RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.JsdJmH/RM_6637.ThuJul40521212024 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: 1720095681 Database = /dev/shm/rModeler.JsdJmH/GCF_000239395.1_NeoBri1.0 - Sequences = 9083 - Bases = 847883811 - N50 = 4459736 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 22251195-23840500 | [ 1 ] 20661890-22251194 | [ ] 19072586-20661890 | [ 2 ] 17483281-19072585 | [ ] 15893977-17483281 | [ 1 ] 14304672-15893976 | [ 3 ] 12715368-14304672 | [ 2 ] 11126063-12715367 | [ 3 ] 9536759-11126063 | [ 4 ] 7947454-9536758 | [ 2 ] 6358150-7947454 | [ 9 ] 4768845-6358149 | [ 13 ] 3179541-4768845 | [ 33 ] 1590236-3179540 | [ 64 ] 932-1590236 |************************************************** [ 8946 ] Storage Throughput = excellent ( 1034.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 49498489 bp ( 40024043 non ambiguous ) - Num Contigs Represented = 830 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:03 (hh:mm:ss) Elapsed Time Round Time: 00:23:52 (hh:mm:ss) Elapsed Time : 560 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 00:00:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10323 repeats masked totaling 1302113 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 12270228 bp Num Contigs Represented = 299 Non ambiguous bp: Initial: 10015040 bp After Masking: 8671511 bp Masked: 13.42 % -- Input Database Coverage: 12270228 bp out of 847883811 bp ( 1.45 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 99681 Comparison Time: 00:07:35 (hh:mm:ss) Elapsed Time, 8129 HSPs Collected Number of families returned by RECON: 1466 Round Time: 00:08:24 (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 : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30526 repeats masked totaling 3925523 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 37228181 bp Num Contigs Represented = 653 Non ambiguous bp: Initial: 30008923 bp After Masking: 25954889 bp Masked: 13.51 % -- Input Database Coverage: 49498409 bp out of 847883811 bp ( 5.84 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 831405 Comparison Time: 00:42:32 (hh:mm:ss) Elapsed Time, 62975 HSPs Collected Number of families returned by RECON: 5404 Round Time: 00:46:02 (hh:mm:ss) Elapsed Time : 127 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104689 repeats masked totaling 14588064 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 110871232 bp Num Contigs Represented = 1520 Non ambiguous bp: Initial: 90022418 bp After Masking: 75067599 bp Masked: 16.61 % -- Input Database Coverage: 160369641 bp out of 847883811 bp ( 18.91 % ) Sampling Time: 00:04:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 7451730 Comparison Time: 05:00:35 (hh:mm:ss) Elapsed Time, 239337 HSPs Collected Number of families returned by RECON: 17818 Round Time: 05:18:40 (hh:mm:ss) Elapsed Time : 415 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 376253 repeats masked totaling 54698552 bp(s). - TE Masking time 00:09:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 335381027 bp Num Contigs Represented = 3892 Non ambiguous bp: Initial: 270008943 bp After Masking: 214224115 bp Masked: 20.66 % -- Input Database Coverage: 495750668 bp out of 847883811 bp ( 58.47 % ) Sampling Time: 00:18:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 66891961 Comparison Time: 40:24:26 (hh:mm:ss) Elapsed Time, 669398 HSPs Collected Number of families returned by RECON: 70991 Round Time: 42:53:56 (hh:mm:ss) Elapsed Time : 1007 families discovered. RepeatScout/RECON discovery complete: 2121 families found Classification Time: 01:13:53 (hh:mm:ss) Elapsed Time Program Time: 50:44:47 (hh:mm:ss) Elapsed Time