RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.X0fZtN/RM_640169.MonApr211255422025 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: 1745265340 Database = /dev/shm/rModeler.X0fZtN/GCA_965226575.1_fPagPag1.hap1.1 - Sequences = 576 - Bases = 825699107 - N50 = 33887174 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 36075963-38652747 | [ 4 ] 33499180-36075963 | [ 7 ] 30922397-33499180 | [ 4 ] 28345614-30922397 | [ 4 ] 25768831-28345614 | [ 2 ] 23192048-25768831 | [ 2 ] 20615265-23192048 | [ 1 ] 18038481-20615264 | [ ] 15461698-18038481 | [ ] 12884915-15461698 | [ ] 10308132-12884915 | [ ] 7731349-10308132 | [ ] 5154566-7731349 | [ ] 2577783-5154566 | [ ] 1000-2577783 |************************************************** [ 552 ] Storage Throughput = excellent ( 1681.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043036 bp ( 40038236 non ambiguous ) - Num Contigs Represented = 101 - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:21 (hh:mm:ss) Elapsed Time Round Time: 00:10:27 (hh:mm:ss) Elapsed Time : 579 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 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10106 repeats masked totaling 1270205 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10017440 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10015240 bp After Masking: 8012978 bp Masked: 19.99 % -- Input Database Coverage: 10017440 bp out of 825699107 bp ( 1.21 % ) Sampling Time: 00:00:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:57 (hh:mm:ss) Elapsed Time, 7851 HSPs Collected Number of families returned by RECON: 1751 Round Time: 00:03:48 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32569 repeats masked totaling 4210278 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30025516 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 30022916 bp After Masking: 23949410 bp Masked: 20.23 % -- Input Database Coverage: 40042956 bp out of 825699107 bp ( 4.85 % ) Sampling Time: 00:02:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 291466 Comparison Time: 00:12:50 (hh:mm:ss) Elapsed Time, 64649 HSPs Collected Number of families returned by RECON: 6203 Round Time: 00:15:45 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 116881 repeats masked totaling 15193697 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90048884 bp Num Contigs Represented = 188 Non ambiguous bp: Initial: 90036884 bp After Masking: 68157652 bp Masked: 24.30 % -- Input Database Coverage: 130091840 bp out of 825699107 bp ( 15.76 % ) Sampling Time: 00:05:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2600340 Comparison Time: 01:20:56 (hh:mm:ss) Elapsed Time, 318035 HSPs Collected Number of families returned by RECON: 19654 Round Time: 01:44:37 (hh:mm:ss) Elapsed Time : 560 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 432752 repeats masked totaling 61128516 bp(s). - TE Masking time 00:03:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270062274 bp Num Contigs Represented = 349 Non ambiguous bp: Initial: 270025874 bp After Masking: 189494414 bp Masked: 29.82 % -- Input Database Coverage: 400154114 bp out of 825699107 bp ( 48.46 % ) Sampling Time: 00:17:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23498940 Comparison Time: 09:29:00 (hh:mm:ss) Elapsed Time, 927924 HSPs Collected Number of families returned by RECON: 66505 Round Time: 10:38:27 (hh:mm:ss) Elapsed Time : 1362 families discovered. RepeatScout/RECON discovery complete: 2681 families found Classification Time: 00:58:54 (hh:mm:ss) Elapsed Time Program Time: 13:51:58 (hh:mm:ss) Elapsed Time