RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9wg1Tc/RM_26281.WedJul100417362024 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: 1720610254 Database = /dev/shm/rModeler.9wg1Tc/GCF_001891065.2_H_comes_QL1_v1.1 - Sequences = 32914 - Bases = 492131402 - N50 = 2116684 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 9156558-9810584 | [ 2 ] 8502532-9156557 | [ ] 7848507-8502532 | [ 2 ] 7194481-7848506 | [ 2 ] 6540456-7194481 | [ 1 ] 5886430-6540455 | [ 3 ] 5232404-5886429 | [ 3 ] 4578379-5232404 | [ 3 ] 3924353-4578378 | [ 9 ] 3270328-3924353 | [ 4 ] 2616302-3270327 | [ 15 ] 1962276-2616301 | [ 19 ] 1308251-1962276 | [ 42 ] 654225-1308250 | [ 99 ] 200-654225 |************************************************** [ 32710 ] Storage Throughput = excellent ( 1073.87 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 43164189 bp ( 40018960 non ambiguous ) - Num Contigs Represented = 3050 - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:02 (hh:mm:ss) Elapsed Time Round Time: 00:22:48 (hh:mm:ss) Elapsed Time : 517 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 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9913 repeats masked totaling 1511863 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10862390 bp Num Contigs Represented = 873 Non ambiguous bp: Initial: 10020759 bp After Masking: 8379915 bp Masked: 16.37 % -- Input Database Coverage: 10862390 bp out of 492131402 bp ( 2.21 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 487578 Comparison Time: 00:09:40 (hh:mm:ss) Elapsed Time, 10623 HSPs Collected Number of families returned by RECON: 1844 Round Time: 00:10:37 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32187 repeats masked totaling 4901552 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 32304610 bp Num Contigs Represented = 2299 Non ambiguous bp: Initial: 30001012 bp After Masking: 24620510 bp Masked: 17.93 % -- Input Database Coverage: 43167000 bp out of 492131402 bp ( 8.77 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3929806 Comparison Time: 00:48:27 (hh:mm:ss) Elapsed Time, 65671 HSPs Collected Number of families returned by RECON: 6261 Round Time: 00:52:40 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 115436 repeats masked totaling 17561468 bp(s). - TE Masking time 00:02:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 96436489 bp Num Contigs Represented = 6764 Non ambiguous bp: Initial: 90019994 bp After Masking: 71141466 bp Masked: 20.97 % -- Input Database Coverage: 139603489 bp out of 492131402 bp ( 28.37 % ) Sampling Time: 00:05:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 38303128 Comparison Time: 06:41:46 (hh:mm:ss) Elapsed Time, 291381 HSPs Collected Number of families returned by RECON: 21124 Round Time: 07:06:25 (hh:mm:ss) Elapsed Time : 519 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 441660 repeats masked totaling 66951511 bp(s). - TE Masking time 00:12:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 290114008 bp Num Contigs Represented = 19597 Non ambiguous bp: Initial: 270019683 bp After Masking: 199359537 bp Masked: 26.17 % -- Input Database Coverage: 429717497 bp out of 492131402 bp ( 87.32 % ) Sampling Time: 00:22:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 344675640 Comparison Time: 41:38:30 (hh:mm:ss) Elapsed Time, 797198 HSPs Collected Number of families returned by RECON: 74847 Round Time: 44:26:14 (hh:mm:ss) Elapsed Time : 1016 families discovered. RepeatScout/RECON discovery complete: 2251 families found Classification Time: 01:16:44 (hh:mm:ss) Elapsed Time Program Time: 54:15:28 (hh:mm:ss) Elapsed Time