RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.zPlVg1/RM_8156.SatJul132239192024 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: 1720935557 Database = /dev/shm/rModeler.zPlVg1/GCF_003711565.1_ASM371156v2 - Sequences = 868 - Bases = 366303280 - N50 = 15776270 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 26915982-28838366 | [ 1 ] 24993598-26915981 | [ ] 23071215-24993598 | [ ] 21148831-23071214 | [ ] 19226447-21148830 | [ 1 ] 17304064-19226447 | [ 3 ] 15381680-17304063 | [ 10 ] 13459296-15381679 | [ 1 ] 11536913-13459296 | [ 5 ] 9614529-11536912 | [ 1 ] 7692145-9614528 | [ ] 5769762-7692145 | [ ] 3847378-5769761 | [ ] 1924994-3847377 | [ ] 2611-1924994 |************************************************* [ 846 ] Storage Throughput = excellent ( 1024.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033202 bp ( 40031300 non ambiguous ) - Num Contigs Represented = 117 - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:19 (hh:mm:ss) Elapsed Time Round Time: 00:25:44 (hh:mm:ss) Elapsed Time : 183 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 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2421 repeats masked totaling 814822 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10012435 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10012134 bp After Masking: 8835761 bp Masked: 11.75 % -- Input Database Coverage: 10012435 bp out of 366303280 bp ( 2.73 % ) Sampling Time: 00:00:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34453 Comparison Time: 00:06:01 (hh:mm:ss) Elapsed Time, 1587 HSPs Collected Number of families returned by RECON: 619 Round Time: 00:07:03 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7140 repeats masked totaling 2559303 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020687 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 30019086 bp After Masking: 26215300 bp Masked: 12.67 % -- Input Database Coverage: 40033122 bp out of 366303280 bp ( 10.93 % ) Sampling Time: 00:03:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 318003 Comparison Time: 00:32:41 (hh:mm:ss) Elapsed Time, 14824 HSPs Collected Number of families returned by RECON: 2958 Round Time: 00:36:32 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 23403 repeats masked totaling 7497203 bp(s). - TE Masking time 00:01:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045853 bp Num Contigs Represented = 251 Non ambiguous bp: Initial: 90039052 bp After Masking: 79062874 bp Masked: 12.19 % -- Input Database Coverage: 130078975 bp out of 366303280 bp ( 35.51 % ) Sampling Time: 00:08:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2886003 Comparison Time: 03:54:11 (hh:mm:ss) Elapsed Time, 116590 HSPs Collected Number of families returned by RECON: 14817 Round Time: 04:16:01 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76969 repeats masked totaling 25088779 bp(s). - TE Masking time 00:05:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 236223956 bp Num Contigs Represented = 586 Non ambiguous bp: Initial: 236208253 bp After Masking: 201431859 bp Masked: 14.72 % -- Input Database Coverage: 366302931 bp out of 366303280 bp ( 100.00 % ) Sampling Time: 00:27:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 19678401 Comparison Time: 23:45:17 (hh:mm:ss) Elapsed Time, 421722 HSPs Collected Number of families returned by RECON: 58232 Round Time: 25:23:35 (hh:mm:ss) Elapsed Time : 426 families discovered. RepeatScout/RECON discovery complete: 815 families found Classification Time: 01:10:00 (hh:mm:ss) Elapsed Time Program Time: 31:58:55 (hh:mm:ss) Elapsed Time