RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.UHHW0k/RM_7091.FriJul122006532024 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: 1720840012 Database = /dev/shm/rModeler.UHHW0k/GCF_002910315.2_ASM291031v2 - Sequences = 15253 - Bases = 2169549916 - N50 = 37080635 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 84484858-90519428 | [ 1 ] 78450289-84484858 | [ 1 ] 72415719-78450288 | [ 1 ] 66381150-72415719 | [ 1 ] 60346581-66381150 | [ ] 54312011-60346580 | [ 2 ] 48277442-54312011 | [ 5 ] 42242872-48277441 | [ 2 ] 36208303-42242872 | [ 8 ] 30173734-36208303 | [ 6 ] 24139164-30173733 | [ 5 ] 18104595-24139164 | [ 3 ] 12070025-18104594 | [ 1 ] 6035456-12070025 | [ 3 ] 887-6035456 |************************************************** [ 15214 ] Storage Throughput = excellent ( 1156.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43066789 bp ( 40018675 non ambiguous ) - Num Contigs Represented = 569 - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:38 (hh:mm:ss) Elapsed Time Round Time: 00:23:43 (hh:mm:ss) Elapsed Time : 906 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16142 repeats masked totaling 4245350 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10713642 bp Num Contigs Represented = 162 Non ambiguous bp: Initial: 10012775 bp After Masking: 4870108 bp Masked: 51.36 % -- Input Database Coverage: 10713642 bp out of 2169549916 bp ( 0.49 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 50403 Comparison Time: 00:06:03 (hh:mm:ss) Elapsed Time, 7308 HSPs Collected Number of families returned by RECON: 1238 Round Time: 00:08:21 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46365 repeats masked totaling 12076932 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32353075 bp Num Contigs Represented = 448 Non ambiguous bp: Initial: 30005828 bp After Masking: 15017246 bp Masked: 49.95 % -- Input Database Coverage: 43066717 bp out of 2169549916 bp ( 1.99 % ) Sampling Time: 00:05:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 469965 Comparison Time: 00:27:07 (hh:mm:ss) Elapsed Time, 42012 HSPs Collected Number of families returned by RECON: 3907 Round Time: 00:34:55 (hh:mm:ss) Elapsed Time : 114 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 150988 repeats masked totaling 39077966 bp(s). - TE Masking time 00:02:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 96441270 bp Num Contigs Represented = 1175 Non ambiguous bp: Initial: 90032037 bp After Masking: 42463174 bp Masked: 52.84 % -- Input Database Coverage: 139507987 bp out of 2169549916 bp ( 6.43 % ) Sampling Time: 00:17:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 4180386 Comparison Time: 02:36:12 (hh:mm:ss) Elapsed Time, 284260 HSPs Collected Number of families returned by RECON: 11421 Round Time: 03:09:00 (hh:mm:ss) Elapsed Time : 526 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:39:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 508198 repeats masked totaling 128189179 bp(s). - TE Masking time 00:11:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 289937837 bp Num Contigs Represented = 3090 Non ambiguous bp: Initial: 270035921 bp After Masking: 116092497 bp Masked: 57.01 % -- Input Database Coverage: 429445824 bp out of 2169549916 bp ( 19.79 % ) Sampling Time: 00:57:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 37797165 Comparison Time: 17:55:45 (hh:mm:ss) Elapsed Time, 673134 HSPs Collected Number of families returned by RECON: 39964 Round Time: 19:56:54 (hh:mm:ss) Elapsed Time : 1020 families discovered. RepeatScout/RECON discovery complete: 2573 families found Classification Time: 01:41:23 (hh:mm:ss) Elapsed Time Program Time: 25:54:16 (hh:mm:ss) Elapsed Time