RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.96CTwW/RM_509712.SunJul200419072025 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: 1753010347 Database = /dev/shm/rModeler.96CTwW/GCA_964196065.2_bCalBor7.hap2.2 - Sequences = 281 - Bases = 1211470109 - N50 = 129082959 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206221202-220951217 | [ 1 ] 191491188-206221202 | [ ] 176761173-191491187 | [ ] 162031159-176761173 | [ 1 ] 147301144-162031158 | [ ] 132571130-147301144 | [ ] 117841115-132571129 | [ 1 ] 103111101-117841115 | [ ] 88381086-103111100 | [ ] 73651072-88381086 | [ 1 ] 58921057-73651071 | [ ] 44191043-58921057 | [ 3 ] 29461028-44191042 | [ 2 ] 14731014-29461028 |** [ 11 ] 1000-14731014 |************************************************** [ 261 ] Storage Throughput = excellent ( 1664.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032164 bp ( 40029964 non ambiguous ) - Num Contigs Represented = 73 - Sequence extraction : 00:01:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:53 (hh:mm:ss) Elapsed Time Round Time: 00:17:21 (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 : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1661 repeats masked totaling 748548 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010958 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10009758 bp After Masking: 9021616 bp Masked: 9.87 % -- Input Database Coverage: 10010958 bp out of 1211470109 bp ( 0.83 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:07 (hh:mm:ss) Elapsed Time, 561 HSPs Collected Number of families returned by RECON: 248 Round Time: 00:03:50 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4239 repeats masked totaling 2218288 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30021186 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 30020186 bp After Masking: 26592181 bp Masked: 11.42 % -- Input Database Coverage: 40032144 bp out of 1211470109 bp ( 3.30 % ) Sampling Time: 00:02:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:15:01 (hh:mm:ss) Elapsed Time, 26077 HSPs Collected Number of families returned by RECON: 1505 Round Time: 00:17:52 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14599 repeats masked totaling 6469818 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041414 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 90032014 bp After Masking: 79478747 bp Masked: 11.72 % -- Input Database Coverage: 130073558 bp out of 1211470109 bp ( 10.74 % ) Sampling Time: 00:07:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 01:31:55 (hh:mm:ss) Elapsed Time, 114481 HSPs Collected Number of families returned by RECON: 8187 Round Time: 01:48:59 (hh:mm:ss) Elapsed Time : 74 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60465 repeats masked totaling 24433425 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270058268 bp Num Contigs Represented = 170 Non ambiguous bp: Initial: 270035840 bp After Masking: 233803979 bp Masked: 13.42 % -- Input Database Coverage: 400131826 bp out of 1211470109 bp ( 33.03 % ) Sampling Time: 00:24:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23014720 Comparison Time: 10:47:14 (hh:mm:ss) Elapsed Time, 232414 HSPs Collected Number of families returned by RECON: 48433 Round Time: 11:24:51 (hh:mm:ss) Elapsed Time : 253 families discovered. RepeatScout/RECON discovery complete: 414 families found Classification Time: 00:14:07 (hh:mm:ss) Elapsed Time Program Time: 14:07:00 (hh:mm:ss) Elapsed Time