RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.AuRu2P/RM_2957416.FriDec80300542023 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: 1702033253 Database = /dev/shm/rModeler.AuRu2P/GCA_960531495.1_fZeuFab8.1 - Sequences = 191 - Bases = 804731948 - N50 = 34678564 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 61378446-65762550 | [ 1 ] 56994343-61378446 | [ ] 52610240-56994343 | [ 1 ] 48226136-52610239 | [ ] 43842033-48226136 | [ ] 39457930-43842033 | [ 1 ] 35073826-39457929 |* [ 4 ] 30689723-35073826 |*** [ 11 ] 26305620-30689723 | [ 3 ] 21921516-26305619 | [ 1 ] 17537413-21921516 | [ ] 13153310-17537413 | [ ] 8769206-13153309 | [ ] 4385103-8769206 | [ ] 1000-4385103 |************************************************** [ 169 ] Storage Throughput = excellent ( 1354.58 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017455 bp ( 40008874 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:22 (hh:mm:ss) Elapsed Time Round Time: 00:30:46 (hh:mm:ss) Elapsed Time : 743 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11975 repeats masked totaling 2155299 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009096 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10006915 bp After Masking: 6747606 bp Masked: 32.57 % -- Input Database Coverage: 10009096 bp out of 804731948 bp ( 1.24 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:53 (hh:mm:ss) Elapsed Time, 7413 HSPs Collected Number of families returned by RECON: 1476 Round Time: 00:10:15 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35764 repeats masked totaling 6746428 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008279 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30001879 bp After Masking: 19582650 bp Masked: 34.73 % -- Input Database Coverage: 40017375 bp out of 804731948 bp ( 4.97 % ) Sampling Time: 00:15:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:27:33 (hh:mm:ss) Elapsed Time, 63784 HSPs Collected Number of families returned by RECON: 4905 Round Time: 00:44:14 (hh:mm:ss) Elapsed Time : 131 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 118099 repeats masked totaling 21902566 bp(s). - TE Masking time 00:01:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045542 bp Num Contigs Represented = 65 Non ambiguous bp: Initial: 90023742 bp After Masking: 57772980 bp Masked: 35.82 % -- Input Database Coverage: 130062917 bp out of 804731948 bp ( 16.16 % ) Sampling Time: 00:54:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 03:04:44 (hh:mm:ss) Elapsed Time, 284241 HSPs Collected Number of families returned by RECON: 15621 Round Time: 04:09:44 (hh:mm:ss) Elapsed Time : 559 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:13:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 432691 repeats masked totaling 79412541 bp(s). - TE Masking time 00:09:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270061806 bp Num Contigs Represented = 102 Non ambiguous bp: Initial: 270000709 bp After Masking: 159712500 bp Masked: 40.85 % -- Input Database Coverage: 400124723 bp out of 804731948 bp ( 49.72 % ) Sampling Time: 02:28:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 20:52:20 (hh:mm:ss) Elapsed Time, 749678 HSPs Collected Number of families returned by RECON: 49819 Round Time: 24:17:08 (hh:mm:ss) Elapsed Time : 1087 families discovered. RepeatScout/RECON discovery complete: 2537 families found Classification Time: 01:21:58 (hh:mm:ss) Elapsed Time Program Time: 31:14:05 (hh:mm:ss) Elapsed Time