RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.KCofxN/RM_3287169.FriNov151320292024 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: 1731705629 Database = /scratch/tmp/rModeler.KCofxN/GCA_038363095.1_mArtLit.hap1 - Sequences = 419 - Bases = 2293600955 - N50 = 176201619 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 229047550-245407277 | [ 1 ] 212687824-229047550 | [ 1 ] 196328098-212687824 | [ ] 179968372-196328098 | [ 2 ] 163608646-179968372 | [ 1 ] 147248920-163608646 | [ 3 ] 130889194-147248920 | [ 2 ] 114529468-130889194 | [ 1 ] 98169742-114529468 | [ 2 ] 81810016-98169742 | [ ] 65450290-81810016 | [ ] 49090564-65450290 | [ 2 ] 32730838-49090564 | [ 1 ] 16371112-32730838 | [ 1 ] 11386-16371112 |************************************************** [ 402 ] Storage Throughput = excellent ( 1496.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40006674 bp ( 40006274 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:53 (hh:mm:ss) Elapsed Time Round Time: 00:13:51 (hh:mm:ss) Elapsed Time : 214 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 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7902 repeats masked totaling 2401232 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015110 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 10014910 bp After Masking: 7495009 bp Masked: 25.16 % -- Input Database Coverage: 10015110 bp out of 2293600955 bp ( 0.44 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:17 (hh:mm:ss) Elapsed Time, 10972 HSPs Collected Number of families returned by RECON: 902 Round Time: 00:04:06 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28695 repeats masked totaling 8288442 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031561 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30031361 bp After Masking: 21284312 bp Masked: 29.13 % -- Input Database Coverage: 40046671 bp out of 2293600955 bp ( 1.75 % ) Sampling Time: 00:01:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:16:10 (hh:mm:ss) Elapsed Time, 435523 HSPs Collected Number of families returned by RECON: 2142 Round Time: 00:18:38 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92665 repeats masked totaling 25559460 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015312 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90014612 bp After Masking: 63190930 bp Masked: 29.80 % -- Input Database Coverage: 130061983 bp out of 2293600955 bp ( 5.67 % ) Sampling Time: 00:06:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:36:43 (hh:mm:ss) Elapsed Time, 3952602 HSPs Collected Number of families returned by RECON: 7826 Round Time: 01:45:57 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 309348 repeats masked totaling 85814677 bp(s). - TE Masking time 00:02:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270022533 bp Num Contigs Represented = 85 Non ambiguous bp: Initial: 270021633 bp After Masking: 180662466 bp Masked: 33.09 % -- Input Database Coverage: 400084516 bp out of 2293600955 bp ( 17.44 % ) Sampling Time: 00:18:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22913065 Comparison Time: 10:49:03 (hh:mm:ss) Elapsed Time, 30206924 HSPs Collected Number of families returned by RECON: 33419 Round Time: 11:25:18 (hh:mm:ss) Elapsed Time : 385 families discovered. RepeatScout/RECON discovery complete: 839 families found Classification Time: 00:20:31 (hh:mm:ss) Elapsed Time Program Time: 14:08:21 (hh:mm:ss) Elapsed Time