29:38:06 (hh:mm:ss) Elapsed Time