RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.slyB3X/RM_18843.SatJul62344212024 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: 1720334659 Database = /dev/shm/rModeler.slyB3X/GCF_001443325.1_P_mexicana-1.0 - Sequences = 18102 - Bases = 801710366 - N50 = 275424 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1459025-1563227 | [ 2 ] 1354823-1459024 | [ 1 ] 1250621-1354822 | [ 3 ] 1146419-1250620 | [ 4 ] 1042218-1146419 | [ 5 ] 938016-1042217 | [ 9 ] 833814-938015 | [ 20 ] 729612-833813 | [ 40 ] 625410-729611 | [ 52 ] 521209-625410 | [ 92 ] 417007-521208 | [ 158 ] 312805-417006 | [ 313 ] 208603-312804 |* [ 540 ] 104401-208602 |*** [ 1038 ] 200-104401 |************************************************** [ 15825 ] Storage Throughput = excellent ( 1049.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 47045583 bp ( 40019605 non ambiguous ) - Num Contigs Represented = 1836 - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:48 (hh:mm:ss) Elapsed Time Round Time: 00:24:18 (hh:mm:ss) Elapsed Time : 485 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9351 repeats masked totaling 1060883 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 11871847 bp Num Contigs Represented = 501 Non ambiguous bp: Initial: 10037696 bp After Masking: 8879282 bp Masked: 11.54 % -- Input Database Coverage: 11871847 bp out of 801710366 bp ( 1.48 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 137026 Comparison Time: 00:08:32 (hh:mm:ss) Elapsed Time, 10888 HSPs Collected Number of families returned by RECON: 1739 Round Time: 00:09:27 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30293 repeats masked totaling 3660862 bp(s). - TE Masking time 00:00:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 35232478 bp Num Contigs Represented = 1424 Non ambiguous bp: Initial: 30020627 bp After Masking: 26113963 bp Masked: 13.01 % -- Input Database Coverage: 47104325 bp out of 801710366 bp ( 5.88 % ) Sampling Time: 00:01:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1209790 Comparison Time: 00:48:28 (hh:mm:ss) Elapsed Time, 52848 HSPs Collected Number of families returned by RECON: 5446 Round Time: 00:51:51 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109145 repeats masked totaling 14390183 bp(s). - TE Masking time 00:01:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 106866539 bp Num Contigs Represented = 3764 Non ambiguous bp: Initial: 90018623 bp After Masking: 74826005 bp Masked: 16.88 % -- Input Database Coverage: 153970864 bp out of 801710366 bp ( 19.21 % ) Sampling Time: 00:04:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 11103828 Comparison Time: 05:47:16 (hh:mm:ss) Elapsed Time, 231982 HSPs Collected Number of families returned by RECON: 17901 Round Time: 06:05:51 (hh:mm:ss) Elapsed Time : 433 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 402131 repeats masked totaling 56613087 bp(s). - TE Masking time 00:10:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 318092068 bp Num Contigs Represented = 8702 Non ambiguous bp: Initial: 270026276 bp After Masking: 211081125 bp Masked: 21.83 % -- Input Database Coverage: 472062932 bp out of 801710366 bp ( 58.88 % ) Sampling Time: 00:19:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 94483131 Comparison Time: 45:18:39 (hh:mm:ss) Elapsed Time, 593148 HSPs Collected Number of families returned by RECON: 67185 Round Time: 47:32:40 (hh:mm:ss) Elapsed Time : 948 families discovered. RepeatScout/RECON discovery complete: 2020 families found Classification Time: 01:23:35 (hh:mm:ss) Elapsed Time Program Time: 56:27:42 (hh:mm:ss) Elapsed Time