RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.TKKGyZ/RM_1265565.SatFeb151805492025 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: 1739671548 Database = /dev/shm/rModeler.TKKGyZ/GCA_964212085.1_pySymPilo4.1 - Sequences = 1832 - Bases = 1272363524 - N50 = 14180732 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 22928576-24566260 | [ 2 ] 21290892-22928576 | [ 2 ] 19653208-21290892 | [ 1 ] 18015524-19653208 | [ 8 ] 16377840-18015524 | [ 10 ] 14740156-16377840 | [ 10 ] 13102472-14740156 | [ 10 ] 11464788-13102472 | [ 16 ] 9827104-11464788 | [ 11 ] 8189420-9827104 | [ 6 ] 6551736-8189420 | [ 2 ] 4914052-6551736 | [ 2 ] 3276368-4914052 | [ 4 ] 1638684-3276368 | [ 6 ] 1000-1638684 |************************************************* [ 1742 ] Storage Throughput = excellent ( 1863.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031316 bp ( 40008390 non ambiguous ) - Num Contigs Represented = 207 - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:05:53 (hh:mm:ss) Elapsed Time Round Time: 00:09:49 (hh:mm:ss) Elapsed Time : 308 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20203 repeats masked totaling 2071370 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10009052 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 10005872 bp After Masking: 7394580 bp Masked: 26.10 % -- Input Database Coverage: 10009052 bp out of 1272363524 bp ( 0.79 % ) Sampling Time: 00:00:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32896 Comparison Time: 00:02:57 (hh:mm:ss) Elapsed Time, 4637 HSPs Collected Number of families returned by RECON: 1160 Round Time: 00:03:33 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 61701 repeats masked totaling 6621799 bp(s). - TE Masking time 00:00:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30022184 bp Num Contigs Represented = 182 Non ambiguous bp: Initial: 30002438 bp After Masking: 21706429 bp Masked: 27.65 % -- Input Database Coverage: 40031236 bp out of 1272363524 bp ( 3.15 % ) Sampling Time: 00:01:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 304590 Comparison Time: 00:13:09 (hh:mm:ss) Elapsed Time, 36669 HSPs Collected Number of families returned by RECON: 4943 Round Time: 00:16:07 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 195372 repeats masked totaling 20774115 bp(s). - TE Masking time 00:01:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90059376 bp Num Contigs Represented = 351 Non ambiguous bp: Initial: 90008457 bp After Masking: 64184627 bp Masked: 28.69 % -- Input Database Coverage: 130090612 bp out of 1272363524 bp ( 10.22 % ) Sampling Time: 00:04:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2720278 Comparison Time: 01:09:13 (hh:mm:ss) Elapsed Time, 270949 HSPs Collected Number of families returned by RECON: 19794 Round Time: 01:23:05 (hh:mm:ss) Elapsed Time : 238 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 647229 repeats masked totaling 76093171 bp(s). - TE Masking time 00:04:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270169433 bp Num Contigs Represented = 686 Non ambiguous bp: Initial: 270019381 bp After Masking: 178854376 bp Masked: 33.76 % -- Input Database Coverage: 400260045 bp out of 1272363524 bp ( 31.46 % ) Sampling Time: 00:14:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24231241 Comparison Time: 07:49:23 (hh:mm:ss) Elapsed Time, 982774 HSPs Collected Number of families returned by RECON: 76908 Round Time: 08:55:05 (hh:mm:ss) Elapsed Time : 811 families discovered. RepeatScout/RECON discovery complete: 1418 families found Classification Time: 00:58:47 (hh:mm:ss) Elapsed Time Program Time: 11:46:26 (hh:mm:ss) Elapsed Time