RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.pdvq5x/RM_3418212.WedJul241254412024 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: 1721850871 Database = /dev/shm/rModeler.pdvq5x/GCF_022539355.2_HSTE1.2 - Sequences = 53 - Bases = 602165188 Storage Throughput = fair ( 659.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033174 bp ( 40006986 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:11 (hh:mm:ss) Elapsed Time Round Time: 00:34:43 (hh:mm:ss) Elapsed Time : 375 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 00:00:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7504 repeats masked totaling 1014990 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041947 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10037051 bp After Masking: 8714962 bp Masked: 13.17 % -- Input Database Coverage: 10041947 bp out of 602165188 bp ( 1.67 % ) Sampling Time: 00:01:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 01:01:57 (hh:mm:ss) Elapsed Time, 5123 HSPs Collected Number of families returned by RECON: 1220 Round Time: 01:05:14 (hh:mm:ss) Elapsed Time : 11 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 00:02:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24452 repeats masked totaling 3414884 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031159 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30009867 bp After Masking: 25692134 bp Masked: 14.39 % -- Input Database Coverage: 40073106 bp out of 602165188 bp ( 6.65 % ) Sampling Time: 00:03:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 03:30:57 (hh:mm:ss) Elapsed Time, 37945 HSPs Collected Number of families returned by RECON: 4968 Round Time: 03:42:19 (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 : 00:01:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80017 repeats masked totaling 11116619 bp(s). - TE Masking time 00:01:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90083009 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 90034311 bp After Masking: 76284897 bp Masked: 15.27 % -- Input Database Coverage: 130156115 bp out of 602165188 bp ( 21.61 % ) Sampling Time: 00:09:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 12:11:11 (hh:mm:ss) Elapsed Time, 223259 HSPs Collected Number of families returned by RECON: 19246 Round Time: 12:56:33 (hh:mm:ss) Elapsed Time : 384 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 297551 repeats masked totaling 44593841 bp(s). - TE Masking time 00:07:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270180643 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 270032625 bp After Masking: 217192476 bp Masked: 19.57 % -- Input Database Coverage: 400336758 bp out of 602165188 bp ( 66.48 % ) Sampling Time: 00:30:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 47:57:59 (hh:mm:ss) Elapsed Time, 745138 HSPs Collected Number of families returned by RECON: 74492 Round Time: 50:05:10 (hh:mm:ss) Elapsed Time : 976 families discovered. RepeatScout/RECON discovery complete: 1833 families found Classification Time: 01:20:18 (hh:mm:ss) Elapsed Time Program Time: 69:44:17 (hh:mm:ss) Elapsed Time