RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2zGouP/RM_2177.SunJul210933462024 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: 1721579625 Database = /dev/shm/rModeler.2zGouP/GCF_016859285.1_ASM1685928v1 - Sequences = 1482 - Bases = 691780295 - N50 = 29433144 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 33251331-35626355 | [ 3 ] 30876307-33251330 | [ 3 ] 28501284-30876307 | [ 6 ] 26126260-28501283 | [ 6 ] 23751236-26126259 | [ 2 ] 21376213-23751236 | [ 2 ] 19001189-21376212 | [ 1 ] 16626165-19001188 | [ ] 14251142-16626165 | [ 1 ] 11876118-14251141 | [ ] 9501094-11876117 | [ ] 7126071-9501094 | [ ] 4751047-7126070 | [ ] 2376023-4751046 | [ ] 1000-2376023 |************************************************** [ 1458 ] Storage Throughput = good ( 826.48 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019530 bp ( 40001530 non ambiguous ) - Num Contigs Represented = 120 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:27 (hh:mm:ss) Elapsed Time Round Time: 00:25:27 (hh:mm:ss) Elapsed Time : 327 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (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... 8810 repeats masked totaling 1091458 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014883 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 10011383 bp After Masking: 8651785 bp Masked: 13.58 % -- Input Database Coverage: 10014883 bp out of 691780295 bp ( 1.45 % ) Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35245 Comparison Time: 00:09:15 (hh:mm:ss) Elapsed Time, 8455 HSPs Collected Number of families returned by RECON: 1533 Round Time: 00:10:46 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27254 repeats masked totaling 3241004 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30044567 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 30030067 bp After Masking: 25931251 bp Masked: 13.65 % -- Input Database Coverage: 40059450 bp out of 691780295 bp ( 5.79 % ) Sampling Time: 00:02:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 322806 Comparison Time: 00:49:49 (hh:mm:ss) Elapsed Time, 53852 HSPs Collected Number of families returned by RECON: 5236 Round Time: 00:55:13 (hh:mm:ss) Elapsed Time : 120 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 95529 repeats masked totaling 12502537 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045441 bp Num Contigs Represented = 233 Non ambiguous bp: Initial: 90018803 bp After Masking: 75026455 bp Masked: 16.65 % -- Input Database Coverage: 130104891 bp out of 691780295 bp ( 18.81 % ) Sampling Time: 00:08:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2878800 Comparison Time: 05:55:00 (hh:mm:ss) Elapsed Time, 243803 HSPs Collected Number of families returned by RECON: 18411 Round Time: 06:20:38 (hh:mm:ss) Elapsed Time : 390 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 353408 repeats masked totaling 50114751 bp(s). - TE Masking time 00:08:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270117047 bp Num Contigs Represented = 596 Non ambiguous bp: Initial: 270030529 bp After Masking: 212744471 bp Masked: 21.21 % -- Input Database Coverage: 400221938 bp out of 691780295 bp ( 57.85 % ) Sampling Time: 00:30:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25794153 Comparison Time: 54:57:25 (hh:mm:ss) Elapsed Time, 710353 HSPs Collected Number of families returned by RECON: 70371 Round Time: 58:27:35 (hh:mm:ss) Elapsed Time : 1035 families discovered. RepeatScout/RECON discovery complete: 1893 families found Classification Time: 01:19:41 (hh:mm:ss) Elapsed Time Program Time: 67:39:20 (hh:mm:ss) Elapsed Time