RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Ge8JQk/RM_19649.MonJul81153162024 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: 1720464794 Database = /dev/shm/rModeler.Ge8JQk/GCF_001515645.1_SAMN03320097.WGS_v1.1 - Sequences = 31277 - Bases = 1750287761 - N50 = 1160397 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 8437607-9040279 | [ 1 ] 7834935-8437606 | [ ] 7232263-7834934 | [ ] 6629591-7232262 | [ 2 ] 6026919-6629590 | [ 1 ] 5424247-6026918 | [ 3 ] 4821575-5424246 | [ 6 ] 4218903-4821574 | [ 10 ] 3616231-4218902 | [ 17 ] 3013559-3616230 | [ 23 ] 2410887-3013558 | [ 42 ] 1808215-2410886 | [ 90 ] 1205543-1808214 | [ 197 ] 602871-1205542 | [ 418 ] 200-602871 |************************************************** [ 30467 ] Storage Throughput = excellent ( 1051.99 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 44798944 bp ( 40031309 non ambiguous ) - Num Contigs Represented = 1468 - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:02 (hh:mm:ss) Elapsed Time Round Time: 00:26:44 (hh:mm:ss) Elapsed Time : 1187 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18438 repeats masked totaling 2965326 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11260518 bp Num Contigs Represented = 415 Non ambiguous bp: Initial: 10024799 bp After Masking: 6859207 bp Masked: 31.58 % -- Input Database Coverage: 11260518 bp out of 1750287761 bp ( 0.64 % ) Sampling Time: 00:01:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 99681 Comparison Time: 00:07:33 (hh:mm:ss) Elapsed Time, 9579 HSPs Collected Number of families returned by RECON: 1632 Round Time: 00:09:50 (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 : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55665 repeats masked totaling 8962761 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 33538346 bp Num Contigs Represented = 1162 Non ambiguous bp: Initial: 30006430 bp After Masking: 20493980 bp Masked: 31.70 % -- Input Database Coverage: 44798864 bp out of 1750287761 bp ( 2.56 % ) Sampling Time: 00:03:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 957036 Comparison Time: 00:38:28 (hh:mm:ss) Elapsed Time, 54563 HSPs Collected Number of families returned by RECON: 5835 Round Time: 00:44:14 (hh:mm:ss) Elapsed Time : 140 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 179799 repeats masked totaling 28619588 bp(s). - TE Masking time 00:03:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 100564226 bp Num Contigs Represented = 2863 Non ambiguous bp: Initial: 90000971 bp After Masking: 59788915 bp Masked: 33.57 % -- Input Database Coverage: 145363090 bp out of 1750287761 bp ( 8.31 % ) Sampling Time: 00:09:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 8166861 Comparison Time: 04:21:54 (hh:mm:ss) Elapsed Time, 365952 HSPs Collected Number of families returned by RECON: 18138 Round Time: 04:50:46 (hh:mm:ss) Elapsed Time : 737 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 633860 repeats masked totaling 102681352 bp(s). - TE Masking time 00:20:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 300963666 bp Num Contigs Represented = 6783 Non ambiguous bp: Initial: 270006281 bp After Masking: 162269475 bp Masked: 39.90 % -- Input Database Coverage: 446326756 bp out of 1750287761 bp ( 25.50 % ) Sampling Time: 00:36:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 72282276 Comparison Time: 31:45:21 (hh:mm:ss) Elapsed Time, 838825 HSPs Collected Number of families returned by RECON: 60238 Round Time: 34:26:50 (hh:mm:ss) Elapsed Time : 1323 families discovered. RepeatScout/RECON discovery complete: 3402 families found Classification Time: 01:59:37 (hh:mm:ss) Elapsed Time Program Time: 42:38:01 (hh:mm:ss) Elapsed Time