RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.fZBgKX/RM_711939.ThuMar141830522024 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: 1710466251 Database = /dev/shm/rModeler.fZBgKX/GCA_035609145.1_aEleCoq1.hap1 - Sequences = 957 - Bases = 3371316047 - N50 = 304122739 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 502246707-538120716 | [ 1 ] 466372698-502246706 | [ ] 430498689-466372697 | [ ] 394624681-430498689 | [ ] 358750672-394624680 | [ ] 322876663-358750671 | [ 1 ] 287002654-322876662 | [ 2 ] 251128646-287002654 | [ 1 ] 215254637-251128645 | [ 2 ] 179380628-215254636 | [ 1 ] 143506619-179380627 | [ 2 ] 107632611-143506619 | [ 3 ] 71758602-107632610 | [ ] 35884593-71758601 | [ ] 10585-35884593 |************************************************** [ 944 ] Storage Throughput = excellent ( 1252.77 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015683 bp ( 40014883 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:06:13 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:33 (hh:mm:ss) Elapsed Time Round Time: 00:33:12 (hh:mm:ss) Elapsed Time : 976 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21426 repeats masked totaling 4511157 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029270 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10028670 bp After Masking: 4189700 bp Masked: 58.22 % -- Input Database Coverage: 10029270 bp out of 3371316047 bp ( 0.30 % ) Sampling Time: 00:03:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 35641 HSPs Collected Number of families returned by RECON: 1573 Round Time: 00:09:26 (hh:mm:ss) Elapsed Time : 35 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66939 repeats masked totaling 14167017 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026492 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30026292 bp After Masking: 12193123 bp Masked: 59.39 % -- Input Database Coverage: 40055762 bp out of 3371316047 bp ( 1.19 % ) Sampling Time: 00:10:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:20:46 (hh:mm:ss) Elapsed Time, 65811 HSPs Collected Number of families returned by RECON: 4974 Round Time: 00:33:17 (hh:mm:ss) Elapsed Time : 161 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:13:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 214595 repeats masked totaling 44958052 bp(s). - TE Masking time 00:02:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039617 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 90033731 bp After Masking: 33303494 bp Masked: 63.01 % -- Input Database Coverage: 130095379 bp out of 3371316047 bp ( 3.86 % ) Sampling Time: 00:34:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 01:47:20 (hh:mm:ss) Elapsed Time, 452747 HSPs Collected Number of families returned by RECON: 12193 Round Time: 02:35:29 (hh:mm:ss) Elapsed Time : 564 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:38:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:50:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 737809 repeats masked totaling 155403667 bp(s). - TE Masking time 00:10:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019369 bp Num Contigs Represented = 261 Non ambiguous bp: Initial: 270009514 bp After Masking: 83121963 bp Masked: 69.22 % -- Input Database Coverage: 400114748 bp out of 3371316047 bp ( 11.87 % ) Sampling Time: 01:40:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 11:24:32 (hh:mm:ss) Elapsed Time, 883032 HSPs Collected Number of families returned by RECON: 30120 Round Time: 13:47:55 (hh:mm:ss) Elapsed Time : 1344 families discovered. RepeatScout/RECON discovery complete: 3080 families found Classification Time: 01:35:31 (hh:mm:ss) Elapsed Time Program Time: 19:14:50 (hh:mm:ss) Elapsed Time