RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.mOGcrR/RM_27259.MonDec21728002024 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: 1733189277 Database = /scratch/tmp/rModeler.mOGcrR/GCA_022682495.2_HLdesRot8A.1 - Sequences = 573 - Bases = 2119704833 - N50 = 167477801 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198107767-212258161 | [ 3 ] 183957374-198107767 | [ ] 169806981-183957374 | [ 1 ] 155656588-169806981 | [ 2 ] 141506195-155656588 | [ ] 127355801-141506194 | [ 2 ] 113205408-127355801 | [ 2 ] 99055015-113205408 | [ 3 ] 84904622-99055015 | [ 1 ] 70754229-84904622 | [ ] 56603835-70754228 | [ ] 42453442-56603835 | [ ] 28303049-42453442 | [ ] 14152656-28303049 | [ ] 2263-14152656 |************************************************** [ 559 ] Storage Throughput = fair ( 545.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035041 bp ( 40031609 non ambiguous ) - Num Contigs Represented = 52 - Sequence extraction : 00:03:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:13 (hh:mm:ss) Elapsed Time Round Time: 00:33:03 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:46 (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... 7947 repeats masked totaling 2299984 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030997 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10030525 bp After Masking: 7629480 bp Masked: 23.94 % -- Input Database Coverage: 10030997 bp out of 2119704833 bp ( 0.47 % ) Sampling Time: 00:01:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:08 (hh:mm:ss) Elapsed Time, 184445 HSPs Collected Number of families returned by RECON: 804 Round Time: 00:13:14 (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 : 00:02:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28387 repeats masked totaling 7849406 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30003964 bp Num Contigs Represented = 40 Non ambiguous bp: Initial: 30001004 bp After Masking: 21700538 bp Masked: 27.67 % -- Input Database Coverage: 40034961 bp out of 2119704833 bp ( 1.89 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:27:39 (hh:mm:ss) Elapsed Time, 30232 HSPs Collected Number of families returned by RECON: 2447 Round Time: 00:34:17 (hh:mm:ss) Elapsed Time : 61 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 92877 repeats masked totaling 25011063 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044931 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 90033491 bp After Masking: 64111539 bp Masked: 28.79 % -- Input Database Coverage: 130079892 bp out of 2119704833 bp ( 6.14 % ) Sampling Time: 00:11:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:18:48 (hh:mm:ss) Elapsed Time, 109621 HSPs Collected Number of families returned by RECON: 9157 Round Time: 03:35:48 (hh:mm:ss) Elapsed Time : 176 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 317162 repeats masked totaling 84378755 bp(s). - TE Masking time 00:05:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270064322 bp Num Contigs Represented = 203 Non ambiguous bp: Initial: 270033945 bp After Masking: 181964299 bp Masked: 32.61 % -- Input Database Coverage: 400144214 bp out of 2119704833 bp ( 18.88 % ) Sampling Time: 00:36:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23048655 Comparison Time: 25:43:08 (hh:mm:ss) Elapsed Time, 1211423 HSPs Collected Number of families returned by RECON: 39516 Round Time: 27:36:01 (hh:mm:ss) Elapsed Time : 372 families discovered. RepeatScout/RECON discovery complete: 829 families found Classification Time: 00:36:12 (hh:mm:ss) Elapsed Time Program Time: 33:08:36 (hh:mm:ss) Elapsed Time