RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.WK47xO/RM_3367397.ThuDec51546142024 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: 1733442373 Database = /scratch/tmp/rModeler.WK47xO/GCA_964204955.1_kaStyClav1.hap2.1 - Sequences = 243 - Bases = 381580332 - N50 = 24803888 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 30686284-32878090 | [ 1 ] 28494478-30686284 | [ 1 ] 26302672-28494478 | [ ] 24110866-26302672 |* [ 7 ] 21919060-24110866 | [ 1 ] 19727254-21919060 | [ 4 ] 17535448-19727254 | [ ] 15343642-17535448 | [ ] 13151836-15343642 | [ 1 ] 10960030-13151836 | [ ] 8768224-10960030 | [ ] 6576418-8768224 | [ ] 4384612-6576418 | [ ] 2192806-4384612 | [ 1 ] 1000-2192806 |************************************************** [ 227 ] Storage Throughput = excellent ( 1425.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030911 bp ( 40030311 non ambiguous ) - Num Contigs Represented = 71 - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:23 (hh:mm:ss) Elapsed Time Round Time: 00:13:46 (hh:mm:ss) Elapsed Time : 865 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17044 repeats masked totaling 3357829 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10010782 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10010582 bp After Masking: 6185572 bp Masked: 38.21 % -- Input Database Coverage: 10010782 bp out of 381580332 bp ( 2.62 % ) Sampling Time: 00:00:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:59 (hh:mm:ss) Elapsed Time, 13632 HSPs Collected Number of families returned by RECON: 826 Round Time: 00:04:18 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49251 repeats masked totaling 10855735 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30020049 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 30019649 bp After Masking: 17552554 bp Masked: 41.53 % -- Input Database Coverage: 40030831 bp out of 381580332 bp ( 10.49 % ) Sampling Time: 00:02:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:13:16 (hh:mm:ss) Elapsed Time, 31261 HSPs Collected Number of families returned by RECON: 3227 Round Time: 00:16:10 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 156851 repeats masked totaling 32032011 bp(s). - TE Masking time 00:01:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022911 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 90021711 bp After Masking: 52747359 bp Masked: 41.41 % -- Input Database Coverage: 130053742 bp out of 381580332 bp ( 34.08 % ) Sampling Time: 00:06:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 01:18:29 (hh:mm:ss) Elapsed Time, 302477 HSPs Collected Number of families returned by RECON: 10243 Round Time: 01:29:05 (hh:mm:ss) Elapsed Time : 431 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 475624 repeats masked totaling 100709342 bp(s). - TE Masking time 00:06:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 251526258 bp Num Contigs Represented = 217 Non ambiguous bp: Initial: 251522858 bp After Masking: 136139790 bp Masked: 45.87 % -- Input Database Coverage: 381580000 bp out of 381580332 bp ( 100.00 % ) Sampling Time: 00:18:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 20285265 Comparison Time: 07:13:49 (hh:mm:ss) Elapsed Time, 733065 HSPs Collected Number of families returned by RECON: 28621 Round Time: 08:07:21 (hh:mm:ss) Elapsed Time : 926 families discovered. RepeatScout/RECON discovery complete: 2299 families found Classification Time: 01:22:05 (hh:mm:ss) Elapsed Time Program Time: 11:32:45 (hh:mm:ss) Elapsed Time