RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.0nZzlY/RM_1294093.TueNov190943032024 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: 1732038182 Database = /scratch/tmp/rModeler.0nZzlY/GCA_963924565.1_kaAscAspe10.1 - Sequences = 75 - Bases = 308571401 Storage Throughput = excellent ( 1429.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040917 bp ( 40033817 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:00:20 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:21 (hh:mm:ss) Elapsed Time Round Time: 00:10:31 (hh:mm:ss) Elapsed Time : 847 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18089 repeats masked totaling 2965439 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017580 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10015780 bp After Masking: 6616627 bp Masked: 33.94 % -- Input Database Coverage: 10017580 bp out of 308571401 bp ( 3.25 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:03:03 (hh:mm:ss) Elapsed Time, 6316 HSPs Collected Number of families returned by RECON: 858 Round Time: 00:04:03 (hh:mm:ss) Elapsed Time : 6 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56706 repeats masked totaling 9203972 bp(s). - TE Masking time 00:00:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023334 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30018034 bp After Masking: 19607638 bp Masked: 34.68 % -- Input Database Coverage: 40040914 bp out of 308571401 bp ( 12.98 % ) Sampling Time: 00:01:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:14:56 (hh:mm:ss) Elapsed Time, 37720 HSPs Collected Number of families returned by RECON: 3285 Round Time: 00:20:30 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 175698 repeats masked totaling 28733421 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027686 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 90006499 bp After Masking: 57908242 bp Masked: 35.66 % -- Input Database Coverage: 130068600 bp out of 308571401 bp ( 42.15 % ) Sampling Time: 00:05:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:31:36 (hh:mm:ss) Elapsed Time, 254198 HSPs Collected Number of families returned by RECON: 10847 Round Time: 01:40:16 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 382495 repeats masked totaling 64862758 bp(s). - TE Masking time 00:04:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 178502699 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 178457186 bp After Masking: 107184985 bp Masked: 39.94 % -- Input Database Coverage: 308571299 bp out of 308571401 bp ( 100.00 % ) Sampling Time: 00:12:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 10059855 Comparison Time: 05:39:44 (hh:mm:ss) Elapsed Time, 472229 HSPs Collected Number of families returned by RECON: 23133 Round Time: 06:01:40 (hh:mm:ss) Elapsed Time : 470 families discovered. RepeatScout/RECON discovery complete: 1728 families found Classification Time: 00:50:56 (hh:mm:ss) Elapsed Time Program Time: 09:07:56 (hh:mm:ss) Elapsed Time