RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.DFW9dz/RM_1164430.TueNov121201082024 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: 1731441668 Database = /scratch/tmp/rModeler.DFW9dz/GCF_963930695.1_fLabBer1.1 - Sequences = 131 - Bases = 720210020 - N50 = 31292968 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 35473738-38007505 |* [ 3 ] 32939971-35473738 |** [ 5 ] 30406204-32939971 |** [ 5 ] 27872437-30406204 | [ 2 ] 25338670-27872437 |* [ 4 ] 22804903-25338670 |* [ 3 ] 20271136-22804903 | [ 1 ] 17737369-20271136 | [ ] 15203602-17737369 | [ ] 12669835-15203602 | [ 1 ] 10136068-12669835 | [ ] 7602301-10136068 | [ ] 5068534-7602301 | [ ] 2534767-5068534 | [ ] 1000-2534767 |************************************************** [ 107 ] Storage Throughput = excellent ( 1628.02 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40042246 bp ( 40033406 non ambiguous ) - Num Contigs Represented = 34 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:14 (hh:mm:ss) Elapsed Time Round Time: 00:11:02 (hh:mm:ss) Elapsed Time : 498 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 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7406 repeats masked totaling 1252563 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020219 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10018219 bp After Masking: 8055276 bp Masked: 19.59 % -- Input Database Coverage: 10020219 bp out of 720210020 bp ( 1.39 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 5445 HSPs Collected Number of families returned by RECON: 1204 Round Time: 00:04:33 (hh:mm:ss) Elapsed Time : 12 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 00:02:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24614 repeats masked totaling 4226605 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022002 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30015162 bp After Masking: 23811701 bp Masked: 20.67 % -- Input Database Coverage: 40042221 bp out of 720210020 bp ( 5.56 % ) Sampling Time: 00:03:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:13:09 (hh:mm:ss) Elapsed Time, 44458 HSPs Collected Number of families returned by RECON: 4454 Round Time: 00:17:11 (hh:mm:ss) Elapsed Time : 114 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 00:07:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 84248 repeats masked totaling 14385919 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90056156 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 90031556 bp After Masking: 70028989 bp Masked: 22.22 % -- Input Database Coverage: 130098377 bp out of 720210020 bp ( 18.06 % ) Sampling Time: 00:08:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 01:27:39 (hh:mm:ss) Elapsed Time, 219650 HSPs Collected Number of families returned by RECON: 15071 Round Time: 01:48:36 (hh:mm:ss) Elapsed Time : 440 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 00:23:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 307709 repeats masked totaling 54764533 bp(s). - TE Masking time 00:03:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270081870 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 270018862 bp After Masking: 198801601 bp Masked: 26.37 % -- Input Database Coverage: 400180247 bp out of 720210020 bp ( 55.56 % ) Sampling Time: 00:29:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 10:33:33 (hh:mm:ss) Elapsed Time, 785194 HSPs Collected Number of families returned by RECON: 60514 Round Time: 11:38:34 (hh:mm:ss) Elapsed Time : 1074 families discovered. RepeatScout/RECON discovery complete: 2138 families found Classification Time: 00:50:58 (hh:mm:ss) Elapsed Time Program Time: 14:50:54 (hh:mm:ss) Elapsed Time