RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/535/GCA_011100535.1_mCalJac1.pat/trackData/repeatModeler/RM_16077.SatDec241330332022 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: 1671917431 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/535/GCA_011100535.1_mCalJac1.pat/trackData/repeatModeler/GCA_011100535.1_mCalJac1.pat - Sequences = 336 - Bases = 2682316413 - N50 = 156129252 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202510801-216975769 | [ 2 ] 188045833-202510800 | [ 1 ] 173580866-188045833 | [ ] 159115898-173580865 | [ 3 ] 144650930-159115897 | [ 1 ] 130185963-144650930 | [ 2 ] 115720995-130185962 | [ 4 ] 101256027-115720994 | [ 1 ] 86791060-101256027 | [ 2 ] 72326092-86791059 | [ 1 ] 57861124-72326091 | [ ] 43396157-57861124 | [ 5 ] 28931189-43396156 | [ ] 14466221-28931188 | [ ] 1254-14466221 |************************************************** [ 314 ] Storage Throughput = good ( 835.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40047734 bp ( 40003290 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:03:00 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:30 (hh:mm:ss) Elapsed Time Round Time: 00:23:48 (hh:mm:ss) Elapsed Time : 230 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14274 repeats masked totaling 2903533 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041167 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10028482 bp After Masking: 7013573 bp Masked: 30.06 % -- Input Database Coverage: 10041167 bp out of 2682316413 bp ( 0.37 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:24 (hh:mm:ss) Elapsed Time, 6832 HSPs Collected Number of families returned by RECON: 929 Round Time: 00:07:34 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49240 repeats masked totaling 9815873 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30046492 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30014733 bp After Masking: 19649939 bp Masked: 34.53 % -- Input Database Coverage: 40087659 bp out of 2682316413 bp ( 1.49 % ) Sampling Time: 00:03:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:24:55 (hh:mm:ss) Elapsed Time, 26550 HSPs Collected Number of families returned by RECON: 2272 Round Time: 00:32:15 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 153421 repeats masked totaling 31601851 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90316178 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 90014690 bp After Masking: 56726423 bp Masked: 36.98 % -- Input Database Coverage: 130403837 bp out of 2682316413 bp ( 4.86 % ) Sampling Time: 00:12:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 02:39:24 (hh:mm:ss) Elapsed Time, 96040 HSPs Collected Number of families returned by RECON: 8376 Round Time: 03:02:31 (hh:mm:ss) Elapsed Time : 175 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 500471 repeats masked totaling 102923239 bp(s). - TE Masking time 00:04:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271249020 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 270025142 bp After Masking: 162228212 bp Masked: 39.92 % -- Input Database Coverage: 401652857 bp out of 2682316413 bp ( 14.97 % ) Sampling Time: 00:39:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23116600 Comparison Time: 20:25:40 (hh:mm:ss) Elapsed Time, 582531 HSPs Collected Number of families returned by RECON: 34345 Round Time: 22:05:26 (hh:mm:ss) Elapsed Time : 409 families discovered. RepeatScout/RECON discovery complete: 904 families found Classification Time: 00:35:41 (hh:mm:ss) Elapsed Time Program Time: 26:47:16 (hh:mm:ss) Elapsed Time