RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/555/GCA_011100555.1_mCalJac1.pat.X/trackData/repeatModeler/RM_16115.SatDec241330432022 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: 1671917442 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/011/100/555/GCA_011100555.1_mCalJac1.pat.X/trackData/repeatModeler/GCA_011100555.1_mCalJac1.pat.X - Sequences = 353 - Bases = 2829727687 - N50 = 156129252 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 202510801-216975769 | [ 2 ] 188045833-202510800 | [ 1 ] 173580866-188045833 | [ ] 159115898-173580865 | [ 3 ] 144650930-159115897 | [ 2 ] 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 |************************************************** [ 330 ] Storage Throughput = good ( 874.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40231523 bp ( 40037454 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:02:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:11:32 (hh:mm:ss) Elapsed Time Round Time: 00:22:40 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14774 repeats masked totaling 3120133 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10078917 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10032326 bp After Masking: 6721497 bp Masked: 33.00 % -- Input Database Coverage: 10078917 bp out of 2829727687 bp ( 0.36 % ) Sampling Time: 00:01:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:24 (hh:mm:ss) Elapsed Time, 7056 HSPs Collected Number of families returned by RECON: 845 Round Time: 00:07:42 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 48181 repeats masked totaling 9858373 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30152526 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30005048 bp After Masking: 19637120 bp Masked: 34.55 % -- Input Database Coverage: 40231443 bp out of 2829727687 bp ( 1.42 % ) Sampling Time: 00:04:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:24:47 (hh:mm:ss) Elapsed Time, 27765 HSPs Collected Number of families returned by RECON: 2371 Round Time: 00:32:33 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 156456 repeats masked totaling 32446963 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90419790 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 90000566 bp After Masking: 56161872 bp Masked: 37.60 % -- Input Database Coverage: 130651233 bp out of 2829727687 bp ( 4.62 % ) Sampling Time: 00:12:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 02:41:06 (hh:mm:ss) Elapsed Time, 106248 HSPs Collected Number of families returned by RECON: 7689 Round Time: 03:03:23 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 496732 repeats masked totaling 104337176 bp(s). - TE Masking time 00:04:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271130178 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 270009042 bp After Masking: 160960884 bp Masked: 40.39 % -- Input Database Coverage: 401781411 bp out of 2829727687 bp ( 14.20 % ) Sampling Time: 00:36:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23062236 Comparison Time: 20:21:58 (hh:mm:ss) Elapsed Time, 833954 HSPs Collected Number of families returned by RECON: 32465 Round Time: 21:49:41 (hh:mm:ss) Elapsed Time : 410 families discovered. RepeatScout/RECON discovery complete: 929 families found Classification Time: 00:33:13 (hh:mm:ss) Elapsed Time Program Time: 26:29:12 (hh:mm:ss) Elapsed Time