RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/refseqBuild/GCF/901/709/675/GCF_901709675.1_fSynAcu1.2/trackData/repeatModeler/RM_5769.SunDec252242392022 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: 1672036958 Database = /hive/data/genomes/asmHubs/refseqBuild/GCF/901/709/675/GCF_901709675.1_fSynAcu1.2/trackData/repeatModeler/GCF_901709675.1_fSynAcu1.2 - Sequences = 87 - Bases = 324331233 Storage Throughput = good ( 749.03 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025808 bp ( 40022608 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:22 (hh:mm:ss) Elapsed Time Round Time: 00:24:27 (hh:mm:ss) Elapsed Time : 363 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5393 repeats masked totaling 1387892 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018726 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10018526 bp After Masking: 8349478 bp Masked: 16.66 % -- Input Database Coverage: 10018726 bp out of 324331233 bp ( 3.09 % ) Sampling Time: 00:00:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:21 (hh:mm:ss) Elapsed Time, 6989 HSPs Collected Number of families returned by RECON: 1165 Round Time: 00:08:08 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17404 repeats masked totaling 4407242 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007029 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30004029 bp After Masking: 24862565 bp Masked: 17.14 % -- Input Database Coverage: 40025755 bp out of 324331233 bp ( 12.34 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:34:30 (hh:mm:ss) Elapsed Time, 33964 HSPs Collected Number of families returned by RECON: 4755 Round Time: 00:41:50 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61392 repeats masked totaling 14698132 bp(s). - TE Masking time 00:01:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90017061 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 90014761 bp After Masking: 73088250 bp Masked: 18.80 % -- Input Database Coverage: 130042816 bp out of 324331233 bp ( 40.10 % ) Sampling Time: 00:06:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 03:57:30 (hh:mm:ss) Elapsed Time, 216002 HSPs Collected Number of families returned by RECON: 18132 Round Time: 04:48:33 (hh:mm:ss) Elapsed Time : 362 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 170591 repeats masked totaling 38145235 bp(s). - TE Masking time 00:06:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 194288063 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 194279863 bp After Masking: 151164939 bp Masked: 22.19 % -- Input Database Coverage: 324330879 bp out of 324331233 bp ( 100.00 % ) Sampling Time: 00:16:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 11934055 Comparison Time: 16:25:38 (hh:mm:ss) Elapsed Time, 343051 HSPs Collected Number of families returned by RECON: 45510 Round Time: 18:29:11 (hh:mm:ss) Elapsed Time : 590 families discovered. RepeatScout/RECON discovery complete: 1391 families found Classification Time: 01:07:22 (hh:mm:ss) Elapsed Time Program Time: 25:39:31 (hh:mm:ss) Elapsed Time