RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.El8GPT/RM_2846612.SunJul200323102025 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: 1753006990 Database = /dev/shm/rModeler.El8GPT/GCA_964145185.2_mMinSch1.hap2.2 - Sequences = 168 - Bases = 1699631453 - N50 = 90604512 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 189193595-202706705 | [ 1 ] 175680486-189193595 | [ 1 ] 162167376-175680485 | [ ] 148654267-162167376 | [ ] 135141157-148654266 | [ ] 121628048-135141157 | [ ] 108114938-121628047 | [ ] 94601829-108114938 | [ 2 ] 81088719-94601828 |** [ 6 ] 67575610-81088719 | [ 2 ] 54062500-67575609 |* [ 3 ] 40549391-54062500 |* [ 3 ] 27036281-40549390 | [ 2 ] 13523172-27036281 | [ 1 ] 10063-13523172 |************************************************** [ 147 ] Storage Throughput = excellent ( 1696.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40036790 bp ( 40036790 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:41 (hh:mm:ss) Elapsed Time Round Time: 00:10:49 (hh:mm:ss) Elapsed Time : 149 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7303 repeats masked totaling 1544168 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031250 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10031250 bp After Masking: 8156946 bp Masked: 18.68 % -- Input Database Coverage: 10031250 bp out of 1699631453 bp ( 0.59 % ) Sampling Time: 00:00:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:04 (hh:mm:ss) Elapsed Time, 8130 HSPs Collected Number of families returned by RECON: 859 Round Time: 00:04:07 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24764 repeats masked totaling 5259281 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005460 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30005460 bp After Masking: 23928182 bp Masked: 20.25 % -- Input Database Coverage: 40036710 bp out of 1699631453 bp ( 2.36 % ) Sampling Time: 00:02:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 280875 Comparison Time: 00:13:50 (hh:mm:ss) Elapsed Time, 30031 HSPs Collected Number of families returned by RECON: 2595 Round Time: 00:16:27 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 85988 repeats masked totaling 18628021 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90002132 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 90001132 bp After Masking: 69141910 bp Masked: 23.18 % -- Input Database Coverage: 130038842 bp out of 1699631453 bp ( 7.65 % ) Sampling Time: 00:06:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 01:18:59 (hh:mm:ss) Elapsed Time, 118686 HSPs Collected Number of families returned by RECON: 10047 Round Time: 01:27:03 (hh:mm:ss) Elapsed Time : 171 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 294581 repeats masked totaling 62879841 bp(s). - TE Masking time 00:01:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270019027 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 270016427 bp After Masking: 200124638 bp Masked: 25.88 % -- Input Database Coverage: 400057869 bp out of 1699631453 bp ( 23.54 % ) Sampling Time: 00:21:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 09:22:58 (hh:mm:ss) Elapsed Time, 1493785 HSPs Collected Number of families returned by RECON: 45750 Round Time: 09:57:31 (hh:mm:ss) Elapsed Time : 371 families discovered. RepeatScout/RECON discovery complete: 775 families found Classification Time: 00:13:04 (hh:mm:ss) Elapsed Time Program Time: 12:09:01 (hh:mm:ss) Elapsed Time