RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BTwqdF/RM_588997.SunMay40838492025 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: 1746373127 Database = /dev/shm/rModeler.BTwqdF/GCA_048934315.1_UKy_Petmar_22M1.pri1.0 - Sequences = 1203 - Bases = 1808332251 - N50 = 13878235 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35160697-37671560 | [ 1 ] 32649835-35160697 | [ 1 ] 30138973-32649835 | [ ] 27628111-30138973 | [ 1 ] 25117249-27628111 | [ 2 ] 22606387-25117249 | [ 8 ] 20095525-22606387 | [ 3 ] 17584662-20095524 | [ 9 ] 15073800-17584662 | [ 8 ] 12562938-15073800 |* [ 24 ] 10052076-12562938 | [ 11 ] 7541214-10052076 | [ 10 ] 5030352-7541214 | [ 20 ] 2519490-5030352 |* [ 35 ] 8628-2519490 |************************************************** [ 1070 ] Storage Throughput = excellent ( 1905.23 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018751 bp ( 40016351 non ambiguous ) - Num Contigs Represented = 298 - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:40 (hh:mm:ss) Elapsed Time Round Time: 00:21:26 (hh:mm:ss) Elapsed Time : 594 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19780 repeats masked totaling 3632913 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031244 bp Num Contigs Represented = 127 Non ambiguous bp: Initial: 10031044 bp After Masking: 2903619 bp Masked: 71.05 % -- Input Database Coverage: 10031244 bp out of 1808332251 bp ( 0.55 % ) Sampling Time: 00:07:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:36 (hh:mm:ss) Elapsed Time, 5582 HSPs Collected Number of families returned by RECON: 546 Round Time: 00:12:38 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 55086 repeats masked totaling 11219652 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027507 bp Num Contigs Represented = 262 Non ambiguous bp: Initial: 30025307 bp After Masking: 7731516 bp Masked: 74.25 % -- Input Database Coverage: 40058751 bp out of 1808332251 bp ( 2.22 % ) Sampling Time: 00:24:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:09:25 (hh:mm:ss) Elapsed Time, 14861 HSPs Collected Number of families returned by RECON: 1783 Round Time: 00:33:39 (hh:mm:ss) Elapsed Time : 36 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:10:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 184108 repeats masked totaling 33972553 bp(s). - TE Masking time 00:01:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90042618 bp Num Contigs Represented = 398 Non ambiguous bp: Initial: 90037018 bp After Masking: 24607551 bp Masked: 72.67 % -- Input Database Coverage: 130101369 bp out of 1808332251 bp ( 7.19 % ) Sampling Time: 01:12:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2582128 Comparison Time: 00:38:48 (hh:mm:ss) Elapsed Time, 143742 HSPs Collected Number of families returned by RECON: 5383 Round Time: 01:58:03 (hh:mm:ss) Elapsed Time : 273 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 03:16:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 586750 repeats masked totaling 108471786 bp(s). - TE Masking time 00:03:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031241 bp Num Contigs Represented = 675 Non ambiguous bp: Initial: 270015841 bp After Masking: 68248721 bp Masked: 74.72 % -- Input Database Coverage: 400132610 bp out of 1808332251 bp ( 22.13 % ) Sampling Time: 03:21:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23375703 Comparison Time: 03:53:19 (hh:mm:ss) Elapsed Time, 1247917 HSPs Collected Number of families returned by RECON: 15145 Round Time: 07:20:13 (hh:mm:ss) Elapsed Time : 664 families discovered. RepeatScout/RECON discovery complete: 1576 families found Classification Time: 00:31:13 (hh:mm:ss) Elapsed Time Program Time: 10:57:12 (hh:mm:ss) Elapsed Time