RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.LG03C4/RM_1413147.ThuNov141446502024 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: 1731624410 Database = /scratch/tmp/rModeler.LG03C4/GCA_964273445.1_bStrDea1.hap1.1 - Sequences = 2451 - Bases = 1290957608 - N50 = 82231490 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 198996841-213210830 | [ 1 ] 184782852-198996840 | [ ] 170568864-184782852 | [ ] 156354875-170568863 | [ 1 ] 142140886-156354874 | [ ] 127926898-142140886 | [ ] 113712909-127926897 | [ 1 ] 99498920-113712908 | [ ] 85284932-99498920 | [ ] 71070943-85284931 | [ 3 ] 56856954-71070942 | [ 2 ] 42642966-56856954 | [ ] 28428977-42642965 | [ ] 14214988-28428976 | [ 8 ] 1000-14214988 |************************************************** [ 2435 ] Storage Throughput = excellent ( 1347.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020223 bp ( 40014423 non ambiguous ) - Num Contigs Represented = 183 - Sequence extraction : 00:01:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:16 (hh:mm:ss) Elapsed Time Round Time: 00:12:35 (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 : 00:00:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1936 repeats masked totaling 675111 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040290 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 10039890 bp After Masking: 8073923 bp Masked: 19.58 % -- Input Database Coverage: 10040290 bp out of 1290957608 bp ( 0.78 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33930 Comparison Time: 00:03:19 (hh:mm:ss) Elapsed Time, 646 HSPs Collected Number of families returned by RECON: 225 Round Time: 00:04:14 (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 : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5702 repeats masked totaling 1875695 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30019859 bp Num Contigs Represented = 150 Non ambiguous bp: Initial: 30014459 bp After Masking: 24010753 bp Masked: 20.00 % -- Input Database Coverage: 40060149 bp out of 1290957608 bp ( 3.10 % ) Sampling Time: 00:02:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 300700 Comparison Time: 00:15:55 (hh:mm:ss) Elapsed Time, 8685 HSPs Collected Number of families returned by RECON: 1226 Round Time: 00:18:51 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17102 repeats masked totaling 5710464 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035729 bp Num Contigs Represented = 330 Non ambiguous bp: Initial: 90026567 bp After Masking: 72927874 bp Masked: 18.99 % -- Input Database Coverage: 130095878 bp out of 1290957608 bp ( 10.08 % ) Sampling Time: 00:09:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2697003 Comparison Time: 01:39:19 (hh:mm:ss) Elapsed Time, 46659 HSPs Collected Number of families returned by RECON: 6950 Round Time: 01:49:49 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 64771 repeats masked totaling 20664682 bp(s). - TE Masking time 00:01:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270050584 bp Num Contigs Represented = 844 Non ambiguous bp: Initial: 270024628 bp After Masking: 215334684 bp Masked: 20.25 % -- Input Database Coverage: 400146462 bp out of 1290957608 bp ( 31.00 % ) Sampling Time: 00:28:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24559536 Comparison Time: 11:00:02 (hh:mm:ss) Elapsed Time, 196566 HSPs Collected Number of families returned by RECON: 44518 Round Time: 11:47:20 (hh:mm:ss) Elapsed Time : 222 families discovered. RepeatScout/RECON discovery complete: 390 families found Classification Time: 00:13:58 (hh:mm:ss) Elapsed Time Program Time: 14:26:47 (hh:mm:ss) Elapsed Time