RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.GC1ZUb/RM_307602.FriJan191009572024 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: 1705687792 Database = /dev/shm/rModeler.GC1ZUb/GCA_028885625.2_NHGRI_mPonPyg2-v2.0_pri - Sequences = 25 - Bases = 3220935163 Storage Throughput = good ( 770.80 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40121471 bp ( 40031207 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:12 (hh:mm:ss) Elapsed Time Round Time: 00:29:51 (hh:mm:ss) Elapsed Time : 240 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12887 repeats masked totaling 2961075 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000275 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000275 bp After Masking: 6394216 bp Masked: 36.06 % -- Input Database Coverage: 10000275 bp out of 3220935163 bp ( 0.31 % ) Sampling Time: 00:03:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:31:49 (hh:mm:ss) Elapsed Time, 7160 HSPs Collected Number of families returned by RECON: 904 Round Time: 00:36:42 (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 : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43584 repeats masked totaling 9582706 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30121116 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30030852 bp After Masking: 17860464 bp Masked: 40.53 % -- Input Database Coverage: 40121391 bp out of 3220935163 bp ( 1.25 % ) Sampling Time: 00:10:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 02:29:17 (hh:mm:ss) Elapsed Time, 27409 HSPs Collected Number of families returned by RECON: 2273 Round Time: 02:45:17 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140460 repeats masked totaling 30799300 bp(s). - TE Masking time 00:01:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90363353 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 90006518 bp After Masking: 51469084 bp Masked: 42.82 % -- Input Database Coverage: 130484744 bp out of 3220935163 bp ( 4.05 % ) Sampling Time: 00:31:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 04:52:09 (hh:mm:ss) Elapsed Time, 118493 HSPs Collected Number of families returned by RECON: 7844 Round Time: 05:27:13 (hh:mm:ss) Elapsed Time : 197 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:25:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 458024 repeats masked totaling 100084827 bp(s). - TE Masking time 00:04:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270841652 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 270026485 bp After Masking: 148070623 bp Masked: 45.16 % -- Input Database Coverage: 401326396 bp out of 3220935163 bp ( 12.46 % ) Sampling Time: 01:40:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22919835 Comparison Time: 19:33:56 (hh:mm:ss) Elapsed Time, 310790 HSPs Collected Number of families returned by RECON: 32056 Round Time: 21:38:20 (hh:mm:ss) Elapsed Time : 405 families discovered. RepeatScout/RECON discovery complete: 924 families found Classification Time: 00:36:00 (hh:mm:ss) Elapsed Time Program Time: 31:33:23 (hh:mm:ss) Elapsed Time