RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.TVpE30/RM_21267.FriDec60840262024 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: 1733503225 Database = /scratch/tmp/rModeler.TVpE30/GCA_037157625.1_bLatDis1.hap2 - Sequences = 413 - Bases = 1123412812 - N50 = 154797005 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 155982754-167123045 | [ 2 ] 144842464-155982754 | [ 1 ] 133702173-144842463 | [ ] 122561883-133702173 | [ 2 ] 111421593-122561883 | [ ] 100281302-111421592 | [ ] 89141012-100281302 | [ 1 ] 78000721-89141011 | [ ] 66860431-78000721 | [ ] 55720141-66860431 | [ ] 44579850-55720140 | [ ] 33439560-44579850 | [ ] 22299269-33439559 | [ 3 ] 11158979-22299269 | [ 6 ] 18689-11158979 |************************************************** [ 398 ] Storage Throughput = fair ( 591.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40098939 bp ( 40016776 non ambiguous ) - Num Contigs Represented = 75 - Sequence extraction : 00:02:24 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:27:07 (hh:mm:ss) Elapsed Time Round Time: 00:34:42 (hh:mm:ss) Elapsed Time : 91 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3042 repeats masked totaling 967896 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10053293 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10013293 bp After Masking: 8244745 bp Masked: 17.66 % -- Input Database Coverage: 10053293 bp out of 1123412812 bp ( 0.89 % ) Sampling Time: 00:02:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:43 (hh:mm:ss) Elapsed Time, 9757 HSPs Collected Number of families returned by RECON: 208 Round Time: 00:08:52 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10741 repeats masked totaling 3260525 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30045566 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 30003403 bp After Masking: 25002713 bp Masked: 16.67 % -- Input Database Coverage: 40098859 bp out of 1123412812 bp ( 3.57 % ) Sampling Time: 00:05:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:31:51 (hh:mm:ss) Elapsed Time, 4965 HSPs Collected Number of families returned by RECON: 1175 Round Time: 00:38:05 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32720 repeats masked totaling 9581161 bp(s). - TE Masking time 00:00:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90409376 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 90006209 bp After Masking: 75206918 bp Masked: 16.44 % -- Input Database Coverage: 130508235 bp out of 1123412812 bp ( 11.62 % ) Sampling Time: 00:19:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 05:04:00 (hh:mm:ss) Elapsed Time, 166214 HSPs Collected Number of families returned by RECON: 7549 Round Time: 05:31:35 (hh:mm:ss) Elapsed Time : 52 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 115057 repeats masked totaling 32712409 bp(s). - TE Masking time 00:04:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270772330 bp Num Contigs Represented = 260 Non ambiguous bp: Initial: 270006045 bp After Masking: 221486178 bp Masked: 17.97 % -- Input Database Coverage: 401280565 bp out of 1123412812 bp ( 35.72 % ) Sampling Time: 00:57:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23252790 Comparison Time: 35:56:22 (hh:mm:ss) Elapsed Time, 1192773 HSPs Collected Number of families returned by RECON: 52001 Round Time: 38:12:53 (hh:mm:ss) Elapsed Time : 188 families discovered. RepeatScout/RECON discovery complete: 344 families found Classification Time: 00:30:00 (hh:mm:ss) Elapsed Time Program Time: 45:36:07 (hh:mm:ss) Elapsed Time