RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.AuZlSI/RM_20630.TueDec51010572023 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: 1701799855 Database = /dev/shm/rModeler.AuZlSI/GCA_031468815.1_bMorBas2.hap2 - Sequences = 421 - Bases = 1294804326 - N50 = 85674795 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 158834230-170178824 | [ 1 ] 147489637-158834230 | [ ] 136145044-147489637 | [ ] 124800451-136145044 | [ 1 ] 113455858-124800451 | [ 1 ] 102111265-113455858 | [ ] 90766672-102111265 | [ ] 79422079-90766672 | [ 3 ] 68077486-79422079 | [ ] 56732893-68077486 | [ 1 ] 45388300-56732893 | [ 1 ] 34043707-45388300 | [ 3 ] 22699114-34043707 | [ 6 ] 11354521-22699114 | [ 4 ] 9928-11354521 |************************************************** [ 400 ] Storage Throughput = excellent ( 1185.70 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40039374 bp ( 40037574 non ambiguous ) - Num Contigs Represented = 77 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:10 (hh:mm:ss) Elapsed Time Round Time: 00:30:00 (hh:mm:ss) Elapsed Time : 37 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1205 repeats masked totaling 690387 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10036472 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 10036072 bp After Masking: 9061585 bp Masked: 9.71 % -- Input Database Coverage: 10036472 bp out of 1294804326 bp ( 0.78 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:18 (hh:mm:ss) Elapsed Time, 866 HSPs Collected Number of families returned by RECON: 244 Round Time: 00:07:38 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3548 repeats masked totaling 1854897 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002885 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 30001485 bp After Masking: 27495615 bp Masked: 8.35 % -- Input Database Coverage: 40039357 bp out of 1294804326 bp ( 3.09 % ) Sampling Time: 00:03:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:37:03 (hh:mm:ss) Elapsed Time, 6185 HSPs Collected Number of families returned by RECON: 1544 Round Time: 00:42:37 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12164 repeats masked totaling 6317022 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029740 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 90025540 bp After Masking: 81478629 bp Masked: 9.49 % -- Input Database Coverage: 130069097 bp out of 1294804326 bp ( 10.05 % ) Sampling Time: 00:10:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 04:38:26 (hh:mm:ss) Elapsed Time, 52433 HSPs Collected Number of families returned by RECON: 8739 Round Time: 05:23:03 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50987 repeats masked totaling 27680293 bp(s). - TE Masking time 00:08:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270046386 bp Num Contigs Represented = 220 Non ambiguous bp: Initial: 270037896 bp After Masking: 236670512 bp Masked: 12.36 % -- Input Database Coverage: 400115483 bp out of 1294804326 bp ( 30.90 % ) Sampling Time: 00:36:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23062236 Comparison Time: 38:01:10 (hh:mm:ss) Elapsed Time, 212302 HSPs Collected Number of families returned by RECON: 56026 Round Time: 40:03:07 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatScout/RECON discovery complete: 324 families found Classification Time: 00:56:35 (hh:mm:ss) Elapsed Time Program Time: 47:43:00 (hh:mm:ss) Elapsed Time