RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BiefYE/RM_894065.FriDec131229372024 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: 1734121776 Database = /dev/shm/rModeler.BiefYE/GCF_031143425.1_aPleWal1.hap1.20221129 - Sequences = 308 - Bases = 10434412033 - N50 = 1725456226 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1872667923-2006429847 | [ 1 ] 1738906000-1872667923 | [ ] 1605144077-1738906000 | [ 1 ] 1471382154-1605144077 | [ 1 ] 1337620231-1471382154 | [ ] 1203858308-1337620231 | [ ] 1070096385-1203858308 | [ 2 ] 936334461-1070096384 | [ 2 ] 802572538-936334461 | [ ] 668810615-802572538 | [ 1 ] 535048692-668810615 | [ ] 401286769-535048692 | [ ] 267524846-401286769 | [ ] 133762923-267524846 | [ ] 1000-133762923 |************************************************** [ 300 ] Storage Throughput = fair ( 493.62 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030119 bp ( 40028839 non ambiguous ) - Num Contigs Represented = 17 - Sequence extraction : 00:46:43 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:04 (hh:mm:ss) Elapsed Time Round Time: 01:54:59 (hh:mm:ss) Elapsed Time : 590 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:11:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10552 repeats masked totaling 5180184 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040076 bp Num Contigs Represented = 9 Non ambiguous bp: Initial: 10039676 bp After Masking: 4317804 bp Masked: 56.99 % -- Input Database Coverage: 10040076 bp out of 10434412033 bp ( 0.10 % ) Sampling Time: 00:13:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:09:32 (hh:mm:ss) Elapsed Time, 13637 HSPs Collected Number of families returned by RECON: 973 Round Time: 00:24:38 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:35:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32708 repeats masked totaling 15839104 bp(s). - TE Masking time 00:02:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30029963 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 30029083 bp After Masking: 12241934 bp Masked: 59.23 % -- Input Database Coverage: 40070039 bp out of 10434412033 bp ( 0.38 % ) Sampling Time: 00:41:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:44:35 (hh:mm:ss) Elapsed Time, 64245 HSPs Collected Number of families returned by RECON: 3018 Round Time: 01:35:30 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 01:45:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105559 repeats masked totaling 51089673 bp(s). - TE Masking time 00:08:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041782 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90039782 bp After Masking: 32931394 bp Masked: 63.43 % -- Input Database Coverage: 130111821 bp out of 10434412033 bp ( 1.25 % ) Sampling Time: 02:03:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 04:14:00 (hh:mm:ss) Elapsed Time, 211409 HSPs Collected Number of families returned by RECON: 8237 Round Time: 06:35:12 (hh:mm:ss) Elapsed Time : 328 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 05:16:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 359862 repeats masked totaling 170890761 bp(s). - TE Masking time 00:35:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022549 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 270017709 bp After Masking: 82034819 bp Masked: 69.62 % -- Input Database Coverage: 400134370 bp out of 10434412033 bp ( 3.83 % ) Sampling Time: 06:23:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22831903 Comparison Time: 26:47:08 (hh:mm:ss) Elapsed Time, 625410 HSPs Collected Number of families returned by RECON: 22540 Round Time: 34:15:56 (hh:mm:ss) Elapsed Time : 751 families discovered. RepeatScout/RECON discovery complete: 1775 families found Classification Time: 03:24:11 (hh:mm:ss) Elapsed Time Program Time: 48:10:26 (hh:mm:ss) Elapsed Time