RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mNn8H0/RM_20206.MonJan90059152023 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: 1673254754 Database = /dev/shm/rModeler.mNn8H0/GCA_014839835.1_bDryPub1.pri - Sequences = 181 - Bases = 1187956536 - 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 |************************************************** [ 147 ] Storage Throughput = excellent ( 1171.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40054980 bp ( 40014113 non ambiguous ) - Num Contigs Represented = 53 - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:52 (hh:mm:ss) Elapsed Time Round Time: 00:30:15 (hh:mm:ss) Elapsed Time : 189 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8615 repeats masked totaling 2334860 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034072 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 10033972 bp After Masking: 7476601 bp Masked: 25.49 % -- Input Database Coverage: 10034072 bp out of 1187956536 bp ( 0.84 % ) Sampling Time: 00:01:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:32 (hh:mm:ss) Elapsed Time, 652 HSPs Collected Number of families returned by RECON: 246 Round Time: 00:07:43 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27504 repeats masked totaling 7477113 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30060759 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 30019992 bp After Masking: 21700191 bp Masked: 27.71 % -- Input Database Coverage: 40094831 bp out of 1187956536 bp ( 3.38 % ) Sampling Time: 00:03:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:33:08 (hh:mm:ss) Elapsed Time, 5524 HSPs Collected Number of families returned by RECON: 1403 Round Time: 00:36:51 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79479 repeats masked totaling 21325761 bp(s). - TE Masking time 00:01:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90314757 bp Num Contigs Represented = 73 Non ambiguous bp: Initial: 90008181 bp After Masking: 66080353 bp Masked: 26.58 % -- Input Database Coverage: 130409588 bp out of 1187956536 bp ( 10.98 % ) Sampling Time: 00:10:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 03:47:56 (hh:mm:ss) Elapsed Time, 40197 HSPs Collected Number of families returned by RECON: 9480 Round Time: 04:00:54 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 244392 repeats masked totaling 66604074 bp(s). - TE Masking time 00:05:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270730955 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 270020947 bp After Masking: 196281435 bp Masked: 27.31 % -- Input Database Coverage: 401140543 bp out of 1187956536 bp ( 33.77 % ) Sampling Time: 00:30:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 30:08:44 (hh:mm:ss) Elapsed Time, 186989 HSPs Collected Number of families returned by RECON: 63178 Round Time: 31:38:03 (hh:mm:ss) Elapsed Time : 199 families discovered. RepeatScout/RECON discovery complete: 467 families found Classification Time: 00:25:41 (hh:mm:ss) Elapsed Time Program Time: 37:19:27 (hh:mm:ss) Elapsed Time