RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KGQ4ZM/RM_25988.ThuDec70048542023 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: 1701938933 Database = /dev/shm/rModeler.KGQ4ZM/GCA_949628215.1_bGulAri2.1 - Sequences = 353 - Bases = 1279134750 - N50 = 131340911 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204624085-219240020 | [ 1 ] 190008150-204624084 | [ ] 175392216-190008150 | [ ] 160776281-175392215 | [ 1 ] 146160346-160776280 | [ ] 131544412-146160346 | [ ] 116928477-131544411 | [ 1 ] 102312542-116928476 | [ ] 87696608-102312542 | [ ] 73080673-87696607 | [ 2 ] 58464738-73080672 | [ 2 ] 43848804-58464738 | [ 2 ] 29232869-43848803 | [ 2 ] 14616934-29232868 |* [ 7 ] 1000-14616934 |************************************************** [ 335 ] Storage Throughput = excellent ( 1177.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40004647 bp ( 40003447 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:32 (hh:mm:ss) Elapsed Time Round Time: 00:43:28 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1588 repeats masked totaling 810835 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023531 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10023131 bp After Masking: 8943835 bp Masked: 10.77 % -- Input Database Coverage: 10023531 bp out of 1279134750 bp ( 0.78 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:50 (hh:mm:ss) Elapsed Time, 442 HSPs Collected Number of families returned by RECON: 211 Round Time: 00:09:18 (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 : 00:01:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5039 repeats masked totaling 2597946 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021100 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 30020300 bp After Masking: 26877144 bp Masked: 10.47 % -- Input Database Coverage: 40044631 bp out of 1279134750 bp ( 3.13 % ) Sampling Time: 00:03:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:39:40 (hh:mm:ss) Elapsed Time, 7979 HSPs Collected Number of families returned by RECON: 1268 Round Time: 00:44:24 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17409 repeats masked totaling 7748136 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90016430 bp Num Contigs Represented = 101 Non ambiguous bp: Initial: 90013630 bp After Masking: 79762854 bp Masked: 11.39 % -- Input Database Coverage: 130061061 bp out of 1279134750 bp ( 10.17 % ) Sampling Time: 00:12:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 04:30:23 (hh:mm:ss) Elapsed Time, 275402 HSPs Collected Number of families returned by RECON: 8112 Round Time: 04:44:48 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61866 repeats masked totaling 26217952 bp(s). - TE Masking time 00:02:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026398 bp Num Contigs Represented = 177 Non ambiguous bp: Initial: 270015198 bp After Masking: 236577002 bp Masked: 12.38 % -- Input Database Coverage: 400087459 bp out of 1279134750 bp ( 31.28 % ) Sampling Time: 00:37:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22967253 Comparison Time: 35:13:34 (hh:mm:ss) Elapsed Time, 735318 HSPs Collected Number of families returned by RECON: 53011 Round Time: 36:44:10 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatScout/RECON discovery complete: 333 families found Classification Time: 00:32:52 (hh:mm:ss) Elapsed Time Program Time: 43:39:00 (hh:mm:ss) Elapsed Time