RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.SvYDxC/RM_1823687.TueDec100019162024 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: 1733818755 Database = /scratch/tmp/rModeler.SvYDxC/GCA_040937895.1_aHypRig1.alt - Sequences = 14077 - Bases = 9708340052 - N50 = 1711533 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 17442028-18687325 | [ 1 ] 16196732-17442028 | [ 2 ] 14951436-16196732 | [ 1 ] 13706140-14951436 | [ 1 ] 12460844-13706140 | [ 6 ] 11215548-12460844 | [ 6 ] 9970252-11215548 | [ 3 ] 8724955-9970251 | [ 8 ] 7479659-8724955 | [ 17 ] 6234363-7479659 | [ 48 ] 4989067-6234363 | [ 65 ] 3743771-4989067 | [ 192 ] 2498475-3743771 |** [ 511 ] 1253179-2498475 |****** [ 1449 ] 7883-1253179 |************************************************** [ 11767 ] Storage Throughput = excellent ( 1575.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028445 bp ( 40028445 non ambiguous ) - Num Contigs Represented = 912 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:03 (hh:mm:ss) Elapsed Time Round Time: 00:21:45 (hh:mm:ss) Elapsed Time : 1125 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21593 repeats masked totaling 5250253 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010141 bp Num Contigs Represented = 251 Non ambiguous bp: Initial: 10010141 bp After Masking: 3523081 bp Masked: 64.80 % -- Input Database Coverage: 10010141 bp out of 9708340052 bp ( 0.10 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34191 Comparison Time: 00:03:13 (hh:mm:ss) Elapsed Time, 9384 HSPs Collected Number of families returned by RECON: 1213 Round Time: 00:04:23 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64172 repeats masked totaling 15532783 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018226 bp Num Contigs Represented = 700 Non ambiguous bp: Initial: 30018226 bp After Masking: 10386293 bp Masked: 65.40 % -- Input Database Coverage: 40028367 bp out of 9708340052 bp ( 0.41 % ) Sampling Time: 00:04:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:12:10 (hh:mm:ss) Elapsed Time, 62926 HSPs Collected Number of families returned by RECON: 3997 Round Time: 00:17:43 (hh:mm:ss) Elapsed Time : 114 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 204964 repeats masked totaling 48897666 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90007369 bp Num Contigs Represented = 1847 Non ambiguous bp: Initial: 90007369 bp After Masking: 29305717 bp Masked: 67.44 % -- Input Database Coverage: 130035736 bp out of 9708340052 bp ( 1.34 % ) Sampling Time: 00:11:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2685403 Comparison Time: 00:51:48 (hh:mm:ss) Elapsed Time, 274894 HSPs Collected Number of families returned by RECON: 11516 Round Time: 01:08:27 (hh:mm:ss) Elapsed Time : 532 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 679178 repeats masked totaling 158715299 bp(s). - TE Masking time 00:04:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270038383 bp Num Contigs Represented = 4048 Non ambiguous bp: Initial: 270037983 bp After Masking: 74652144 bp Masked: 72.35 % -- Input Database Coverage: 400074119 bp out of 9708340052 bp ( 4.12 % ) Sampling Time: 00:41:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24099153 Comparison Time: 04:42:38 (hh:mm:ss) Elapsed Time, 779894 HSPs Collected Number of families returned by RECON: 29152 Round Time: 05:45:55 (hh:mm:ss) Elapsed Time : 1288 families discovered. RepeatScout/RECON discovery complete: 3080 families found Classification Time: 00:48:11 (hh:mm:ss) Elapsed Time Program Time: 08:26:24 (hh:mm:ss) Elapsed Time