RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4ZsAFI/RM_8261.SatDec20901352023 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: 1701536494 Database = /dev/shm/rModeler.4ZsAFI/GCA_030144785.1_sHypSab1.hap2 - Sequences = 1412 - Bases = 3635158545 - N50 = 166194756 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 201489980-215882050 | [ 2 ] 187097910-201489980 | [ 2 ] 172705840-187097910 | [ 4 ] 158313770-172705840 | [ 2 ] 143921700-158313770 | [ ] 129529630-143921700 | [ ] 115137560-129529630 | [ 1 ] 100745490-115137560 | [ 3 ] 86353420-100745490 | [ 2 ] 71961350-86353420 | [ 4 ] 57569280-71961350 | [ 3 ] 43177210-57569280 | [ 4 ] 28785140-43177210 | [ 4 ] 14393070-28785140 | [ ] 1000-14393070 |************************************************** [ 1381 ] Storage Throughput = excellent ( 1016.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40017073 bp ( 40013673 non ambiguous ) - Num Contigs Represented = 98 - Sequence extraction : 00:02:44 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:58 (hh:mm:ss) Elapsed Time Round Time: 00:32:36 (hh:mm:ss) Elapsed Time : 635 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19014 repeats masked totaling 5141504 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030931 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10030531 bp After Masking: 3634419 bp Masked: 63.77 % -- Input Database Coverage: 10030931 bp out of 3635158545 bp ( 0.28 % ) Sampling Time: 00:03:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:04:19 (hh:mm:ss) Elapsed Time, 3718 HSPs Collected Number of families returned by RECON: 625 Round Time: 00:08:26 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56739 repeats masked totaling 15437035 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30026062 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 30023062 bp After Masking: 10658796 bp Masked: 64.50 % -- Input Database Coverage: 40056993 bp out of 3635158545 bp ( 1.10 % ) Sampling Time: 00:13:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:18:39 (hh:mm:ss) Elapsed Time, 22617 HSPs Collected Number of families returned by RECON: 1902 Round Time: 00:32:33 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:31:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 174370 repeats masked totaling 47434465 bp(s). - TE Masking time 00:02:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026211 bp Num Contigs Represented = 187 Non ambiguous bp: Initial: 90015704 bp After Masking: 30890876 bp Masked: 65.68 % -- Input Database Coverage: 130083204 bp out of 3635158545 bp ( 3.58 % ) Sampling Time: 00:40:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 01:46:58 (hh:mm:ss) Elapsed Time, 118259 HSPs Collected Number of families returned by RECON: 5437 Round Time: 02:31:32 (hh:mm:ss) Elapsed Time : 249 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:18:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:20:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 576825 repeats masked totaling 152764679 bp(s). - TE Masking time 00:09:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270026777 bp Num Contigs Represented = 421 Non ambiguous bp: Initial: 270000476 bp After Masking: 82805771 bp Masked: 69.33 % -- Input Database Coverage: 400109981 bp out of 3635158545 bp ( 11.01 % ) Sampling Time: 01:48:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23205078 Comparison Time: 12:14:46 (hh:mm:ss) Elapsed Time, 322595 HSPs Collected Number of families returned by RECON: 13923 Round Time: 14:25:29 (hh:mm:ss) Elapsed Time : 495 families discovered. RepeatScout/RECON discovery complete: 1449 families found Classification Time: 01:09:00 (hh:mm:ss) Elapsed Time Program Time: 19:19:36 (hh:mm:ss) Elapsed Time