RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ELcEkK/RM_27457.TueJul21716232024 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: 1719965775 Database = /dev/shm/rModeler.ELcEkK/GCA_038355195.1_fOsmMor3.pri - Sequences = 365 - Bases = 497673479 - N50 = 18964683 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 24571031-26325141 | [ 1 ] 22816921-24571031 | [ 2 ] 21062811-22816921 | [ 4 ] 19308701-21062811 | [ 2 ] 17554591-19308701 | [ 5 ] 15800481-17554591 | [ 3 ] 14046371-15800481 | [ 3 ] 12292261-14046371 | [ 2 ] 10538151-12292261 | [ 5 ] 8784041-10538151 | [ ] 7029931-8784041 | [ 1 ] 5275821-7029931 | [ ] 3521711-5275821 | [ ] 1767601-3521711 | [ ] 13491-1767601 |************************************************** [ 337 ] Storage Throughput = excellent ( 1028.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045226 bp ( 40015595 non ambiguous ) - Num Contigs Represented = 66 - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:47 (hh:mm:ss) Elapsed Time Round Time: 00:32:11 (hh:mm:ss) Elapsed Time : 383 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5197 repeats masked totaling 1216317 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007815 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10001621 bp After Masking: 7979534 bp Masked: 20.22 % -- Input Database Coverage: 10007815 bp out of 497673479 bp ( 2.01 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:36:30 (hh:mm:ss) Elapsed Time, 8268 HSPs Collected Number of families returned by RECON: 1432 Round Time: 00:39:48 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17859 repeats masked totaling 4192362 bp(s). - TE Masking time 00:00:40 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037408 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30013971 bp After Masking: 22819016 bp Masked: 23.97 % -- Input Database Coverage: 40045223 bp out of 497673479 bp ( 8.05 % ) Sampling Time: 00:04:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 02:11:30 (hh:mm:ss) Elapsed Time, 58398 HSPs Collected Number of families returned by RECON: 5513 Round Time: 02:20:21 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59503 repeats masked totaling 14508273 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90104087 bp Num Contigs Represented = 116 Non ambiguous bp: Initial: 90041328 bp After Masking: 67123026 bp Masked: 25.45 % -- Input Database Coverage: 130149310 bp out of 497673479 bp ( 26.15 % ) Sampling Time: 00:14:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2611755 Comparison Time: 05:59:51 (hh:mm:ss) Elapsed Time, 357210 HSPs Collected Number of families returned by RECON: 20509 Round Time: 06:31:56 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:34:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 228674 repeats masked totaling 55750264 bp(s). - TE Masking time 00:12:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270230412 bp Num Contigs Represented = 237 Non ambiguous bp: Initial: 270034310 bp After Masking: 189304405 bp Masked: 29.90 % -- Input Database Coverage: 400379722 bp out of 497673479 bp ( 80.45 % ) Sampling Time: 00:50:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23396220 Comparison Time: 32:58:33 (hh:mm:ss) Elapsed Time, 1349364 HSPs Collected Number of families returned by RECON: 77639 Round Time: 36:34:27 (hh:mm:ss) Elapsed Time : 760 families discovered. RepeatScout/RECON discovery complete: 1552 families found Classification Time: 01:41:06 (hh:mm:ss) Elapsed Time Program Time: 48:19:49 (hh:mm:ss) Elapsed Time