RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.PpjnPE/RM_52885.SunNov171201212024 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: 1731873681 Database = /scratch/tmp/rModeler.PpjnPE/GCF_963932015.1_bAnaAcu1.1 - Sequences = 394 - Bases = 1189296988 - N50 = 119285422 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 191341003-205008147 | [ 1 ] 177673860-191341003 | [ ] 164006717-177673860 | [ ] 150339574-164006717 | [ 1 ] 136672431-150339574 | [ ] 123005288-136672431 | [ ] 109338145-123005288 | [ 1 ] 95671001-109338144 | [ ] 82003858-95671001 | [ ] 68336715-82003858 | [ 2 ] 54669572-68336715 | [ 1 ] 41002429-54669572 | [ ] 27335286-41002429 | [ 4 ] 13668143-27335286 |* [ 9 ] 1000-13668143 |************************************************** [ 375 ] Storage Throughput = excellent ( 1452.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40037328 bp ( 40031548 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:28 (hh:mm:ss) Elapsed Time Round Time: 00:10:31 (hh:mm:ss) Elapsed Time : 72 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1521 repeats masked totaling 543650 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10038870 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10036690 bp After Masking: 8795930 bp Masked: 12.36 % -- Input Database Coverage: 10038870 bp out of 1189296988 bp ( 0.84 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:03:34 (hh:mm:ss) Elapsed Time, 376 HSPs Collected Number of families returned by RECON: 242 Round Time: 00:04:16 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5947 repeats masked totaling 2099175 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30038507 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 30034907 bp After Masking: 26113910 bp Masked: 13.05 % -- Input Database Coverage: 40077377 bp out of 1189296988 bp ( 3.37 % ) Sampling Time: 00:02:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:17:33 (hh:mm:ss) Elapsed Time, 25151 HSPs Collected Number of families returned by RECON: 1432 Round Time: 00:19:47 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18232 repeats masked totaling 6103649 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034627 bp Num Contigs Represented = 125 Non ambiguous bp: Initial: 90022450 bp After Masking: 78472678 bp Masked: 12.83 % -- Input Database Coverage: 130112004 bp out of 1189296988 bp ( 10.94 % ) Sampling Time: 00:05:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2568511 Comparison Time: 02:04:36 (hh:mm:ss) Elapsed Time, 151215 HSPs Collected Number of families returned by RECON: 9677 Round Time: 02:12:15 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 63494 repeats masked totaling 21124695 bp(s). - TE Masking time 00:01:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270049027 bp Num Contigs Represented = 224 Non ambiguous bp: Initial: 270019767 bp After Masking: 233471541 bp Masked: 13.54 % -- Input Database Coverage: 400161031 bp out of 1189296988 bp ( 33.65 % ) Sampling Time: 00:16:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 15:48:57 (hh:mm:ss) Elapsed Time, 876952 HSPs Collected Number of families returned by RECON: 60841 Round Time: 16:31:22 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatScout/RECON discovery complete: 342 families found Classification Time: 00:15:10 (hh:mm:ss) Elapsed Time Program Time: 19:33:21 (hh:mm:ss) Elapsed Time