RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.wRdWO2/RM_29399.MonJul150713562024 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: 1721052835 Database = /dev/shm/rModeler.wRdWO2/GCF_008692095.1_UIUC_Espe_1.0 - Sequences = 3119 - Bases = 854806606 - N50 = 30652338 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 36219267-38806284 | [ 4 ] 33632251-36219267 | [ 3 ] 31045235-33632251 | [ 4 ] 28458218-31045234 | [ 3 ] 25871202-28458218 | [ 2 ] 23284186-25871202 | [ 5 ] 20697169-23284185 | [ 1 ] 18110153-20697169 | [ 1 ] 15523137-18110153 | [ 1 ] 12936120-15523136 | [ ] 10349104-12936120 | [ ] 7762088-10349104 | [ ] 5175071-7762087 | [ ] 2588055-5175071 | [ ] 1039-2588055 |************************************************** [ 3095 ] Storage Throughput = excellent ( 1032.83 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40197273 bp ( 40016157 non ambiguous ) - Num Contigs Represented = 228 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:21 (hh:mm:ss) Elapsed Time Round Time: 00:26:53 (hh:mm:ss) Elapsed Time : 856 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12549 repeats masked totaling 1951400 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10053829 bp Num Contigs Represented = 81 Non ambiguous bp: Initial: 10001980 bp After Masking: 7429098 bp Masked: 25.72 % -- Input Database Coverage: 10053829 bp out of 854806606 bp ( 1.18 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 34716 Comparison Time: 00:06:20 (hh:mm:ss) Elapsed Time, 17476 HSPs Collected Number of families returned by RECON: 1593 Round Time: 00:08:13 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38414 repeats masked totaling 6105579 bp(s). - TE Masking time 00:00:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30143364 bp Num Contigs Represented = 180 Non ambiguous bp: Initial: 30014097 bp After Masking: 22411476 bp Masked: 25.33 % -- Input Database Coverage: 40197193 bp out of 854806606 bp ( 4.70 % ) Sampling Time: 00:03:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 322003 Comparison Time: 00:33:02 (hh:mm:ss) Elapsed Time, 65595 HSPs Collected Number of families returned by RECON: 5737 Round Time: 00:40:26 (hh:mm:ss) Elapsed Time : 169 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 128896 repeats masked totaling 20888300 bp(s). - TE Masking time 00:02:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90415261 bp Num Contigs Represented = 484 Non ambiguous bp: Initial: 90029892 bp After Masking: 64390298 bp Masked: 28.48 % -- Input Database Coverage: 130612454 bp out of 854806606 bp ( 15.28 % ) Sampling Time: 00:10:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2982903 Comparison Time: 03:49:28 (hh:mm:ss) Elapsed Time, 349592 HSPs Collected Number of families returned by RECON: 16514 Round Time: 04:24:24 (hh:mm:ss) Elapsed Time : 636 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:20:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 466796 repeats masked totaling 80232751 bp(s). - TE Masking time 00:15:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271325187 bp Num Contigs Represented = 1238 Non ambiguous bp: Initial: 270032023 bp After Masking: 175885000 bp Masked: 34.87 % -- Input Database Coverage: 401937641 bp out of 854806606 bp ( 47.02 % ) Sampling Time: 00:40:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26677860 Comparison Time: 35:42:03 (hh:mm:ss) Elapsed Time, 858610 HSPs Collected Number of families returned by RECON: 52735 Round Time: 38:34:31 (hh:mm:ss) Elapsed Time : 1350 families discovered. RepeatScout/RECON discovery complete: 3025 families found Classification Time: 02:30:31 (hh:mm:ss) Elapsed Time Program Time: 46:44:58 (hh:mm:ss) Elapsed Time