RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.OqncR0/RM_24958.SunDec31046592023 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: 1701629218 Database = /dev/shm/rModeler.OqncR0/GCA_030867065.1_rAllMis1 - Sequences = 670 - Bases = 2373280586 - N50 = 304933920 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 449207987-481293216 | [ 1 ] 417122759-449207987 | [ ] 385037530-417122758 | [ ] 352952302-385037530 | [ ] 320867074-352952302 | [ ] 288781845-320867073 | [ 2 ] 256696617-288781845 | [ ] 224611388-256696616 | [ 1 ] 192526160-224611388 | [ 1 ] 160440932-192526160 | [ ] 128355703-160440931 | [ 1 ] 96270475-128355703 | [ 1 ] 64185246-96270474 | [ 6 ] 32100018-64185246 | [ 1 ] 14790-32100018 |************************************************** [ 656 ] Storage Throughput = excellent ( 1123.19 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40072388 bp ( 40011506 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:05:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:53 (hh:mm:ss) Elapsed Time Round Time: 00:32:20 (hh:mm:ss) Elapsed Time : 591 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12923 repeats masked totaling 2872590 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038259 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10023719 bp After Masking: 7067809 bp Masked: 29.49 % -- Input Database Coverage: 10038259 bp out of 2373280586 bp ( 0.42 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:29 (hh:mm:ss) Elapsed Time, 13378 HSPs Collected Number of families returned by RECON: 1481 Round Time: 00:07:58 (hh:mm:ss) Elapsed Time : 30 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40743 repeats masked totaling 8943357 bp(s). - TE Masking time 00:00:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30074048 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 30027706 bp After Masking: 20603192 bp Masked: 31.39 % -- Input Database Coverage: 40112307 bp out of 2373280586 bp ( 1.69 % ) Sampling Time: 00:07:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:27:57 (hh:mm:ss) Elapsed Time, 66223 HSPs Collected Number of families returned by RECON: 4423 Round Time: 00:38:15 (hh:mm:ss) Elapsed Time : 130 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:11:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 134508 repeats masked totaling 29727764 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90237896 bp Num Contigs Represented = 68 Non ambiguous bp: Initial: 90030649 bp After Masking: 59076153 bp Masked: 34.38 % -- Input Database Coverage: 130350203 bp out of 2373280586 bp ( 5.49 % ) Sampling Time: 00:20:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 03:06:03 (hh:mm:ss) Elapsed Time, 272435 HSPs Collected Number of families returned by RECON: 12330 Round Time: 03:49:09 (hh:mm:ss) Elapsed Time : 404 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:35:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 483429 repeats masked totaling 106705657 bp(s). - TE Masking time 00:12:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270651843 bp Num Contigs Represented = 138 Non ambiguous bp: Initial: 270027934 bp After Masking: 160059732 bp Masked: 40.72 % -- Input Database Coverage: 401002046 bp out of 2373280586 bp ( 16.90 % ) Sampling Time: 01:08:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23069028 Comparison Time: 22:29:52 (hh:mm:ss) Elapsed Time, 577158 HSPs Collected Number of families returned by RECON: 39912 Round Time: 24:44:34 (hh:mm:ss) Elapsed Time : 1040 families discovered. RepeatScout/RECON discovery complete: 2195 families found Classification Time: 01:38:36 (hh:mm:ss) Elapsed Time Program Time: 31:30:52 (hh:mm:ss) Elapsed Time