RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.OajZor/RM_21985.WedJan40946232023 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: 1672854382 Database = /dev/shm/rModeler.OajZor/GCA_009819655.1_bSylAtr1.pri - Sequences = 189 - Bases = 1066786587 - N50 = 88576696 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 142981509-153194430 | [ 1 ] 132768589-142981509 | [ ] 122555669-132768589 | [ ] 112342749-122555669 | [ 2 ] 102129829-112342749 | [ ] 91916909-102129829 | [ ] 81703989-91916909 | [ 1 ] 71491068-81703988 | [ 2 ] 61278148-71491068 | [ 1 ] 51065228-61278148 | [ ] 40852308-51065228 | [ ] 30639388-40852308 | [ 3 ] 20426468-30639388 |* [ 5 ] 10213548-20426468 |** [ 7 ] 628-10213548 |************************************************** [ 167 ] Storage Throughput = excellent ( 1090.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40395746 bp ( 40034648 non ambiguous ) - Num Contigs Represented = 42 - Sequence extraction : 00:01:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:23:09 (hh:mm:ss) Elapsed Time Round Time: 00:27:56 (hh:mm:ss) Elapsed Time : 113 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2717 repeats masked totaling 635193 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10119508 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10005627 bp After Masking: 9253211 bp Masked: 7.52 % -- Input Database Coverage: 10119508 bp out of 1066786587 bp ( 0.95 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:43 (hh:mm:ss) Elapsed Time, 1005 HSPs Collected Number of families returned by RECON: 367 Round Time: 00:08:47 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7928 repeats masked totaling 1722016 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30276236 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 30029019 bp After Masking: 27921621 bp Masked: 7.02 % -- Input Database Coverage: 40395744 bp out of 1066786587 bp ( 3.79 % ) Sampling Time: 00:03:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 289180 Comparison Time: 00:45:15 (hh:mm:ss) Elapsed Time, 6419 HSPs Collected Number of families returned by RECON: 1896 Round Time: 00:48:46 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24359 repeats masked totaling 5312579 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91034222 bp Num Contigs Represented = 62 Non ambiguous bp: Initial: 90020225 bp After Masking: 83216094 bp Masked: 7.56 % -- Input Database Coverage: 131429966 bp out of 1066786587 bp ( 12.32 % ) Sampling Time: 00:08:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 05:32:43 (hh:mm:ss) Elapsed Time, 53337 HSPs Collected Number of families returned by RECON: 12241 Round Time: 05:45:14 (hh:mm:ss) Elapsed Time : 75 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 82493 repeats masked totaling 19214176 bp(s). - TE Masking time 00:03:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273012662 bp Num Contigs Represented = 108 Non ambiguous bp: Initial: 270012456 bp After Masking: 246885304 bp Masked: 8.57 % -- Input Database Coverage: 404442628 bp out of 1066786587 bp ( 37.91 % ) Sampling Time: 00:26:19 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23512653 Comparison Time: 45:49:23 (hh:mm:ss) Elapsed Time, 276056 HSPs Collected Number of families returned by RECON: 79551 Round Time: 47:56:44 (hh:mm:ss) Elapsed Time : 228 families discovered. RepeatScout/RECON discovery complete: 429 families found Classification Time: 00:31:30 (hh:mm:ss) Elapsed Time Program Time: 55:38:57 (hh:mm:ss) Elapsed Time