RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2qgB46/RM_28585.ThuJul41942042024 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: 1720147323 Database = /dev/shm/rModeler.2qgB46/GCF_000523025.1_Cse_v1.0 - Sequences = 29643 - Bases = 470199494 - N50 = 20052193 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 32226931-34528841 | [ 1 ] 29925022-32226931 | [ 1 ] 27623112-29925021 | [ 1 ] 25321203-27623112 | [ ] 23019294-25321203 | [ ] 20717384-23019293 | [ 3 ] 18415475-20717384 | [ 8 ] 16113565-18415474 | [ 5 ] 13811656-16113565 | [ 3 ] 11509747-13811656 | [ ] 9207837-11509746 | [ ] 6905928-9207837 | [ ] 4604018-6905927 | [ ] 2302109-4604018 | [ ] 200-2302109 |************************************************** [ 29621 ] Storage Throughput = excellent ( 1051.84 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42241651 bp ( 40014729 non ambiguous ) - Num Contigs Represented = 2789 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:55 (hh:mm:ss) Elapsed Time Round Time: 00:24:38 (hh:mm:ss) Elapsed Time : 221 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 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4415 repeats masked totaling 492616 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10504429 bp Num Contigs Represented = 756 Non ambiguous bp: Initial: 10010875 bp After Masking: 9312186 bp Masked: 6.98 % -- Input Database Coverage: 10504429 bp out of 470199494 bp ( 2.23 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 485605 Comparison Time: 00:09:37 (hh:mm:ss) Elapsed Time, 10006 HSPs Collected Number of families returned by RECON: 1351 Round Time: 00:10:44 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16034 repeats masked totaling 1741117 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31737212 bp Num Contigs Represented = 2056 Non ambiguous bp: Initial: 30003844 bp After Masking: 27724498 bp Masked: 7.60 % -- Input Database Coverage: 42241641 bp out of 470199494 bp ( 8.98 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3910206 Comparison Time: 00:51:16 (hh:mm:ss) Elapsed Time, 36115 HSPs Collected Number of families returned by RECON: 5364 Round Time: 00:54:52 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55372 repeats masked totaling 6297761 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 95084261 bp Num Contigs Represented = 6020 Non ambiguous bp: Initial: 90031059 bp After Masking: 82013678 bp Masked: 8.91 % -- Input Database Coverage: 137325902 bp out of 470199494 bp ( 29.21 % ) Sampling Time: 00:06:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34233675 Comparison Time: 06:12:15 (hh:mm:ss) Elapsed Time, 195147 HSPs Collected Number of families returned by RECON: 23695 Round Time: 06:33:40 (hh:mm:ss) Elapsed Time : 206 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 202450 repeats masked totaling 24574017 bp(s). - TE Masking time 00:05:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 284473715 bp Num Contigs Represented = 17973 Non ambiguous bp: Initial: 270033473 bp After Masking: 240354758 bp Masked: 10.99 % -- Input Database Coverage: 421799617 bp out of 470199494 bp ( 89.71 % ) Sampling Time: 00:20:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 307606806 Comparison Time: 48:50:17 (hh:mm:ss) Elapsed Time, 992878 HSPs Collected Number of families returned by RECON: 99999 Round Time: 53:45:31 (hh:mm:ss) Elapsed Time : 554 families discovered. RepeatScout/RECON discovery complete: 1051 families found Classification Time: 00:34:31 (hh:mm:ss) Elapsed Time Program Time: 62:23:56 (hh:mm:ss) Elapsed Time