RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.yysD78/RM_6057.SatJul130019122024 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: 1720855150 Database = /dev/shm/rModeler.yysD78/GCF_003331165.1_Xiphophorus_hellerii-4.1 - Sequences = 87 - Bases = 732906125 Storage Throughput = excellent ( 1041.82 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40242102 bp ( 40038589 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:40 (hh:mm:ss) Elapsed Time Round Time: 00:26:23 (hh:mm:ss) Elapsed Time : 448 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 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8680 repeats masked totaling 1379005 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10082204 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10032728 bp After Masking: 8487695 bp Masked: 15.40 % -- Input Database Coverage: 10082204 bp out of 732906125 bp ( 1.38 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:46 (hh:mm:ss) Elapsed Time, 10933 HSPs Collected Number of families returned by RECON: 1531 Round Time: 00:08:01 (hh:mm:ss) Elapsed Time : 24 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30237 repeats masked totaling 4886560 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30159884 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30005847 bp After Masking: 24669673 bp Masked: 17.78 % -- Input Database Coverage: 40242088 bp out of 732906125 bp ( 5.49 % ) Sampling Time: 00:02:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:37:58 (hh:mm:ss) Elapsed Time, 70893 HSPs Collected Number of families returned by RECON: 5048 Round Time: 00:42:55 (hh:mm:ss) Elapsed Time : 117 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108942 repeats masked totaling 18493282 bp(s). - TE Masking time 00:02:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90191866 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 90027707 bp After Masking: 70154784 bp Masked: 22.07 % -- Input Database Coverage: 130433954 bp out of 732906125 bp ( 17.80 % ) Sampling Time: 00:07:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 04:19:39 (hh:mm:ss) Elapsed Time, 214892 HSPs Collected Number of families returned by RECON: 15523 Round Time: 04:39:11 (hh:mm:ss) Elapsed Time : 394 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 396067 repeats masked totaling 70409434 bp(s). - TE Masking time 00:12:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270666504 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 270034434 bp After Masking: 195594361 bp Masked: 27.57 % -- Input Database Coverage: 401100458 bp out of 732906125 bp ( 54.73 % ) Sampling Time: 00:28:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 33:00:50 (hh:mm:ss) Elapsed Time, 633373 HSPs Collected Number of families returned by RECON: 56197 Round Time: 35:01:10 (hh:mm:ss) Elapsed Time : 991 families discovered. RepeatScout/RECON discovery complete: 1974 families found Classification Time: 01:46:08 (hh:mm:ss) Elapsed Time Program Time: 42:43:48 (hh:mm:ss) Elapsed Time