RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1AO5Ft/RM_16175.MonDec40331112023 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: 1701689470 Database = /dev/shm/rModeler.1AO5Ft/GCA_030867165.1_bOpiHoa1.hap2 - Sequences = 323 - Bases = 1355639139 - N50 = 81074052 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 146473129-156934390 | [ 1 ] 136011869-146473129 | [ ] 125550609-136011869 | [ 1 ] 115089349-125550609 | [ ] 104628089-115089349 | [ 1 ] 94166829-104628089 | [ 1 ] 83705569-94166829 | [ 1 ] 73244309-83705569 | [ 3 ] 62783049-73244309 | [ ] 52321789-62783049 | [ ] 41860529-52321789 | [ 1 ] 31399269-41860529 | [ 1 ] 20938009-31399269 |* [ 6 ] 10476749-20938009 |* [ 9 ] 15489-10476749 |************************************************** [ 298 ] Storage Throughput = excellent ( 1127.44 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032855 bp ( 40032055 non ambiguous ) - Num Contigs Represented = 79 - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:38 (hh:mm:ss) Elapsed Time Round Time: 01:01:50 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1635 repeats masked totaling 786718 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036703 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10036703 bp After Masking: 8053277 bp Masked: 19.76 % -- Input Database Coverage: 10036703 bp out of 1355639139 bp ( 0.74 % ) Sampling Time: 00:02:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:41 (hh:mm:ss) Elapsed Time, 907 HSPs Collected Number of families returned by RECON: 196 Round Time: 00:08:33 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5808 repeats masked totaling 2685421 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30035995 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 30035195 bp After Masking: 23232367 bp Masked: 22.65 % -- Input Database Coverage: 40072698 bp out of 1355639139 bp ( 2.96 % ) Sampling Time: 00:07:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:30:09 (hh:mm:ss) Elapsed Time, 6024 HSPs Collected Number of families returned by RECON: 923 Round Time: 00:37:50 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19013 repeats masked totaling 8329183 bp(s). - TE Masking time 00:00:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018638 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 90016604 bp After Masking: 69802852 bp Masked: 22.46 % -- Input Database Coverage: 130091336 bp out of 1355639139 bp ( 9.60 % ) Sampling Time: 00:15:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:54:58 (hh:mm:ss) Elapsed Time, 110143 HSPs Collected Number of families returned by RECON: 6018 Round Time: 04:13:42 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61943 repeats masked totaling 27538859 bp(s). - TE Masking time 00:03:45 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017985 bp Num Contigs Represented = 202 Non ambiguous bp: Initial: 270008785 bp After Masking: 205545890 bp Masked: 23.87 % -- Input Database Coverage: 400109321 bp out of 1355639139 bp ( 29.51 % ) Sampling Time: 00:52:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 29:34:59 (hh:mm:ss) Elapsed Time, 537745 HSPs Collected Number of families returned by RECON: 38300 Round Time: 31:04:48 (hh:mm:ss) Elapsed Time : 231 families discovered. RepeatScout/RECON discovery complete: 365 families found Classification Time: 00:40:33 (hh:mm:ss) Elapsed Time Program Time: 37:47:16 (hh:mm:ss) Elapsed Time