RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7gMhE3/RM_11923.ThuJul251342572024 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: 1721940167 Database = /dev/shm/rModeler.7gMhE3/GCF_019703515.2_UBuf_Myxa_2 - Sequences = 353 - Bases = 2340864798 - N50 = 47969982 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 64586347-69199620 | [ 3 ] 59973074-64586346 | [ 1 ] 55359802-59973074 | [ 4 ] 50746529-55359801 | [ 5 ] 46133256-50746528 |** [ 14 ] 41519984-46133256 |* [ 12 ] 36906711-41519983 | [ 4 ] 32293438-36906710 | [ 2 ] 27680166-32293438 | [ 3 ] 23066893-27680165 | [ 2 ] 18453620-23066892 | [ ] 13840348-18453620 | [ ] 9227075-13840347 | [ ] 4613802-9227074 | [ ] 530-4613802 |************************************************** [ 303 ] Storage Throughput = excellent ( 1024.56 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40032133 bp ( 40029633 non ambiguous ) - Num Contigs Represented = 54 - Sequence extraction : 00:00:55 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:55 (hh:mm:ss) Elapsed Time Round Time: 01:22:13 (hh:mm:ss) Elapsed Time : 1431 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22236 repeats masked totaling 5017377 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007394 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 10006394 bp After Masking: 4764634 bp Masked: 52.38 % -- Input Database Coverage: 10007394 bp out of 2340864798 bp ( 0.43 % ) Sampling Time: 00:02:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 01:09:47 (hh:mm:ss) Elapsed Time, 7778 HSPs Collected Number of families returned by RECON: 1501 Round Time: 01:15:03 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:41 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 68542 repeats masked totaling 15522577 bp(s). - TE Masking time 00:01:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30024659 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30023159 bp After Masking: 13771126 bp Masked: 54.13 % -- Input Database Coverage: 40032053 bp out of 2340864798 bp ( 1.71 % ) Sampling Time: 00:04:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 03:50:07 (hh:mm:ss) Elapsed Time, 56315 HSPs Collected Number of families returned by RECON: 4533 Round Time: 04:06:50 (hh:mm:ss) Elapsed Time : 162 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 217744 repeats masked totaling 47635200 bp(s). - TE Masking time 00:04:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90040339 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 90037839 bp After Masking: 40110714 bp Masked: 55.45 % -- Input Database Coverage: 130072392 bp out of 2340864798 bp ( 5.56 % ) Sampling Time: 00:13:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2559453 Comparison Time: 12:18:43 (hh:mm:ss) Elapsed Time, 338012 HSPs Collected Number of families returned by RECON: 11831 Round Time: 13:18:02 (hh:mm:ss) Elapsed Time : 696 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 730617 repeats masked totaling 159893838 bp(s). - TE Masking time 00:20:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270037175 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 270017504 bp After Masking: 103633468 bp Masked: 61.62 % -- Input Database Coverage: 400109567 bp out of 2340864798 bp ( 17.09 % ) Sampling Time: 00:45:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 27:06:04 (hh:mm:ss) Elapsed Time, 588348 HSPs Collected Number of families returned by RECON: 34518 Round Time: 28:50:19 (hh:mm:ss) Elapsed Time : 1098 families discovered. RepeatScout/RECON discovery complete: 3405 families found Classification Time: 01:53:00 (hh:mm:ss) Elapsed Time Program Time: 50:45:28 (hh:mm:ss) Elapsed Time