RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.sVPX6y/RM_2624312.SunDec81801452024 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: 1733709705 Database = /scratch/tmp/rModeler.sVPX6y/GCA_964106205.1_mNeoVis2.hap2.1 - Sequences = 351 - Bases = 2662777898 - N50 = 219869771 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 293079075-314013224 | [ 1 ] 272144927-293079075 | [ ] 251210779-272144927 | [ ] 230276630-251210778 | [ 2 ] 209342482-230276630 | [ 3 ] 188408334-209342482 | [ 1 ] 167474186-188408334 | [ 1 ] 146540037-167474185 | [ 2 ] 125605889-146540037 | [ 2 ] 104671741-125605889 | [ ] 83737593-104671741 | [ 1 ] 62803444-83737592 | [ 1 ] 41869296-62803444 | [ 1 ] 20935148-41869296 | [ ] 1000-20935148 |************************************************** [ 336 ] Storage Throughput = excellent ( 1383.49 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008888 bp ( 40001586 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:02:03 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:15 (hh:mm:ss) Elapsed Time Round Time: 00:13:19 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13104 repeats masked totaling 2916913 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040702 bp Num Contigs Represented = 17 Non ambiguous bp: Initial: 10038800 bp After Masking: 7063477 bp Masked: 29.64 % -- Input Database Coverage: 10040702 bp out of 2662777898 bp ( 0.38 % ) Sampling Time: 00:00:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:03:14 (hh:mm:ss) Elapsed Time, 10837 HSPs Collected Number of families returned by RECON: 757 Round Time: 00:04:10 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41785 repeats masked totaling 9825313 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008027 bp Num Contigs Represented = 23 Non ambiguous bp: Initial: 30002627 bp After Masking: 20038620 bp Masked: 33.21 % -- Input Database Coverage: 40048729 bp out of 2662777898 bp ( 1.50 % ) Sampling Time: 00:02:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:13:31 (hh:mm:ss) Elapsed Time, 103171 HSPs Collected Number of families returned by RECON: 2326 Round Time: 00:16:16 (hh:mm:ss) Elapsed Time : 53 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 127805 repeats masked totaling 29595028 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029245 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 90010045 bp After Masking: 59996715 bp Masked: 33.34 % -- Input Database Coverage: 130077974 bp out of 2662777898 bp ( 4.89 % ) Sampling Time: 00:06:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2541385 Comparison Time: 01:16:43 (hh:mm:ss) Elapsed Time, 1150665 HSPs Collected Number of families returned by RECON: 8960 Round Time: 01:26:12 (hh:mm:ss) Elapsed Time : 151 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 420350 repeats masked totaling 96676828 bp(s). - TE Masking time 00:01:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270102337 bp Num Contigs Represented = 104 Non ambiguous bp: Initial: 270035864 bp After Masking: 171982940 bp Masked: 36.31 % -- Input Database Coverage: 400180311 bp out of 2662777898 bp ( 15.03 % ) Sampling Time: 00:20:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22906296 Comparison Time: 09:04:42 (hh:mm:ss) Elapsed Time, 14810133 HSPs Collected Number of families returned by RECON: 35094 Round Time: 09:38:26 (hh:mm:ss) Elapsed Time : 330 families discovered. RepeatScout/RECON discovery complete: 716 families found Classification Time: 00:14:58 (hh:mm:ss) Elapsed Time Program Time: 11:53:21 (hh:mm:ss) Elapsed Time