RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.mDln0J/RM_37539.WedDec282240112022 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: 1672296010 Database = /dev/shm/rModeler.mDln0J/GCA_910591455.2_fPhoGun1.2 - Sequences = 101 - Bases = 588696950 - N50 = 27020202 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 29569215-31680502 |* [ 2 ] 27457928-29569214 |*** [ 6 ] 25346641-27457927 |* [ 3 ] 23235354-25346640 |** [ 4 ] 21124067-23235353 |*** [ 5 ] 19012780-21124066 | [ 1 ] 16901493-19012779 | [ 1 ] 14790207-16901493 | [ 1 ] 12678920-14790206 | [ ] 10567633-12678919 | [ 1 ] 8456346-10567632 | [ ] 6345059-8456345 | [ ] 4233772-6345058 | [ ] 2122485-4233771 | [ ] 11199-2122485 |************************************************** [ 77 ] Storage Throughput = excellent ( 1414.40 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40045554 bp ( 40035592 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:53 (hh:mm:ss) Elapsed Time Round Time: 00:27:53 (hh:mm:ss) Elapsed Time : 458 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7771 repeats masked totaling 1126183 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030987 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10028187 bp After Masking: 8497383 bp Masked: 15.27 % -- Input Database Coverage: 10030987 bp out of 588696950 bp ( 1.70 % ) Sampling Time: 00:02:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:05:48 (hh:mm:ss) Elapsed Time, 6800 HSPs Collected Number of families returned by RECON: 1502 Round Time: 00:08:04 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22012 repeats masked totaling 3100509 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30014487 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30007325 bp After Masking: 25636229 bp Masked: 14.57 % -- Input Database Coverage: 40045474 bp out of 588696950 bp ( 6.80 % ) Sampling Time: 00:03:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:29:47 (hh:mm:ss) Elapsed Time, 52093 HSPs Collected Number of families returned by RECON: 5929 Round Time: 00:35:25 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:57 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 80293 repeats masked totaling 11190929 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023055 bp Num Contigs Represented = 41 Non ambiguous bp: Initial: 90000855 bp After Masking: 75520677 bp Masked: 16.09 % -- Input Database Coverage: 130068529 bp out of 588696950 bp ( 22.09 % ) Sampling Time: 00:10:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 03:29:43 (hh:mm:ss) Elapsed Time, 263101 HSPs Collected Number of families returned by RECON: 21403 Round Time: 03:54:36 (hh:mm:ss) Elapsed Time : 465 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 299362 repeats masked totaling 44206077 bp(s). - TE Masking time 00:07:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270069837 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 270004599 bp After Masking: 215326295 bp Masked: 20.25 % -- Input Database Coverage: 400138366 bp out of 588696950 bp ( 67.97 % ) Sampling Time: 00:31:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 27:02:01 (hh:mm:ss) Elapsed Time, 775477 HSPs Collected Number of families returned by RECON: 79664 Round Time: 29:26:38 (hh:mm:ss) Elapsed Time : 1069 families discovered. RepeatScout/RECON discovery complete: 2131 families found Classification Time: 01:15:55 (hh:mm:ss) Elapsed Time Program Time: 35:48:31 (hh:mm:ss) Elapsed Time