RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/900/963/305/GCF_900963305.1_fEcheNa1.1/trackData/repeatModeler/RM_7644.MonDec262126132022 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: 1672118772 Database = /hive/data/genomes/asmHubs/refseqBuild/GCF/900/963/305/GCF_900963305.1_fEcheNa1.1/trackData/repeatModeler/GCF_900963305.1_fEcheNa1.1 - Sequences = 38 - Bases = 544229245 Storage Throughput = good ( 747.55 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40076665 bp ( 40035825 non ambiguous ) - Num Contigs Represented = 26 - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:56 (hh:mm:ss) Elapsed Time Round Time: 00:25:57 (hh:mm:ss) Elapsed Time : 242 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3333 repeats masked totaling 563305 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043115 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10002814 bp After Masking: 9340488 bp Masked: 6.62 % -- Input Database Coverage: 10043115 bp out of 544229245 bp ( 1.85 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:31 (hh:mm:ss) Elapsed Time, 3026 HSPs Collected Number of families returned by RECON: 992 Round Time: 00:08:45 (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 : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8540 repeats masked totaling 1518981 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033527 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 30032988 bp After Masking: 28190775 bp Masked: 6.13 % -- Input Database Coverage: 40076642 bp out of 544229245 bp ( 7.36 % ) Sampling Time: 00:01:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:45:21 (hh:mm:ss) Elapsed Time, 23892 HSPs Collected Number of families returned by RECON: 4546 Round Time: 00:51:34 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 34263 repeats masked totaling 6186764 bp(s). - TE Masking time 00:01:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90168928 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90013437 bp After Masking: 82851529 bp Masked: 7.96 % -- Input Database Coverage: 130245570 bp out of 544229245 bp ( 23.93 % ) Sampling Time: 00:05:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 05:42:32 (hh:mm:ss) Elapsed Time, 193189 HSPs Collected Number of families returned by RECON: 19987 Round Time: 06:29:36 (hh:mm:ss) Elapsed Time : 269 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 137964 repeats masked totaling 26848706 bp(s). - TE Masking time 00:09:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270263311 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 270031894 bp After Masking: 240367528 bp Masked: 10.99 % -- Input Database Coverage: 400508881 bp out of 544229245 bp ( 73.59 % ) Sampling Time: 00:22:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 46:05:10 (hh:mm:ss) Elapsed Time, 660894 HSPs Collected Number of families returned by RECON: 89992 Round Time: 52:50:56 (hh:mm:ss) Elapsed Time : 738 families discovered. RepeatScout/RECON discovery complete: 1297 families found Classification Time: 01:31:00 (hh:mm:ss) Elapsed Time Program Time: 62:17:48 (hh:mm:ss) Elapsed Time