RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mfZYWc/RM_145651.MonJul11446412024 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: 1719870400 Database = /dev/shm/rModeler.mfZYWc/GCF_902827115.1_fPseGeo1.1 - Sequences = 1563 - Bases = 1026101545 - N50 = 43034850 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 49864892-53425585 | [ 2 ] 46304200-49864892 | [ 4 ] 42743508-46304200 | [ 5 ] 39182816-42743508 | [ 3 ] 35622124-39182816 | [ ] 32061431-35622123 | [ 4 ] 28500739-32061431 | [ 2 ] 24940047-28500739 | [ 1 ] 21379355-24940047 | [ 2 ] 17818663-21379355 | [ ] 14257970-17818662 | [ ] 10697278-14257970 | [ 1 ] 7136586-10697278 | [ ] 3575894-7136586 | [ ] 15202-3575894 |************************************************** [ 1539 ] Storage Throughput = excellent ( 1289.90 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40044727 bp ( 40018436 non ambiguous ) - Num Contigs Represented = 130 - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:56 (hh:mm:ss) Elapsed Time Round Time: 00:21:47 (hh:mm:ss) Elapsed Time : 1053 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12553 repeats masked totaling 3968191 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028756 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 10021778 bp After Masking: 5524835 bp Masked: 44.87 % -- Input Database Coverage: 10028756 bp out of 1026101545 bp ( 0.98 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:04:30 (hh:mm:ss) Elapsed Time, 4578 HSPs Collected Number of families returned by RECON: 834 Round Time: 00:06:03 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41106 repeats masked totaling 12335860 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30055891 bp Num Contigs Represented = 99 Non ambiguous bp: Initial: 30036578 bp After Masking: 16003079 bp Masked: 46.72 % -- Input Database Coverage: 40084647 bp out of 1026101545 bp ( 3.91 % ) Sampling Time: 00:03:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:18:55 (hh:mm:ss) Elapsed Time, 28459 HSPs Collected Number of families returned by RECON: 2949 Round Time: 00:23:01 (hh:mm:ss) Elapsed Time : 55 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 124389 repeats masked totaling 36319668 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90055505 bp Num Contigs Represented = 282 Non ambiguous bp: Initial: 90005034 bp After Masking: 48404362 bp Masked: 46.22 % -- Input Database Coverage: 130140152 bp out of 1026101545 bp ( 12.68 % ) Sampling Time: 00:09:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2673828 Comparison Time: 01:36:13 (hh:mm:ss) Elapsed Time, 222278 HSPs Collected Number of families returned by RECON: 9145 Round Time: 01:51:52 (hh:mm:ss) Elapsed Time : 463 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:23:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 420698 repeats masked totaling 120847986 bp(s). - TE Masking time 00:09:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270172565 bp Num Contigs Represented = 658 Non ambiguous bp: Initial: 270007095 bp After Masking: 133116906 bp Masked: 50.70 % -- Input Database Coverage: 400312717 bp out of 1026101545 bp ( 39.01 % ) Sampling Time: 00:38:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23995128 Comparison Time: 10:30:18 (hh:mm:ss) Elapsed Time, 574576 HSPs Collected Number of families returned by RECON: 31189 Round Time: 11:43:56 (hh:mm:ss) Elapsed Time : 999 families discovered. RepeatScout/RECON discovery complete: 2577 families found Classification Time: 01:37:44 (hh:mm:ss) Elapsed Time Program Time: 16:04:23 (hh:mm:ss) Elapsed Time