RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.UMKDu5/RM_1782172.WedApr230053002025 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: 1745394779 Database = /data/tmp/rModeler.UMKDu5/GCA_048128725.1_fSymNem1.1_haplotype_1 - Sequences = 86 - Bases = 1079363760 Storage Throughput = excellent ( 1163.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017525 bp ( 40017125 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:00:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:38 (hh:mm:ss) Elapsed Time Round Time: 00:28:05 (hh:mm:ss) Elapsed Time : 1021 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21673 repeats masked totaling 2820591 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003428 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10003428 bp After Masking: 6880941 bp Masked: 31.21 % -- Input Database Coverage: 10003428 bp out of 1079363760 bp ( 0.93 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:37 (hh:mm:ss) Elapsed Time, 15431 HSPs Collected Number of families returned by RECON: 2064 Round Time: 00:11:09 (hh:mm:ss) Elapsed Time : 31 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64979 repeats masked totaling 8671151 bp(s). - TE Masking time 00:00:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014092 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30013692 bp After Masking: 20630037 bp Masked: 31.26 % -- Input Database Coverage: 40017520 bp out of 1079363760 bp ( 3.71 % ) Sampling Time: 00:03:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:28:33 (hh:mm:ss) Elapsed Time, 99614 HSPs Collected Number of families returned by RECON: 6555 Round Time: 00:45:38 (hh:mm:ss) Elapsed Time : 289 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 218322 repeats masked totaling 30555173 bp(s). - TE Masking time 00:03:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90004870 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 90004270 bp After Masking: 57486720 bp Masked: 36.13 % -- Input Database Coverage: 130022390 bp out of 1079363760 bp ( 12.05 % ) Sampling Time: 00:10:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:00:35 (hh:mm:ss) Elapsed Time, 391120 HSPs Collected Number of families returned by RECON: 18081 Round Time: 03:53:59 (hh:mm:ss) Elapsed Time : 712 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 753766 repeats masked totaling 109925381 bp(s). - TE Masking time 00:14:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023399 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 270019099 bp After Masking: 154269306 bp Masked: 42.87 % -- Input Database Coverage: 400045789 bp out of 1079363760 bp ( 37.06 % ) Sampling Time: 00:34:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 20:17:17 (hh:mm:ss) Elapsed Time, 936903 HSPs Collected Number of families returned by RECON: 55534 Round Time: 24:41:42 (hh:mm:ss) Elapsed Time : 1538 families discovered. RepeatScout/RECON discovery complete: 3591 families found Classification Time: 02:08:57 (hh:mm:ss) Elapsed Time Program Time: 32:09:30 (hh:mm:ss) Elapsed Time