RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.K23UT0/RM_1667199.SunMar242322132024 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: 1711347732 Database = /dev/shm/rModeler.K23UT0/GCA_036418255.1_mEquCab1.mat - Sequences = 821 - Bases = 2331848197 - N50 = 90649477 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 179633537-192463451 | [ 1 ] 166803624-179633537 | [ ] 153973711-166803624 | [ ] 141143798-153973711 | [ ] 128313885-141143798 | [ ] 115483972-128313885 | [ 1 ] 102654059-115483972 | [ 2 ] 89824146-102654059 | [ 6 ] 76994233-89824146 | [ 4 ] 64164320-76994233 | [ 2 ] 51334407-64164320 | [ 4 ] 38504494-51334407 | [ 5 ] 25674581-38504494 | [ 5 ] 12844668-25674581 | [ 1 ] 14755-12844668 |************************************************** [ 790 ] Storage Throughput = excellent ( 1016.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40002767 bp ( 40002167 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:31 (hh:mm:ss) Elapsed Time Round Time: 00:25:11 (hh:mm:ss) Elapsed Time : 216 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8697 repeats masked totaling 1963075 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030233 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10030033 bp After Masking: 7620575 bp Masked: 24.02 % -- Input Database Coverage: 10030233 bp out of 2331848197 bp ( 0.43 % ) Sampling Time: 00:01:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:26 (hh:mm:ss) Elapsed Time, 54503 HSPs Collected Number of families returned by RECON: 948 Round Time: 00:09:19 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32588 repeats masked totaling 7448138 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012536 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30012136 bp After Masking: 21385278 bp Masked: 28.74 % -- Input Database Coverage: 40042769 bp out of 2331848197 bp ( 1.72 % ) Sampling Time: 00:03:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:38:38 (hh:mm:ss) Elapsed Time, 1030912 HSPs Collected Number of families returned by RECON: 2817 Round Time: 00:43:40 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104944 repeats masked totaling 24075173 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90020788 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 90019388 bp After Masking: 61309608 bp Masked: 31.89 % -- Input Database Coverage: 130063557 bp out of 2331848197 bp ( 5.58 % ) Sampling Time: 00:09:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2563980 Comparison Time: 03:27:05 (hh:mm:ss) Elapsed Time, 4125507 HSPs Collected Number of families returned by RECON: 9891 Round Time: 03:41:05 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 356110 repeats masked totaling 80433223 bp(s). - TE Masking time 00:04:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044060 bp Num Contigs Represented = 221 Non ambiguous bp: Initial: 270038860 bp After Masking: 177635687 bp Masked: 34.22 % -- Input Database Coverage: 400107617 bp out of 2331848197 bp ( 17.16 % ) Sampling Time: 00:29:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 23:56:54 (hh:mm:ss) Elapsed Time, 31180076 HSPs Collected Number of families returned by RECON: 39628 Round Time: 25:12:06 (hh:mm:ss) Elapsed Time : 371 families discovered. RepeatScout/RECON discovery complete: 840 families found Classification Time: 00:38:06 (hh:mm:ss) Elapsed Time Program Time: 30:49:27 (hh:mm:ss) Elapsed Time