RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.VqG2uR/RM_11944.SunDec80100512024 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: 1733648450 Database = /scratch/tmp/rModeler.VqG2uR/GCA_038363175.2_mArtLit1.hap2 - Sequences = 312 - Bases = 2096453601 - N50 = 180695055 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 227975225-244258554 | [ 1 ] 211691896-227975224 | [ 1 ] 195408567-211691895 | [ ] 179125238-195408566 | [ 3 ] 162841910-179125238 | [ 1 ] 146558581-162841909 | [ 1 ] 130275252-146558580 | [ 1 ] 113991923-130275251 | [ 2 ] 97708594-113991922 | [ 2 ] 81425266-97708594 | [ ] 65141937-81425265 | [ ] 48858608-65141936 | [ 2 ] 32575279-48858607 | [ ] 16291950-32575278 | [ ] 8622-16291950 |************************************************** [ 298 ] Storage Throughput = fair ( 579.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012559 bp ( 40012459 non ambiguous ) - Num Contigs Represented = 29 - Sequence extraction : 00:03:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:50 (hh:mm:ss) Elapsed Time Round Time: 00:36:08 (hh:mm:ss) Elapsed Time : 207 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8896 repeats masked totaling 2334475 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001106 bp Num Contigs Represented = 16 Non ambiguous bp: Initial: 10001006 bp After Masking: 7573206 bp Masked: 24.28 % -- Input Database Coverage: 10001106 bp out of 2096453601 bp ( 0.48 % ) Sampling Time: 00:01:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:19 (hh:mm:ss) Elapsed Time, 26233 HSPs Collected Number of families returned by RECON: 803 Round Time: 00:08:27 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 27724 repeats masked totaling 7633362 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011442 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30011442 bp After Masking: 21947820 bp Masked: 26.87 % -- Input Database Coverage: 40012548 bp out of 2096453601 bp ( 1.91 % ) Sampling Time: 00:04:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:39:41 (hh:mm:ss) Elapsed Time, 716658 HSPs Collected Number of families returned by RECON: 2182 Round Time: 00:45:17 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 91360 repeats masked totaling 24549855 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022018 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90021418 bp After Masking: 63879894 bp Masked: 29.04 % -- Input Database Coverage: 130034566 bp out of 2096453601 bp ( 6.20 % ) Sampling Time: 00:13:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 04:12:54 (hh:mm:ss) Elapsed Time, 3638234 HSPs Collected Number of families returned by RECON: 8315 Round Time: 04:34:12 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:22:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 301370 repeats masked totaling 81775964 bp(s). - TE Masking time 00:05:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034752 bp Num Contigs Represented = 106 Non ambiguous bp: Initial: 270034236 bp After Masking: 183870133 bp Masked: 31.91 % -- Input Database Coverage: 400069318 bp out of 2096453601 bp ( 19.08 % ) Sampling Time: 00:40:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 30:28:51 (hh:mm:ss) Elapsed Time, 20401072 HSPs Collected Number of families returned by RECON: 36709 Round Time: 32:02:46 (hh:mm:ss) Elapsed Time : 414 families discovered. RepeatScout/RECON discovery complete: 847 families found Classification Time: 00:41:34 (hh:mm:ss) Elapsed Time Program Time: 38:48:24 (hh:mm:ss) Elapsed Time