RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WiFAIi/RM_26591.WedJun260106452024 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: 1719389204 Database = /dev/shm/rModeler.WiFAIi/GCF_028885625.2_NHGRI_mPonPyg2-v2.0_pri - Sequences = 26 - Bases = 3220951552 Storage Throughput = excellent ( 1020.29 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40081531 bp ( 40001519 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:56 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:03 (hh:mm:ss) Elapsed Time Round Time: 00:34:02 (hh:mm:ss) Elapsed Time : 252 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13253 repeats masked totaling 3104175 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000447 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000447 bp After Masking: 6021011 bp Masked: 39.79 % -- Input Database Coverage: 10000447 bp out of 3220951552 bp ( 0.31 % ) Sampling Time: 00:03:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:04:59 (hh:mm:ss) Elapsed Time, 5935 HSPs Collected Number of families returned by RECON: 847 Round Time: 00:08:55 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39535 repeats masked totaling 9086769 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30081083 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30001071 bp After Masking: 17738155 bp Masked: 40.87 % -- Input Database Coverage: 40081530 bp out of 3220951552 bp ( 1.24 % ) Sampling Time: 00:14:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:25:12 (hh:mm:ss) Elapsed Time, 25868 HSPs Collected Number of families returned by RECON: 2252 Round Time: 00:41:02 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 131954 repeats masked totaling 30658847 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90123290 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90003290 bp After Masking: 52473661 bp Masked: 41.70 % -- Input Database Coverage: 130204820 bp out of 3220951552 bp ( 4.04 % ) Sampling Time: 00:31:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 02:55:30 (hh:mm:ss) Elapsed Time, 126182 HSPs Collected Number of families returned by RECON: 8364 Round Time: 03:37:32 (hh:mm:ss) Elapsed Time : 190 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:30:44 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 434088 repeats masked totaling 101307965 bp(s). - TE Masking time 00:07:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270647620 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 270010992 bp After Masking: 146459123 bp Masked: 45.76 % -- Input Database Coverage: 400852440 bp out of 3220951552 bp ( 12.45 % ) Sampling Time: 01:51:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 21:45:57 (hh:mm:ss) Elapsed Time, 389131 HSPs Collected Number of families returned by RECON: 31303 Round Time: 24:07:56 (hh:mm:ss) Elapsed Time : 407 families discovered. RepeatScout/RECON discovery complete: 929 families found Classification Time: 00:44:08 (hh:mm:ss) Elapsed Time Program Time: 29:53:35 (hh:mm:ss) Elapsed Time