RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.f1nnPi/RM_565917.ThuNov141559202024 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: 1731628760 Database = /scratch/tmp/rModeler.f1nnPi/GCA_964106855.1_bGruGru1.hap1.1 - Sequences = 754 - Bases = 1352282554 - N50 = 89816460 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 209764276-224747368 | [ 1 ] 194781185-209764276 | [ ] 179798094-194781185 | [ ] 164815003-179798094 | [ 1 ] 149831912-164815003 | [ ] 134848820-149831911 | [ ] 119865729-134848820 | [ 1 ] 104882638-119865729 | [ ] 89899547-104882638 | [ ] 74916456-89899547 | [ 2 ] 59933364-74916455 | [ 1 ] 44950273-59933364 | [ 1 ] 29967182-44950273 | [ 4 ] 14984091-29967182 | [ 8 ] 1000-14984091 |************************************************** [ 735 ] Storage Throughput = excellent ( 1546.13 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40041479 bp ( 40038479 non ambiguous ) - Num Contigs Represented = 106 - Sequence extraction : 00:00:58 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:01 (hh:mm:ss) Elapsed Time Round Time: 00:15:03 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1669 repeats masked totaling 757371 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030082 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10028882 bp After Masking: 8521112 bp Masked: 15.03 % -- Input Database Coverage: 10030082 bp out of 1352282554 bp ( 0.74 % ) Sampling Time: 00:00:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 1442 HSPs Collected Number of families returned by RECON: 250 Round Time: 00:03:46 (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 : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5048 repeats masked totaling 2288956 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011317 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 30009517 bp After Masking: 25170081 bp Masked: 16.13 % -- Input Database Coverage: 40041399 bp out of 1352282554 bp ( 2.96 % ) Sampling Time: 00:02:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:13:15 (hh:mm:ss) Elapsed Time, 8998 HSPs Collected Number of families returned by RECON: 1291 Round Time: 00:15:24 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16580 repeats masked totaling 7426622 bp(s). - TE Masking time 00:00:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023620 bp Num Contigs Represented = 184 Non ambiguous bp: Initial: 90015438 bp After Masking: 76052664 bp Masked: 15.51 % -- Input Database Coverage: 130065019 bp out of 1352282554 bp ( 9.62 % ) Sampling Time: 00:05:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 01:26:08 (hh:mm:ss) Elapsed Time, 69620 HSPs Collected Number of families returned by RECON: 7540 Round Time: 01:34:15 (hh:mm:ss) Elapsed Time : 78 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65867 repeats masked totaling 26667566 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270058819 bp Num Contigs Represented = 355 Non ambiguous bp: Initial: 270033342 bp After Masking: 224123037 bp Masked: 17.00 % -- Input Database Coverage: 400123838 bp out of 1352282554 bp ( 29.59 % ) Sampling Time: 00:18:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23307378 Comparison Time: 11:07:48 (hh:mm:ss) Elapsed Time, 538966 HSPs Collected Number of families returned by RECON: 46583 Round Time: 11:41:51 (hh:mm:ss) Elapsed Time : 235 families discovered. RepeatScout/RECON discovery complete: 398 families found Classification Time: 00:19:21 (hh:mm:ss) Elapsed Time Program Time: 14:09:40 (hh:mm:ss) Elapsed Time