RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.NyaSa4/RM_3917600.MonMay150848572023 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: 1684165736 Database = /dev/shm/rModeler.NyaSa4/GCF_014839835.1_bDryPub1.pri - Sequences = 180 - Bases = 1187939694 - N50 = 44340053 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 130813529-140157326 | [ 1 ] 121469733-130813529 | [ ] 112125936-121469732 | [ ] 102782140-112125936 | [ ] 93438343-102782139 | [ ] 84094547-93438343 | [ ] 74750750-84094546 | [ ] 65406954-74750750 | [ 1 ] 56063157-65406953 | [ 1 ] 46719361-56063157 |* [ 4 ] 37375564-46719360 |* [ 5 ] 28031768-37375564 |* [ 3 ] 18687971-28031767 |*** [ 9 ] 9344175-18687971 |*** [ 10 ] 379-9344175 |************************************************** [ 146 ] Storage Throughput = good ( 990.69 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40104910 bp ( 40010769 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:18 (hh:mm:ss) Elapsed Time Round Time: 00:21:43 (hh:mm:ss) Elapsed Time : 164 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9266 repeats masked totaling 2468730 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10066946 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10026925 bp After Masking: 7317006 bp Masked: 27.03 % -- Input Database Coverage: 10066946 bp out of 1187939694 bp ( 0.85 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:46 (hh:mm:ss) Elapsed Time, 704 HSPs Collected Number of families returned by RECON: 226 Round Time: 00:07:56 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26682 repeats masked totaling 7016864 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30077884 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 30023764 bp After Masking: 22278018 bp Masked: 25.80 % -- Input Database Coverage: 40144830 bp out of 1187939694 bp ( 3.38 % ) Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:31:40 (hh:mm:ss) Elapsed Time, 6438 HSPs Collected Number of families returned by RECON: 1508 Round Time: 00:35:35 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80763 repeats masked totaling 21408690 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90418478 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 90017402 bp After Masking: 66419184 bp Masked: 26.22 % -- Input Database Coverage: 130563308 bp out of 1187939694 bp ( 10.99 % ) Sampling Time: 00:10:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 03:26:24 (hh:mm:ss) Elapsed Time, 38002 HSPs Collected Number of families returned by RECON: 9248 Round Time: 03:40:03 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 255790 repeats masked totaling 67200342 bp(s). - TE Masking time 00:04:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271150250 bp Num Contigs Represented = 105 Non ambiguous bp: Initial: 270036142 bp After Masking: 195181915 bp Masked: 27.72 % -- Input Database Coverage: 401713558 bp out of 1187939694 bp ( 33.82 % ) Sampling Time: 00:31:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23103003 Comparison Time: 25:00:55 (hh:mm:ss) Elapsed Time, 186337 HSPs Collected Number of families returned by RECON: 62026 Round Time: 26:16:00 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatScout/RECON discovery complete: 448 families found Classification Time: 00:24:49 (hh:mm:ss) Elapsed Time Program Time: 31:26:06 (hh:mm:ss) Elapsed Time