RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.sIFjdi/RM_107815.FriJan60843392023 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: 1673023418 Database = /dev/shm/rModeler.sIFjdi/GCA_016695395.2_mHomSap3.mat - Sequences = 950 - Bases = 2902214236 - N50 = 155511006 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 221481558-237301588 | [ 2 ] 205661529-221481558 | [ ] 189841500-205661529 | [ 1 ] 174021471-189841500 | [ 2 ] 158201442-174021471 | [ 1 ] 142381413-158201442 | [ 2 ] 126561384-142381413 | [ 4 ] 110741354-126561383 | [ 1 ] 94921325-110741354 | [ 1 ] 79101296-94921325 | [ 3 ] 63281267-79101296 | [ 2 ] 47461238-63281267 | [ 2 ] 31641209-47461238 | [ 2 ] 15821180-31641209 | [ ] 1151-15821180 |************************************************** [ 927 ] Storage Throughput = excellent ( 1063.74 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40423127 bp ( 40004868 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:19 (hh:mm:ss) Elapsed Time Round Time: 00:30:17 (hh:mm:ss) Elapsed Time : 289 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12982 repeats masked totaling 2914832 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10102932 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10007582 bp After Masking: 6730026 bp Masked: 32.75 % -- Input Database Coverage: 10102932 bp out of 2902214236 bp ( 0.35 % ) Sampling Time: 00:02:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:06:08 (hh:mm:ss) Elapsed Time, 6844 HSPs Collected Number of families returned by RECON: 994 Round Time: 00:08:41 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43284 repeats masked totaling 9592402 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30360115 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 30037206 bp After Masking: 19361430 bp Masked: 35.54 % -- Input Database Coverage: 40463047 bp out of 2902214236 bp ( 1.39 % ) Sampling Time: 00:07:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:28:35 (hh:mm:ss) Elapsed Time, 33092 HSPs Collected Number of families returned by RECON: 2565 Round Time: 00:36:53 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 141893 repeats masked totaling 30867184 bp(s). - TE Masking time 00:01:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90337119 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 90014221 bp After Masking: 55845668 bp Masked: 37.96 % -- Input Database Coverage: 130800166 bp out of 2902214236 bp ( 4.51 % ) Sampling Time: 00:25:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 03:13:23 (hh:mm:ss) Elapsed Time, 114556 HSPs Collected Number of families returned by RECON: 8911 Round Time: 03:43:20 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:35:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 471874 repeats masked totaling 103176573 bp(s). - TE Masking time 00:06:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270772643 bp Num Contigs Represented = 214 Non ambiguous bp: Initial: 270019526 bp After Masking: 157208134 bp Masked: 41.78 % -- Input Database Coverage: 401572809 bp out of 2902214236 bp ( 13.84 % ) Sampling Time: 01:03:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23259610 Comparison Time: 20:55:25 (hh:mm:ss) Elapsed Time, 237563 HSPs Collected Number of families returned by RECON: 33054 Round Time: 22:24:31 (hh:mm:ss) Elapsed Time : 428 families discovered. RepeatScout/RECON discovery complete: 993 families found Classification Time: 00:41:52 (hh:mm:ss) Elapsed Time Program Time: 28:05:34 (hh:mm:ss) Elapsed Time