RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IGbLmU/RM_24708.ThuJun270508402024 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: 1719490119 Database = /dev/shm/rModeler.IGbLmU/GCF_030035675.1_rRhiFlo1.hap2 - Sequences = 76 - Bases = 2307419594 Storage Throughput = excellent ( 1002.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40123303 bp ( 40035586 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:03:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:30 (hh:mm:ss) Elapsed Time Round Time: 00:28:52 (hh:mm:ss) Elapsed Time : 588 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19358 repeats masked totaling 4526017 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040376 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 10017134 bp After Masking: 5218262 bp Masked: 47.91 % -- Input Database Coverage: 10040376 bp out of 2307419594 bp ( 0.44 % ) Sampling Time: 00:01:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:40 (hh:mm:ss) Elapsed Time, 6858 HSPs Collected Number of families returned by RECON: 1213 Round Time: 00:06:37 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58898 repeats masked totaling 14047736 bp(s). - TE Masking time 00:00:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30082847 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30018372 bp After Masking: 15300359 bp Masked: 49.03 % -- Input Database Coverage: 40123223 bp out of 2307419594 bp ( 1.74 % ) Sampling Time: 00:04:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:22:18 (hh:mm:ss) Elapsed Time, 46434 HSPs Collected Number of families returned by RECON: 4041 Round Time: 00:28:34 (hh:mm:ss) Elapsed Time : 118 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:08:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 189712 repeats masked totaling 44841071 bp(s). - TE Masking time 00:02:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90128016 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 90031534 bp After Masking: 43713781 bp Masked: 51.45 % -- Input Database Coverage: 130251239 bp out of 2307419594 bp ( 5.64 % ) Sampling Time: 00:15:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 02:21:35 (hh:mm:ss) Elapsed Time, 201253 HSPs Collected Number of families returned by RECON: 11763 Round Time: 02:46:35 (hh:mm:ss) Elapsed Time : 409 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:24:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 628575 repeats masked totaling 145668433 bp(s). - TE Masking time 00:12:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271067664 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 270021681 bp After Masking: 119345364 bp Masked: 55.80 % -- Input Database Coverage: 401318903 bp out of 2307419594 bp ( 17.39 % ) Sampling Time: 00:47:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22994371 Comparison Time: 17:01:52 (hh:mm:ss) Elapsed Time, 580164 HSPs Collected Number of families returned by RECON: 36476 Round Time: 18:49:41 (hh:mm:ss) Elapsed Time : 1086 families discovered. RepeatScout/RECON discovery complete: 2222 families found Classification Time: 01:31:14 (hh:mm:ss) Elapsed Time Program Time: 24:11:33 (hh:mm:ss) Elapsed Time