RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.nOg0Y9/RM_3266031.MonNov180814412024 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: 1731946481 Database = /scratch/tmp/rModeler.nOg0Y9/GCA_964197995.1_fScaEry2.hap1.1 - Sequences = 755 - Bases = 1229666150 - N50 = 46461436 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 74826970-80171683 | [ 1 ] 69482258-74826970 | [ 1 ] 64137546-69482258 | [ ] 58792834-64137546 | [ 2 ] 53448122-58792834 | [ 1 ] 48103409-53448121 | [ 4 ] 42758697-48103409 | [ 5 ] 37413985-42758697 | [ 7 ] 32069273-37413985 | [ 4 ] 26724561-32069273 | [ ] 21379848-26724560 | [ ] 16035136-21379848 | [ ] 10690424-16035136 | [ ] 5345712-10690424 | [ ] 1000-5345712 |************************************************** [ 730 ] Storage Throughput = excellent ( 1455.81 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016418 bp ( 40010244 non ambiguous ) - Num Contigs Represented = 88 - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:59 (hh:mm:ss) Elapsed Time Round Time: 00:20:41 (hh:mm:ss) Elapsed Time : 1233 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 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15660 repeats masked totaling 3485851 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007392 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10005592 bp After Masking: 5610002 bp Masked: 43.93 % -- Input Database Coverage: 10007392 bp out of 1229666150 bp ( 0.81 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:06 (hh:mm:ss) Elapsed Time, 9587 HSPs Collected Number of families returned by RECON: 1677 Round Time: 00:04:13 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47877 repeats masked totaling 10805993 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008946 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 30004572 bp After Masking: 16744036 bp Masked: 44.20 % -- Input Database Coverage: 40016338 bp out of 1229666150 bp ( 3.25 % ) Sampling Time: 00:04:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289941 Comparison Time: 00:14:32 (hh:mm:ss) Elapsed Time, 95755 HSPs Collected Number of families returned by RECON: 5561 Round Time: 00:20:01 (hh:mm:ss) Elapsed Time : 106 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 151806 repeats masked totaling 33429988 bp(s). - TE Masking time 00:01:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90030295 bp Num Contigs Represented = 153 Non ambiguous bp: Initial: 90019695 bp After Masking: 50267707 bp Masked: 44.16 % -- Input Database Coverage: 130046633 bp out of 1229666150 bp ( 10.58 % ) Sampling Time: 00:10:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2591226 Comparison Time: 01:25:21 (hh:mm:ss) Elapsed Time, 931195 HSPs Collected Number of families returned by RECON: 15679 Round Time: 01:44:35 (hh:mm:ss) Elapsed Time : 744 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:24:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 534589 repeats masked totaling 121009334 bp(s). - TE Masking time 00:08:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270055608 bp Num Contigs Represented = 281 Non ambiguous bp: Initial: 270017037 bp After Masking: 129359653 bp Masked: 52.09 % -- Input Database Coverage: 400102241 bp out of 1229666150 bp ( 32.54 % ) Sampling Time: 00:36:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23362030 Comparison Time: 07:52:45 (hh:mm:ss) Elapsed Time, 5779708 HSPs Collected Number of families returned by RECON: 40672 Round Time: 09:04:26 (hh:mm:ss) Elapsed Time : 1699 families discovered. RepeatScout/RECON discovery complete: 3805 families found Classification Time: 01:23:13 (hh:mm:ss) Elapsed Time Program Time: 12:57:09 (hh:mm:ss) Elapsed Time