RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.dGtqp9/RM_130549.WedNov130636322024 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: 1731508591 Database = /scratch/tmp/rModeler.dGtqp9/GCF_013368605.1_bNycGra1.pri - Sequences = 190 - Bases = 1256393467 - N50 = 99981954 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 124846559-133763977 | [ 2 ] 115929142-124846559 | [ ] 107011724-115929141 | [ 1 ] 98094307-107011724 | [ 2 ] 89176890-98094307 | [ 1 ] 80259472-89176889 | [ 1 ] 71342055-80259472 | [ ] 62424637-71342054 | [ ] 53507220-62424637 | [ 1 ] 44589803-53507220 | [ 1 ] 35672385-44589802 | [ 1 ] 26754968-35672385 | [ 3 ] 17837550-26754967 | [ 2 ] 8920133-17837550 |** [ 9 ] 2716-8920133 |************************************************** [ 166 ] Storage Throughput = excellent ( 1599.22 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40391473 bp ( 40036373 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:41 (hh:mm:ss) Elapsed Time Round Time: 00:11:54 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1971 repeats masked totaling 1153535 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042034 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 10026951 bp After Masking: 8809862 bp Masked: 12.14 % -- Input Database Coverage: 10042034 bp out of 1256393467 bp ( 0.80 % ) Sampling Time: 00:00:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:02:49 (hh:mm:ss) Elapsed Time, 745 HSPs Collected Number of families returned by RECON: 261 Round Time: 00:03:17 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6232 repeats masked totaling 3660238 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30349359 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30009342 bp After Masking: 26112235 bp Masked: 12.99 % -- Input Database Coverage: 40391393 bp out of 1256393467 bp ( 3.21 % ) Sampling Time: 00:01:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:12:54 (hh:mm:ss) Elapsed Time, 7400 HSPs Collected Number of families returned by RECON: 1428 Round Time: 00:14:16 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 20493 repeats masked totaling 10659315 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90433617 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 90015800 bp After Masking: 78797905 bp Masked: 12.46 % -- Input Database Coverage: 130825010 bp out of 1256393467 bp ( 10.41 % ) Sampling Time: 00:03:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 01:23:07 (hh:mm:ss) Elapsed Time, 32651 HSPs Collected Number of families returned by RECON: 8124 Round Time: 01:27:33 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73617 repeats masked totaling 35847219 bp(s). - TE Masking time 00:01:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271309744 bp Num Contigs Represented = 97 Non ambiguous bp: Initial: 270009877 bp After Masking: 232308053 bp Masked: 13.96 % -- Input Database Coverage: 402134754 bp out of 1256393467 bp ( 32.01 % ) Sampling Time: 00:10:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23177836 Comparison Time: 10:45:11 (hh:mm:ss) Elapsed Time, 195272 HSPs Collected Number of families returned by RECON: 51202 Round Time: 11:10:14 (hh:mm:ss) Elapsed Time : 227 families discovered. RepeatScout/RECON discovery complete: 395 families found Classification Time: 00:11:26 (hh:mm:ss) Elapsed Time Program Time: 13:18:40 (hh:mm:ss) Elapsed Time