RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.VNUtgN/RM_1195034.WedNov132218502024 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: 1731565129 Database = /scratch/tmp/rModeler.VNUtgN/GCA_964188355.1_bButBut1.hap1.1 - Sequences = 544 - Bases = 1303700921 - N50 = 47553025 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 83615126-89587085 | [ 2 ] 77643167-83615125 | [ 2 ] 71671209-77643167 | [ ] 65699250-71671208 | [ 1 ] 59727291-65699249 | [ ] 53755333-59727291 | [ 2 ] 47783374-53755332 | [ 1 ] 41811415-47783373 | [ 5 ] 35839457-41811415 | [ 1 ] 29867498-35839456 | [ 6 ] 23895539-29867497 | [ 4 ] 17923581-23895539 | [ 2 ] 11951622-17923580 | [ 2 ] 5979663-11951621 | [ 2 ] 7705-5979663 |************************************************** [ 514 ] Storage Throughput = excellent ( 1554.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014097 bp ( 40012211 non ambiguous ) - Num Contigs Represented = 88 - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:02 (hh:mm:ss) Elapsed Time Round Time: 00:09:45 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1257 repeats masked totaling 549265 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10023376 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 10022290 bp After Masking: 8865409 bp Masked: 11.54 % -- Input Database Coverage: 10023376 bp out of 1303700921 bp ( 0.77 % ) Sampling Time: 00:01:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:55 (hh:mm:ss) Elapsed Time, 562 HSPs Collected Number of families returned by RECON: 254 Round Time: 00:04:22 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3443 repeats masked totaling 1557660 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030564 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 30029764 bp After Masking: 27026936 bp Masked: 10.00 % -- Input Database Coverage: 40053940 bp out of 1303700921 bp ( 3.07 % ) Sampling Time: 00:04:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:13:50 (hh:mm:ss) Elapsed Time, 5257 HSPs Collected Number of families returned by RECON: 1456 Round Time: 00:19:10 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12513 repeats masked totaling 4888231 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90025178 bp Num Contigs Represented = 138 Non ambiguous bp: Initial: 90019178 bp After Masking: 79712045 bp Masked: 11.45 % -- Input Database Coverage: 130079118 bp out of 1303700921 bp ( 9.98 % ) Sampling Time: 00:10:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 01:28:10 (hh:mm:ss) Elapsed Time, 82313 HSPs Collected Number of families returned by RECON: 8545 Round Time: 01:44:07 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:33:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49305 repeats masked totaling 17702388 bp(s). - TE Masking time 00:00:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019630 bp Num Contigs Represented = 270 Non ambiguous bp: Initial: 270001316 bp After Masking: 235615486 bp Masked: 12.74 % -- Input Database Coverage: 400098748 bp out of 1303700921 bp ( 30.69 % ) Sampling Time: 00:37:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23211891 Comparison Time: 12:15:04 (hh:mm:ss) Elapsed Time, 210487 HSPs Collected Number of families returned by RECON: 52520 Round Time: 13:10:09 (hh:mm:ss) Elapsed Time : 253 families discovered. RepeatScout/RECON discovery complete: 396 families found Classification Time: 00:19:33 (hh:mm:ss) Elapsed Time Program Time: 15:47:06 (hh:mm:ss) Elapsed Time