RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2GLkV0/RM_2014270.FriApr250716272025 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: 1745590586 Database = /dev/shm/rModeler.2GLkV0/GCA_048301465.1_ASM4830146v1 - Sequences = 160 - Bases = 662945422 - N50 = 28719643 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32468713-34787836 | [ 1 ] 30149591-32468713 |* [ 5 ] 27830468-30149590 |* [ 5 ] 25511346-27830468 |** [ 6 ] 23192224-25511346 |* [ 4 ] 20873101-23192223 | [ 1 ] 18553979-20873101 | [ ] 16234856-18553978 | [ 1 ] 13915734-16234856 | [ ] 11596612-13915734 | [ 1 ] 9277489-11596611 | [ ] 6958367-9277489 | [ ] 4639244-6958366 | [ 1 ] 2320122-4639244 | [ ] 1000-2320122 |************************************************** [ 135 ] Storage Throughput = excellent ( 1891.92 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019869 bp ( 40019169 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:47 (hh:mm:ss) Elapsed Time Round Time: 00:09:44 (hh:mm:ss) Elapsed Time : 229 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5075 repeats masked totaling 964506 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004778 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10004478 bp After Masking: 8503998 bp Masked: 15.00 % -- Input Database Coverage: 10004778 bp out of 662945422 bp ( 1.51 % ) Sampling Time: 00:00:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:44 (hh:mm:ss) Elapsed Time, 5946 HSPs Collected Number of families returned by RECON: 1367 Round Time: 00:03:39 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15802 repeats masked totaling 3033950 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30015011 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 30014611 bp After Masking: 25003185 bp Masked: 16.70 % -- Input Database Coverage: 40019789 bp out of 662945422 bp ( 6.04 % ) Sampling Time: 00:02:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:12:34 (hh:mm:ss) Elapsed Time, 44487 HSPs Collected Number of families returned by RECON: 5543 Round Time: 00:15:42 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59028 repeats masked totaling 10557176 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90009046 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 90006846 bp After Masking: 73659470 bp Masked: 18.16 % -- Input Database Coverage: 130028835 bp out of 662945422 bp ( 19.61 % ) Sampling Time: 00:08:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 01:17:58 (hh:mm:ss) Elapsed Time, 182909 HSPs Collected Number of families returned by RECON: 19753 Round Time: 01:30:50 (hh:mm:ss) Elapsed Time : 367 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 230416 repeats masked totaling 42904615 bp(s). - TE Masking time 00:02:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270047000 bp Num Contigs Represented = 116 Non ambiguous bp: Initial: 270038600 bp After Masking: 209542017 bp Masked: 22.40 % -- Input Database Coverage: 400075835 bp out of 662945422 bp ( 60.35 % ) Sampling Time: 00:27:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 09:49:25 (hh:mm:ss) Elapsed Time, 901745 HSPs Collected Number of families returned by RECON: 77073 Round Time: 11:06:46 (hh:mm:ss) Elapsed Time : 1046 families discovered. RepeatScout/RECON discovery complete: 1750 families found Classification Time: 00:42:04 (hh:mm:ss) Elapsed Time Program Time: 13:48:45 (hh:mm:ss) Elapsed Time