RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Yt6YOb/RM_1923257.SunJul200007102025 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: 1752995228 Database = /dev/shm/rModeler.Yt6YOb/GCA_048772025.1_bTaeGut7.pat - Sequences = 39 - Bases = 1021668102 Storage Throughput = excellent ( 1147.34 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010431 bp ( 40010431 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:07 (hh:mm:ss) Elapsed Time Round Time: 00:30:18 (hh:mm:ss) Elapsed Time : 140 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2840 repeats masked totaling 653375 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10002925 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10002925 bp After Masking: 8984489 bp Masked: 10.18 % -- Input Database Coverage: 10002925 bp out of 1021668102 bp ( 0.98 % ) Sampling Time: 00:00:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:51 (hh:mm:ss) Elapsed Time, 1266 HSPs Collected Number of families returned by RECON: 250 Round Time: 00:06:52 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8160 repeats masked totaling 1988752 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007504 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 30007504 bp After Masking: 27005575 bp Masked: 10.00 % -- Input Database Coverage: 40010429 bp out of 1021668102 bp ( 3.92 % ) Sampling Time: 00:03:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:36:38 (hh:mm:ss) Elapsed Time, 14268 HSPs Collected Number of families returned by RECON: 1657 Round Time: 00:40:43 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 26241 repeats masked totaling 6223657 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90045854 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 90005735 bp After Masking: 80630272 bp Masked: 10.42 % -- Input Database Coverage: 130056283 bp out of 1021668102 bp ( 12.73 % ) Sampling Time: 00:09:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 04:47:41 (hh:mm:ss) Elapsed Time, 100099 HSPs Collected Number of families returned by RECON: 10548 Round Time: 05:00:58 (hh:mm:ss) Elapsed Time : 94 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 87134 repeats masked totaling 21930830 bp(s). - TE Masking time 00:05:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270002260 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 270002260 bp After Masking: 238148630 bp Masked: 11.80 % -- Input Database Coverage: 400058543 bp out of 1021668102 bp ( 39.16 % ) Sampling Time: 00:31:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22804881 Comparison Time: 39:41:45 (hh:mm:ss) Elapsed Time, 579009 HSPs Collected Number of families returned by RECON: 72006 Round Time: 41:31:19 (hh:mm:ss) Elapsed Time : 246 families discovered. RepeatScout/RECON discovery complete: 485 families found Classification Time: 00:49:58 (hh:mm:ss) Elapsed Time Program Time: 48:40:08 (hh:mm:ss) Elapsed Time