RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.d5S4hd/RM_3318735.MonNov270205442023 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: 1701079544 Database = /dev/shm/rModeler.d5S4hd/GCF_902713425.1_fAciRut3.2_maternal_haplotype - Sequences = 1731 - Bases = 1899810788 - N50 = 44288098 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 112266581-120284971 | [ 2 ] 104248191-112266580 | [ 2 ] 96229802-104248191 | [ ] 88211412-96229801 | [ 1 ] 80193022-88211411 | [ 1 ] 72174633-80193022 | [ ] 64156243-72174632 | [ 2 ] 56137853-64156242 | [ 1 ] 48119464-56137853 | [ 1 ] 40101074-48119463 | [ 2 ] 32082684-40101073 | [ 9 ] 24064295-32082684 | [ 7 ] 16045905-24064294 | [ 1 ] 8027515-16045904 | [ 25 ] 9126-8027515 |************************************************** [ 1677 ] Storage Throughput = excellent ( 1411.01 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009181 bp ( 40006781 non ambiguous ) - Num Contigs Represented = 127 - Sequence extraction : 00:01:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:56 (hh:mm:ss) Elapsed Time Round Time: 00:27:53 (hh:mm:ss) Elapsed Time : 884 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11297 repeats masked totaling 2479655 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038758 bp Num Contigs Represented = 70 Non ambiguous bp: Initial: 10038358 bp After Masking: 6726438 bp Masked: 32.99 % -- Input Database Coverage: 10038758 bp out of 1899810788 bp ( 0.53 % ) Sampling Time: 00:01:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:06 (hh:mm:ss) Elapsed Time, 11125 HSPs Collected Number of families returned by RECON: 1812 Round Time: 00:08:36 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34314 repeats masked totaling 7793122 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010418 bp Num Contigs Represented = 107 Non ambiguous bp: Initial: 30008418 bp After Masking: 19682673 bp Masked: 34.41 % -- Input Database Coverage: 40049176 bp out of 1899810788 bp ( 2.11 % ) Sampling Time: 00:05:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:28:20 (hh:mm:ss) Elapsed Time, 62923 HSPs Collected Number of families returned by RECON: 6025 Round Time: 00:35:23 (hh:mm:ss) Elapsed Time : 139 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118507 repeats masked totaling 25513235 bp(s). - TE Masking time 00:02:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012264 bp Num Contigs Represented = 189 Non ambiguous bp: Initial: 90008864 bp After Masking: 56871720 bp Masked: 36.82 % -- Input Database Coverage: 130061440 bp out of 1899810788 bp ( 6.85 % ) Sampling Time: 00:18:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 02:54:29 (hh:mm:ss) Elapsed Time, 411351 HSPs Collected Number of families returned by RECON: 16813 Round Time: 03:26:17 (hh:mm:ss) Elapsed Time : 686 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 446130 repeats masked totaling 96064879 bp(s). - TE Masking time 00:13:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270018718 bp Num Contigs Represented = 425 Non ambiguous bp: Initial: 270008235 bp After Masking: 150931564 bp Masked: 44.10 % -- Input Database Coverage: 400080158 bp out of 1899810788 bp ( 21.06 % ) Sampling Time: 00:58:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23492085 Comparison Time: 20:33:53 (hh:mm:ss) Elapsed Time, 1114268 HSPs Collected Number of families returned by RECON: 50929 Round Time: 22:51:37 (hh:mm:ss) Elapsed Time : 1540 families discovered. RepeatScout/RECON discovery complete: 3262 families found Classification Time: 02:24:44 (hh:mm:ss) Elapsed Time Program Time: 29:54:30 (hh:mm:ss) Elapsed Time