RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/020/510/985/GCA_020510985.1_fPhoLeu1.pri/trackData/repeatModeler/RM_22304.SunDec252250242022 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: 1672037423 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/020/510/985/GCA_020510985.1_fPhoLeu1.pri/trackData/repeatModeler/GCA_020510985.1_fPhoLeu1.pri - Sequences = 512 - Bases = 6032307556 - N50 = 443879367 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 467820398-501236086 | [ 4 ] 434404710-467820398 | [ 3 ] 400989022-434404710 | [ 2 ] 367573334-400989022 | [ ] 334157646-367573334 | [ 1 ] 300741958-334157646 | [ 4 ] 267326270-300741958 | [ ] 233910582-267326270 | [ ] 200494894-233910582 | [ ] 167079206-200494894 | [ 1 ] 133663518-167079206 | [ ] 100247830-133663518 | [ ] 66832142-100247830 | [ ] 33416454-66832142 | [ ] 766-33416454 |************************************************** [ 497 ] Storage Throughput = good ( 704.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40402053 bp ( 40008599 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:08:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:13 (hh:mm:ss) Elapsed Time Round Time: 00:43:50 (hh:mm:ss) Elapsed Time : 1186 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:02:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18607 repeats masked totaling 7783737 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10121016 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10009587 bp After Masking: 2107515 bp Masked: 78.95 % -- Input Database Coverage: 10121016 bp out of 6032307556 bp ( 0.17 % ) Sampling Time: 00:03:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:04:59 (hh:mm:ss) Elapsed Time, 3421 HSPs Collected Number of families returned by RECON: 967 Round Time: 00:08:56 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:06:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56487 repeats masked totaling 23192924 bp(s). - TE Masking time 00:01:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30320957 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 30038932 bp After Masking: 6454878 bp Masked: 78.51 % -- Input Database Coverage: 40441973 bp out of 6032307556 bp ( 0.67 % ) Sampling Time: 00:09:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:18:42 (hh:mm:ss) Elapsed Time, 36050 HSPs Collected Number of families returned by RECON: 3062 Round Time: 00:32:35 (hh:mm:ss) Elapsed Time : 87 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:19:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 174143 repeats masked totaling 70450629 bp(s). - TE Masking time 00:05:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90781492 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90002448 bp After Masking: 18443356 bp Masked: 79.51 % -- Input Database Coverage: 131223465 bp out of 6032307556 bp ( 2.18 % ) Sampling Time: 00:27:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2586675 Comparison Time: 01:27:27 (hh:mm:ss) Elapsed Time, 223026 HSPs Collected Number of families returned by RECON: 6747 Round Time: 02:20:04 (hh:mm:ss) Elapsed Time : 509 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:58:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 578220 repeats masked totaling 224446324 bp(s). - TE Masking time 00:20:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272420939 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 270023947 bp After Masking: 42372138 bp Masked: 84.31 % -- Input Database Coverage: 403644404 bp out of 6032307556 bp ( 6.69 % ) Sampling Time: 01:27:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23259610 Comparison Time: 07:42:05 (hh:mm:ss) Elapsed Time, 508318 HSPs Collected Number of families returned by RECON: 14397 Round Time: 10:21:21 (hh:mm:ss) Elapsed Time : 1067 families discovered. RepeatScout/RECON discovery complete: 2851 families found Classification Time: 02:15:39 (hh:mm:ss) Elapsed Time Program Time: 16:22:25 (hh:mm:ss) Elapsed Time