RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/017/639/675/GCA_017639675.1_fAplTae1.pri/trackData/repeatModeler/RM_35160.MonDec262121132022 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: 1672118472 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/017/639/675/GCA_017639675.1_fAplTae1.pri/trackData/repeatModeler/GCA_017639675.1_fAplTae1.pri - Sequences = 41 - Bases = 461946147 Storage Throughput = good ( 835.11 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40694375 bp ( 40025641 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:24 (hh:mm:ss) Elapsed Time Round Time: 00:18:12 (hh:mm:ss) Elapsed Time : 215 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2171 repeats masked totaling 494217 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10325418 bp Num Contigs Represented = 21 Non ambiguous bp: Initial: 10005971 bp After Masking: 8311411 bp Masked: 16.94 % -- Input Database Coverage: 10325418 bp out of 461946147 bp ( 2.24 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33411 Comparison Time: 00:06:18 (hh:mm:ss) Elapsed Time, 2844 HSPs Collected Number of families returned by RECON: 960 Round Time: 00:09:02 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6516 repeats masked totaling 1424689 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30368948 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30019661 bp After Masking: 24717377 bp Masked: 17.66 % -- Input Database Coverage: 40694366 bp out of 461946147 bp ( 8.81 % ) Sampling Time: 00:06:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:34:11 (hh:mm:ss) Elapsed Time, 19902 HSPs Collected Number of families returned by RECON: 3938 Round Time: 00:43:28 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22671 repeats masked totaling 4725426 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91505770 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 90031603 bp After Masking: 74042580 bp Masked: 17.76 % -- Input Database Coverage: 132200136 bp out of 461946147 bp ( 28.62 % ) Sampling Time: 00:21:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 04:07:58 (hh:mm:ss) Elapsed Time, 189602 HSPs Collected Number of families returned by RECON: 16863 Round Time: 04:57:01 (hh:mm:ss) Elapsed Time : 270 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:44:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100333 repeats masked totaling 21351960 bp(s). - TE Masking time 00:07:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 274835914 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 270024854 bp After Masking: 217125297 bp Masked: 19.59 % -- Input Database Coverage: 407036050 bp out of 461946147 bp ( 88.11 % ) Sampling Time: 00:55:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23698170 Comparison Time: 30:52:33 (hh:mm:ss) Elapsed Time, 781015 HSPs Collected Number of families returned by RECON: 69713 Round Time: 35:27:53 (hh:mm:ss) Elapsed Time : 740 families discovered. RepeatScout/RECON discovery complete: 1262 families found Classification Time: 00:55:31 (hh:mm:ss) Elapsed Time Program Time: 42:31:07 (hh:mm:ss) Elapsed Time