RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.VVrZCP/RM_2230780.SatMar300455552024 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: 1711799754 Database = /dev/shm/rModeler.VVrZCP/GCA_963930665.1_mMunRee1.1_alternate_haplotype - Sequences = 8892 - Bases = 2863788737 - N50 = 1273668 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 10918083-11697794 | [ 2 ] 10138373-10918083 | [ ] 9358663-10138373 | [ ] 8578952-9358662 | [ ] 7799242-8578952 | [ 5 ] 7019532-7799242 | [ 3 ] 6239822-7019532 | [ 4 ] 5460111-6239821 | [ 7 ] 4680401-5460111 | [ 12 ] 3900691-4680401 | [ 23 ] 3120981-3900691 | [ 47 ] 2341270-3120980 | [ 90 ] 1561560-2341270 |* [ 229 ] 781850-1561560 |**** [ 707 ] 2140-781850 |************************************************** [ 7763 ] Storage Throughput = excellent ( 1500.64 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40025929 bp ( 40025929 non ambiguous ) - Num Contigs Represented = 835 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:26 (hh:mm:ss) Elapsed Time Round Time: 00:33:35 (hh:mm:ss) Elapsed Time : 178 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14413 repeats masked totaling 4014371 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039639 bp Num Contigs Represented = 248 Non ambiguous bp: Initial: 10039639 bp After Masking: 5735971 bp Masked: 42.87 % -- Input Database Coverage: 10039639 bp out of 2863788737 bp ( 0.35 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34453 Comparison Time: 00:05:35 (hh:mm:ss) Elapsed Time, 33662 HSPs Collected Number of families returned by RECON: 494 Round Time: 00:07:21 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43433 repeats masked totaling 12355395 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026191 bp Num Contigs Represented = 668 Non ambiguous bp: Initial: 30026191 bp After Masking: 16695429 bp Masked: 44.40 % -- Input Database Coverage: 40065830 bp out of 2863788737 bp ( 1.40 % ) Sampling Time: 00:05:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 313236 Comparison Time: 00:26:45 (hh:mm:ss) Elapsed Time, 337845 HSPs Collected Number of families returned by RECON: 1850 Round Time: 00:33:05 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 139471 repeats masked totaling 39611613 bp(s). - TE Masking time 00:02:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032956 bp Num Contigs Represented = 1501 Non ambiguous bp: Initial: 90032956 bp After Masking: 47703585 bp Masked: 47.02 % -- Input Database Coverage: 130098786 bp out of 2863788737 bp ( 4.54 % ) Sampling Time: 00:15:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2862028 Comparison Time: 02:42:36 (hh:mm:ss) Elapsed Time, 3328746 HSPs Collected Number of families returned by RECON: 5489 Round Time: 03:03:42 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 442124 repeats masked totaling 122779318 bp(s). - TE Masking time 00:09:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270032598 bp Num Contigs Represented = 2927 Non ambiguous bp: Initial: 270032598 bp After Masking: 138437509 bp Masked: 48.73 % -- Input Database Coverage: 400131384 bp out of 2863788737 bp ( 13.97 % ) Sampling Time: 00:52:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 25443411 Comparison Time: 20:47:08 (hh:mm:ss) Elapsed Time, 41226541 HSPs Collected Number of families returned by RECON: 23554 Round Time: 22:10:12 (hh:mm:ss) Elapsed Time : 331 families discovered. RepeatScout/RECON discovery complete: 715 families found Classification Time: 00:49:57 (hh:mm:ss) Elapsed Time Program Time: 27:17:52 (hh:mm:ss) Elapsed Time