RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qlNLnY/RM_3674133.SatJul200008462024 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: 1721459321 Database = /dev/shm/rModeler.qlNLnY/GCF_023375975.1_AstMex3_surface - Sequences = 109 - Bases = 1373169186 - N50 = 52709103 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 125086559-134019835 | [ 1 ] 116153283-125086558 | [ ] 107220008-116153283 | [ ] 98286732-107220007 | [ ] 89353456-98286731 | [ ] 80420181-89353456 | [ ] 71486905-80420180 | [ 1 ] 62553629-71486904 | [ 1 ] 53620354-62553629 |*** [ 6 ] 44687078-53620353 |**** [ 8 ] 35753802-44687077 |** [ 5 ] 26820527-35753802 |* [ 3 ] 17887251-26820526 | [ ] 8953975-17887250 | [ ] 20700-8953975 |************************************************** [ 84 ] Storage Throughput = good ( 786.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009898 bp ( 40009898 non ambiguous ) - Num Contigs Represented = 45 - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:47 (hh:mm:ss) Elapsed Time Round Time: 00:32:47 (hh:mm:ss) Elapsed Time : 905 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18936 repeats masked totaling 3304264 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001287 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10001287 bp After Masking: 5745700 bp Masked: 42.55 % -- Input Database Coverage: 10001287 bp out of 1373169186 bp ( 0.73 % ) Sampling Time: 00:03:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:24:20 (hh:mm:ss) Elapsed Time, 16423 HSPs Collected Number of families returned by RECON: 1625 Round Time: 00:28:38 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59308 repeats masked totaling 9722078 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008531 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30008531 bp After Masking: 17769980 bp Masked: 40.78 % -- Input Database Coverage: 40009818 bp out of 1373169186 bp ( 2.91 % ) Sampling Time: 00:08:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 01:13:09 (hh:mm:ss) Elapsed Time, 76328 HSPs Collected Number of families returned by RECON: 5678 Round Time: 01:24:57 (hh:mm:ss) Elapsed Time : 150 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 189852 repeats masked totaling 31289900 bp(s). - TE Masking time 00:02:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034609 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90034609 bp After Masking: 50436499 bp Masked: 43.98 % -- Input Database Coverage: 130044427 bp out of 1373169186 bp ( 9.47 % ) Sampling Time: 00:27:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 04:18:29 (hh:mm:ss) Elapsed Time, 339676 HSPs Collected Number of families returned by RECON: 16380 Round Time: 05:01:31 (hh:mm:ss) Elapsed Time : 605 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:09:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 656010 repeats masked totaling 108711901 bp(s). - TE Masking time 00:13:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034435 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270032434 bp After Masking: 134654763 bp Masked: 50.13 % -- Input Database Coverage: 400078862 bp out of 1373169186 bp ( 29.14 % ) Sampling Time: 01:27:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 21:18:49 (hh:mm:ss) Elapsed Time, 888906 HSPs Collected Number of families returned by RECON: 45995 Round Time: 23:43:56 (hh:mm:ss) Elapsed Time : 1215 families discovered. RepeatScout/RECON discovery complete: 2910 families found Classification Time: 01:44:44 (hh:mm:ss) Elapsed Time Program Time: 32:56:33 (hh:mm:ss) Elapsed Time