RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.6RFViR/RM_3353799.SatJul190821392025 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: 1752938497 Database = /dev/shm/rModeler.6RFViR/GCA_048544195.1_ASM4854419v1 - Sequences = 567 - Bases = 553547304 - N50 = 23329580 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 27965107-29962544 | [ 3 ] 25967671-27965107 | [ ] 23970235-25967671 | [ 6 ] 21972798-23970234 | [ 4 ] 19975362-21972798 | [ 5 ] 17977926-19975362 | [ 4 ] 15980490-17977926 | [ 1 ] 13983053-15980489 | [ ] 11985617-13983053 | [ ] 9988181-11985617 | [ 1 ] 7990745-9988181 | [ ] 5993308-7990744 | [ ] 3995872-5993308 | [ ] 1998436-3995872 | [ ] 1000-1998436 |************************************************** [ 543 ] Storage Throughput = excellent ( 1899.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020971 bp ( 40014971 non ambiguous ) - Num Contigs Represented = 80 - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:03 (hh:mm:ss) Elapsed Time Round Time: 00:10:57 (hh:mm:ss) Elapsed Time : 297 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (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... 4598 repeats masked totaling 917813 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041338 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 10039738 bp After Masking: 8212973 bp Masked: 18.20 % -- Input Database Coverage: 10041338 bp out of 553547304 bp ( 1.81 % ) Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:02:46 (hh:mm:ss) Elapsed Time, 2763 HSPs Collected Number of families returned by RECON: 614 Round Time: 00:03:48 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12663 repeats masked totaling 2796003 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019540 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 30015140 bp After Masking: 24981865 bp Masked: 16.77 % -- Input Database Coverage: 40060878 bp out of 553547304 bp ( 7.24 % ) Sampling Time: 00:02:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:12:50 (hh:mm:ss) Elapsed Time, 15138 HSPs Collected Number of families returned by RECON: 2611 Round Time: 00:15:18 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38125 repeats masked totaling 8262828 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025756 bp Num Contigs Represented = 123 Non ambiguous bp: Initial: 90014160 bp After Masking: 75862081 bp Masked: 15.72 % -- Input Database Coverage: 130086634 bp out of 553547304 bp ( 23.50 % ) Sampling Time: 00:06:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2639253 Comparison Time: 01:23:41 (hh:mm:ss) Elapsed Time, 135312 HSPs Collected Number of families returned by RECON: 12055 Round Time: 01:32:19 (hh:mm:ss) Elapsed Time : 232 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151119 repeats masked totaling 33055005 bp(s). - TE Masking time 00:02:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270042306 bp Num Contigs Represented = 329 Non ambiguous bp: Initial: 270002402 bp After Masking: 217641722 bp Masked: 19.39 % -- Input Database Coverage: 400128940 bp out of 553547304 bp ( 72.28 % ) Sampling Time: 00:21:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23932821 Comparison Time: 10:16:25 (hh:mm:ss) Elapsed Time, 537972 HSPs Collected Number of families returned by RECON: 56798 Round Time: 11:01:07 (hh:mm:ss) Elapsed Time : 680 families discovered. RepeatScout/RECON discovery complete: 1245 families found Classification Time: 00:35:29 (hh:mm:ss) Elapsed Time Program Time: 13:38:58 (hh:mm:ss) Elapsed Time