RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Dfi6jP/RM_26407.SunNov101022082024 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: 1731262927 Database = /dev/shm/rModeler.Dfi6jP/GCA_964194415.1_rVipBer3.hap1.1 - Sequences = 479 - Bases = 1695017208 - N50 = 290632359 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 338738936-362934503 | [ 1 ] 314543369-338738935 | [ ] 290347802-314543368 | [ 1 ] 266152235-290347801 | [ ] 241956668-266152234 | [ ] 217761101-241956667 | [ 1 ] 193565534-217761100 | [ ] 169369968-193565534 | [ ] 145174401-169369967 | [ ] 120978834-145174400 | [ 2 ] 96783267-120978833 | [ 1 ] 72587700-96783266 | [ 3 ] 48392133-72587699 | [ ] 24196566-48392132 | [ 2 ] 1000-24196566 |************************************************** [ 468 ] Storage Throughput = excellent ( 1037.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031258 bp ( 40027858 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:04:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:07 (hh:mm:ss) Elapsed Time Round Time: 00:32:13 (hh:mm:ss) Elapsed Time : 469 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13976 repeats masked totaling 3786355 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004065 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 10002465 bp After Masking: 5601152 bp Masked: 44.00 % -- Input Database Coverage: 10004065 bp out of 1695017208 bp ( 0.59 % ) Sampling Time: 00:06:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:56 (hh:mm:ss) Elapsed Time, 4423 HSPs Collected Number of families returned by RECON: 778 Round Time: 00:11:21 (hh:mm:ss) Elapsed Time : 8 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43236 repeats masked totaling 11810839 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027113 bp Num Contigs Represented = 30 Non ambiguous bp: Initial: 30025313 bp After Masking: 16783701 bp Masked: 44.10 % -- Input Database Coverage: 40031178 bp out of 1695017208 bp ( 2.36 % ) Sampling Time: 00:09:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:25:02 (hh:mm:ss) Elapsed Time, 37080 HSPs Collected Number of families returned by RECON: 2765 Round Time: 00:35:26 (hh:mm:ss) Elapsed Time : 73 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:09:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 139637 repeats masked totaling 36722697 bp(s). - TE Masking time 00:02:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90046994 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 90034032 bp After Masking: 48503394 bp Masked: 46.13 % -- Input Database Coverage: 130078172 bp out of 1695017208 bp ( 7.67 % ) Sampling Time: 00:29:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 02:46:28 (hh:mm:ss) Elapsed Time, 147405 HSPs Collected Number of families returned by RECON: 8874 Round Time: 03:22:32 (hh:mm:ss) Elapsed Time : 308 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:27:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:56:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 464137 repeats masked totaling 118292773 bp(s). - TE Masking time 00:09:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270042951 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 270010551 bp After Masking: 137625655 bp Masked: 49.03 % -- Input Database Coverage: 400121123 bp out of 1695017208 bp ( 23.61 % ) Sampling Time: 01:34:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23082615 Comparison Time: 20:58:09 (hh:mm:ss) Elapsed Time, 392331 HSPs Collected Number of families returned by RECON: 30899 Round Time: 23:08:20 (hh:mm:ss) Elapsed Time : 697 families discovered. RepeatScout/RECON discovery complete: 1555 families found Classification Time: 01:07:15 (hh:mm:ss) Elapsed Time Program Time: 28:57:07 (hh:mm:ss) Elapsed Time