RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wfU3AQ/RM_25286.WedJul170323382024 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: 1721211810 Database = /dev/shm/rModeler.wfU3AQ/GCF_012432095.1_ASM1243209v1 - Sequences = 353 - Bases = 886586436 - N50 = 34194882 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 52723259-56488920 | [ 1 ] 48957598-52723258 | [ 1 ] 45191937-48957597 | [ 2 ] 41426277-45191937 | [ ] 37660616-41426276 | [ 1 ] 33894955-37660615 |* [ 7 ] 30129294-33894954 |* [ 8 ] 26363634-30129294 | [ 4 ] 22597973-26363633 | [ 1 ] 18832312-22597972 | [ ] 15066651-18832311 | [ ] 11300991-15066651 | [ ] 7535330-11300990 | [ ] 3769669-7535329 | [ ] 4009-3769669 |************************************************** [ 328 ] Storage Throughput = excellent ( 1028.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40155855 bp ( 40024548 non ambiguous ) - Num Contigs Represented = 41 - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:58 (hh:mm:ss) Elapsed Time Round Time: 00:47:56 (hh:mm:ss) Elapsed Time : 1188 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 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16439 repeats masked totaling 3262657 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10045780 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10032329 bp After Masking: 6589696 bp Masked: 34.32 % -- Input Database Coverage: 10045780 bp out of 886586436 bp ( 1.13 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:39:35 (hh:mm:ss) Elapsed Time, 7035 HSPs Collected Number of families returned by RECON: 1778 Round Time: 00:42:51 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49205 repeats masked totaling 9655081 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30149931 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 30032075 bp After Masking: 19764491 bp Masked: 34.19 % -- Input Database Coverage: 40195711 bp out of 886586436 bp ( 4.53 % ) Sampling Time: 00:03:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 02:01:17 (hh:mm:ss) Elapsed Time, 58013 HSPs Collected Number of families returned by RECON: 5779 Round Time: 02:10:39 (hh:mm:ss) Elapsed Time : 115 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 157551 repeats masked totaling 30417730 bp(s). - TE Masking time 00:04:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90346998 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90014356 bp After Masking: 57871897 bp Masked: 35.71 % -- Input Database Coverage: 130542709 bp out of 886586436 bp ( 14.72 % ) Sampling Time: 00:11:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2607186 Comparison Time: 07:25:16 (hh:mm:ss) Elapsed Time, 408152 HSPs Collected Number of families returned by RECON: 17004 Round Time: 08:07:03 (hh:mm:ss) Elapsed Time : 785 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 571226 repeats masked totaling 111437071 bp(s). - TE Masking time 00:25:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270966289 bp Num Contigs Represented = 146 Non ambiguous bp: Initial: 270013540 bp After Masking: 153458930 bp Masked: 43.17 % -- Input Database Coverage: 401508998 bp out of 886586436 bp ( 45.29 % ) Sampling Time: 00:47:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23519511 Comparison Time: 45:06:29 (hh:mm:ss) Elapsed Time, 898047 HSPs Collected Number of families returned by RECON: 49161 Round Time: 47:54:57 (hh:mm:ss) Elapsed Time : 1535 families discovered. RepeatScout/RECON discovery complete: 3631 families found Classification Time: 02:35:39 (hh:mm:ss) Elapsed Time Program Time: 62:19:05 (hh:mm:ss) Elapsed Time