RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.uiyi93/RM_3158.SatJan70934382023 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: 1673112877 Database = /dev/shm/rModeler.uiyi93/GCA_902686455.1_mSciVul1.1 - Sequences = 638 - Bases = 2878591032 - N50 = 162823747 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198981385-213194295 | [ 2 ] 184768476-198981385 | [ 2 ] 170555567-184768476 | [ 2 ] 156342658-170555567 | [ 1 ] 142129749-156342658 | [ 3 ] 127916840-142129749 | [ 2 ] 113703931-127916840 | [ 1 ] 99491022-113703931 | [ 1 ] 85278113-99491022 | [ 2 ] 71065204-85278113 | [ 2 ] 56852295-71065204 | [ ] 42639386-56852295 | [ ] 28426477-42639386 | [ 2 ] 14213568-28426477 | [ 3 ] 659-14213568 |************************************************** [ 615 ] Storage Throughput = good ( 963.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 41873390 bp ( 40010199 non ambiguous ) - Num Contigs Represented = 67 - Sequence extraction : 00:03:14 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:01 (hh:mm:ss) Elapsed Time Round Time: 00:35:14 (hh:mm:ss) Elapsed Time : 191 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8952 repeats masked totaling 2470511 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10599759 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10017292 bp After Masking: 7481081 bp Masked: 25.32 % -- Input Database Coverage: 10599759 bp out of 2878591032 bp ( 0.37 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 35511 Comparison Time: 00:07:13 (hh:mm:ss) Elapsed Time, 6695 HSPs Collected Number of families returned by RECON: 866 Round Time: 00:09:19 (hh:mm:ss) Elapsed Time : 19 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29791 repeats masked totaling 8000279 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31313551 bp Num Contigs Represented = 56 Non ambiguous bp: Initial: 30032827 bp After Masking: 21829277 bp Masked: 27.32 % -- Input Database Coverage: 41913310 bp out of 2878591032 bp ( 1.46 % ) Sampling Time: 00:03:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 307720 Comparison Time: 00:35:40 (hh:mm:ss) Elapsed Time, 22340 HSPs Collected Number of families returned by RECON: 2377 Round Time: 00:40:53 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:17 (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... 99176 repeats masked totaling 26567659 bp(s). - TE Masking time 00:01:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 95875748 bp Num Contigs Represented = 91 Non ambiguous bp: Initial: 90024191 bp After Masking: 62708712 bp Masked: 30.34 % -- Input Database Coverage: 137789058 bp out of 2878591032 bp ( 4.79 % ) Sampling Time: 00:11:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2890810 Comparison Time: 03:55:38 (hh:mm:ss) Elapsed Time, 99322 HSPs Collected Number of families returned by RECON: 8279 Round Time: 04:13:10 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:21:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 352999 repeats masked totaling 89586647 bp(s). - TE Masking time 00:07:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 287187586 bp Num Contigs Represented = 164 Non ambiguous bp: Initial: 270020156 bp After Masking: 178180667 bp Masked: 34.01 % -- Input Database Coverage: 424976644 bp out of 2878591032 bp ( 14.76 % ) Sampling Time: 00:38:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26075031 Comparison Time: 29:37:17 (hh:mm:ss) Elapsed Time, 411989 HSPs Collected Number of families returned by RECON: 35919 Round Time: 30:48:42 (hh:mm:ss) Elapsed Time : 399 families discovered. RepeatScout/RECON discovery complete: 846 families found Classification Time: 00:53:18 (hh:mm:ss) Elapsed Time Program Time: 37:20:37 (hh:mm:ss) Elapsed Time