RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/902/652/985/GCF_902652985.1_xPecMax1.1/trackData/repeatModeler/RM_18373.SatDec241533242022 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: 1671924803 Database = /hive/data/genomes/asmHubs/refseqBuild/GCF/902/652/985/GCF_902652985.1_xPecMax1.1/trackData/repeatModeler/GCF_902652985.1_xPecMax1.1 - Sequences = 3983 - Bases = 918306378 - N50 = 45552881 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 56071616-60076705 | [ 1 ] 52066527-56071615 | [ 3 ] 48061439-52066527 | [ 1 ] 44056350-48061438 | [ 6 ] 40051262-44056350 | [ 1 ] 36046173-40051261 | [ 4 ] 32041085-36046173 | [ 3 ] 28035996-32041084 | [ ] 24030908-28035996 | [ ] 20025819-24030907 | [ ] 16020731-20025819 | [ ] 12015642-16020730 | [ ] 8010554-12015642 | [ ] 4005465-8010553 | [ ] 377-4005465 |************************************************** [ 3964 ] Storage Throughput = good ( 746.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031893 bp ( 40002083 non ambiguous ) - Num Contigs Represented = 210 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:49 (hh:mm:ss) Elapsed Time Round Time: 00:24:13 (hh:mm:ss) Elapsed Time : 574 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8381 repeats masked totaling 1452971 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043275 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 10037075 bp After Masking: 6139084 bp Masked: 38.84 % -- Input Database Coverage: 10043275 bp out of 918306378 bp ( 1.09 % ) Sampling Time: 00:03:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 40755 Comparison Time: 00:06:37 (hh:mm:ss) Elapsed Time, 6650 HSPs Collected Number of families returned by RECON: 1171 Round Time: 00:10:56 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26334 repeats masked totaling 4651178 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028684 bp Num Contigs Represented = 151 Non ambiguous bp: Initial: 30005074 bp After Masking: 17990236 bp Masked: 40.04 % -- Input Database Coverage: 40071959 bp out of 918306378 bp ( 4.36 % ) Sampling Time: 00:10:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 340725 Comparison Time: 00:32:44 (hh:mm:ss) Elapsed Time, 43527 HSPs Collected Number of families returned by RECON: 4001 Round Time: 00:48:47 (hh:mm:ss) Elapsed Time : 76 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 81637 repeats masked totaling 14590673 bp(s). - TE Masking time 00:02:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90073929 bp Num Contigs Represented = 458 Non ambiguous bp: Initial: 90014174 bp After Masking: 53603109 bp Masked: 40.45 % -- Input Database Coverage: 130145888 bp out of 918306378 bp ( 14.17 % ) Sampling Time: 00:29:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 3178981 Comparison Time: 03:30:35 (hh:mm:ss) Elapsed Time, 258097 HSPs Collected Number of families returned by RECON: 11896 Round Time: 04:33:28 (hh:mm:ss) Elapsed Time : 439 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:16:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 301673 repeats masked totaling 57124113 bp(s). - TE Masking time 00:12:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270237649 bp Num Contigs Represented = 1310 Non ambiguous bp: Initial: 270015711 bp After Masking: 147393642 bp Masked: 45.41 % -- Input Database Coverage: 400383537 bp out of 918306378 bp ( 43.60 % ) Sampling Time: 01:35:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 28467285 Comparison Time: 24:31:38 (hh:mm:ss) Elapsed Time, 752681 HSPs Collected Number of families returned by RECON: 34038 Round Time: 29:19:11 (hh:mm:ss) Elapsed Time : 1106 families discovered. RepeatScout/RECON discovery complete: 2208 families found Classification Time: 02:22:13 (hh:mm:ss) Elapsed Time Program Time: 37:38:48 (hh:mm:ss) Elapsed Time