RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.eoAcaU/RM_150685.MonJan21156572023 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: 1672689416 Database = /dev/shm/rModeler.eoAcaU/GCA_014839685.1_fAnaAna1.pri - Sequences = 33 - Bases = 867632993 Storage Throughput = excellent ( 1053.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40005182 bp ( 40004282 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:14 (hh:mm:ss) Elapsed Time Round Time: 00:17:06 (hh:mm:ss) Elapsed Time : 623 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14791 repeats masked totaling 2198791 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001041 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000741 bp After Masking: 7660228 bp Masked: 23.40 % -- Input Database Coverage: 10001041 bp out of 867632993 bp ( 1.15 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:45 (hh:mm:ss) Elapsed Time, 12641 HSPs Collected Number of families returned by RECON: 1654 Round Time: 00:07:50 (hh:mm:ss) Elapsed Time : 34 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49847 repeats masked totaling 7975328 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004061 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30003461 bp After Masking: 21641677 bp Masked: 27.87 % -- Input Database Coverage: 40005102 bp out of 867632993 bp ( 4.61 % ) Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:31:16 (hh:mm:ss) Elapsed Time, 56892 HSPs Collected Number of families returned by RECON: 4822 Round Time: 00:34:27 (hh:mm:ss) Elapsed Time : 161 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 165946 repeats masked totaling 27456117 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90092603 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90021316 bp After Masking: 61582559 bp Masked: 31.59 % -- Input Database Coverage: 130097705 bp out of 867632993 bp ( 14.99 % ) Sampling Time: 00:05:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 03:06:10 (hh:mm:ss) Elapsed Time, 241720 HSPs Collected Number of families returned by RECON: 14230 Round Time: 03:21:36 (hh:mm:ss) Elapsed Time : 419 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 562753 repeats masked totaling 96091269 bp(s). - TE Masking time 00:06:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270111446 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 270014463 bp After Masking: 170527962 bp Masked: 36.84 % -- Input Database Coverage: 400209151 bp out of 867632993 bp ( 46.13 % ) Sampling Time: 00:19:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 20:43:08 (hh:mm:ss) Elapsed Time, 691597 HSPs Collected Number of families returned by RECON: 50213 Round Time: 22:11:18 (hh:mm:ss) Elapsed Time : 894 families discovered. RepeatScout/RECON discovery complete: 2131 families found Classification Time: 00:59:44 (hh:mm:ss) Elapsed Time Program Time: 27:32:01 (hh:mm:ss) Elapsed Time