RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FqeWJ5/RM_17271.MonJan150248272024 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: 1705315700 Database = /dev/shm/rModeler.FqeWJ5/GCA_949820135.1_mSylFlo1.10 - Sequences = 99 - Bases = 2848420111 Storage Throughput = excellent ( 1133.72 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019200 bp ( 40018900 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:02:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:25 (hh:mm:ss) Elapsed Time Round Time: 00:33:15 (hh:mm:ss) Elapsed Time : 144 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13004 repeats masked totaling 3212268 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001493 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10001393 bp After Masking: 5807950 bp Masked: 41.93 % -- Input Database Coverage: 10001493 bp out of 2848420111 bp ( 0.35 % ) Sampling Time: 00:04:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:28:33 (hh:mm:ss) Elapsed Time, 5139 HSPs Collected Number of families returned by RECON: 556 Round Time: 00:34:40 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:08 (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... 39575 repeats masked totaling 9348758 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30017700 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 30017500 bp After Masking: 16875800 bp Masked: 43.78 % -- Input Database Coverage: 40019193 bp out of 2848420111 bp ( 1.40 % ) Sampling Time: 00:09:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:55:15 (hh:mm:ss) Elapsed Time, 19220 HSPs Collected Number of families returned by RECON: 1618 Round Time: 01:08:13 (hh:mm:ss) Elapsed Time : 41 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 129719 repeats masked totaling 30652344 bp(s). - TE Masking time 00:02:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018817 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 90018017 bp After Masking: 50174002 bp Masked: 44.26 % -- Input Database Coverage: 130038010 bp out of 2848420111 bp ( 4.57 % ) Sampling Time: 00:30:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:48:54 (hh:mm:ss) Elapsed Time, 62312 HSPs Collected Number of families returned by RECON: 6249 Round Time: 04:22:47 (hh:mm:ss) Elapsed Time : 115 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:08:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 412394 repeats masked totaling 97072768 bp(s). - TE Masking time 00:07:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270020926 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 270017926 bp After Masking: 145681999 bp Masked: 46.05 % -- Input Database Coverage: 400058936 bp out of 2848420111 bp ( 14.04 % ) Sampling Time: 01:35:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22818390 Comparison Time: 21:29:25 (hh:mm:ss) Elapsed Time, 173854 HSPs Collected Number of families returned by RECON: 26738 Round Time: 23:34:36 (hh:mm:ss) Elapsed Time : 328 families discovered. RepeatScout/RECON discovery complete: 638 families found Classification Time: 00:29:10 (hh:mm:ss) Elapsed Time Program Time: 30:42:41 (hh:mm:ss) Elapsed Time