RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.xNilZd/RM_27930.SunJul71026032024 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: 1720373162 Database = /dev/shm/rModeler.xNilZd/GCF_001444195.1_X_couchianus-1.0 - Sequences = 68 - Bases = 688541509 Storage Throughput = excellent ( 1014.14 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40141512 bp ( 40036480 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:35 (hh:mm:ss) Elapsed Time Round Time: 00:28:08 (hh:mm:ss) Elapsed Time : 410 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8850 repeats masked totaling 1371472 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001171 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10000971 bp After Masking: 8488358 bp Masked: 15.12 % -- Input Database Coverage: 10001171 bp out of 688541509 bp ( 1.45 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:58 (hh:mm:ss) Elapsed Time, 10684 HSPs Collected Number of families returned by RECON: 1507 Round Time: 00:07:12 (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 : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28319 repeats masked totaling 4800593 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30140261 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30035429 bp After Masking: 24786467 bp Masked: 17.48 % -- Input Database Coverage: 40141432 bp out of 688541509 bp ( 5.83 % ) Sampling Time: 00:02:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:34:52 (hh:mm:ss) Elapsed Time, 51730 HSPs Collected Number of families returned by RECON: 5159 Round Time: 00:39:02 (hh:mm:ss) Elapsed Time : 121 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 106443 repeats masked totaling 17196879 bp(s). - TE Masking time 00:02:00 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90050845 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 90001527 bp After Masking: 71443640 bp Masked: 20.62 % -- Input Database Coverage: 130192277 bp out of 688541509 bp ( 18.91 % ) Sampling Time: 00:08:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 04:19:21 (hh:mm:ss) Elapsed Time, 206334 HSPs Collected Number of families returned by RECON: 16349 Round Time: 04:39:19 (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 : 00:04:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:14:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 394283 repeats masked totaling 65026703 bp(s). - TE Masking time 00:11:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270411664 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 270022129 bp After Masking: 200764075 bp Masked: 25.65 % -- Input Database Coverage: 400603941 bp out of 688541509 bp ( 58.18 % ) Sampling Time: 00:30:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22940151 Comparison Time: 33:45:09 (hh:mm:ss) Elapsed Time, 550864 HSPs Collected Number of families returned by RECON: 58155 Round Time: 35:47:38 (hh:mm:ss) Elapsed Time : 962 families discovered. RepeatScout/RECON discovery complete: 1923 families found Classification Time: 01:39:58 (hh:mm:ss) Elapsed Time Program Time: 43:21:17 (hh:mm:ss) Elapsed Time