RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SRofuJ/RM_11429.MonJan82243352024 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: 1704782614 Database = /dev/shm/rModeler.SRofuJ/GCA_963692335.1_fOsmEpe2.1 - Sequences = 1008 - Bases = 508737883 - N50 = 18663607 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 25582896-27410175 | [ 1 ] 23755618-25582896 | [ 3 ] 21928340-23755618 | [ 3 ] 20101061-21928339 | [ 1 ] 18273783-20101061 | [ 6 ] 16446505-18273783 | [ 1 ] 14619226-16446504 | [ 4 ] 12791948-14619226 | [ 3 ] 10964670-12791948 | [ 2 ] 9137391-10964669 | [ 3 ] 7310113-9137391 | [ 1 ] 5482835-7310113 | [ ] 3655556-5482834 | [ ] 1828278-3655556 | [ ] 1000-1828278 |************************************************* [ 980 ] Storage Throughput = excellent ( 1021.83 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40058511 bp ( 40018189 non ambiguous ) - Num Contigs Represented = 132 - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:46 (hh:mm:ss) Elapsed Time Round Time: 00:28:31 (hh:mm:ss) Elapsed Time : 397 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4976 repeats masked totaling 1288465 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018352 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10008352 bp After Masking: 7737565 bp Masked: 22.69 % -- Input Database Coverage: 10018352 bp out of 508737883 bp ( 1.97 % ) Sampling Time: 00:01:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:06:50 (hh:mm:ss) Elapsed Time, 6912 HSPs Collected Number of families returned by RECON: 1370 Round Time: 00:08:46 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16588 repeats masked totaling 4676165 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30040079 bp Num Contigs Represented = 114 Non ambiguous bp: Initial: 30009757 bp After Masking: 21981225 bp Masked: 26.75 % -- Input Database Coverage: 40058431 bp out of 508737883 bp ( 7.87 % ) Sampling Time: 00:04:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 318801 Comparison Time: 00:38:12 (hh:mm:ss) Elapsed Time, 69358 HSPs Collected Number of families returned by RECON: 5721 Round Time: 00:47:10 (hh:mm:ss) Elapsed Time : 50 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 54728 repeats masked totaling 14897946 bp(s). - TE Masking time 00:01:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90127110 bp Num Contigs Represented = 226 Non ambiguous bp: Initial: 90035933 bp After Masking: 65922027 bp Masked: 26.78 % -- Input Database Coverage: 130185541 bp out of 508737883 bp ( 25.59 % ) Sampling Time: 00:15:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2802528 Comparison Time: 04:25:38 (hh:mm:ss) Elapsed Time, 456007 HSPs Collected Number of families returned by RECON: 21997 Round Time: 05:05:13 (hh:mm:ss) Elapsed Time : 341 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:36:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 216810 repeats masked totaling 55415814 bp(s). - TE Masking time 00:10:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270288960 bp Num Contigs Represented = 554 Non ambiguous bp: Initial: 270029965 bp After Masking: 187903166 bp Masked: 30.41 % -- Input Database Coverage: 400474501 bp out of 508737883 bp ( 78.72 % ) Sampling Time: 00:50:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24904153 Comparison Time: 32:03:31 (hh:mm:ss) Elapsed Time, 1313785 HSPs Collected Number of families returned by RECON: 77427 Round Time: 35:31:57 (hh:mm:ss) Elapsed Time : 759 families discovered. RepeatScout/RECON discovery complete: 1550 families found Classification Time: 01:41:05 (hh:mm:ss) Elapsed Time Program Time: 43:42:42 (hh:mm:ss) Elapsed Time