RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WUWnDB/RM_23137.WedMay170648072023 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: 1684331286 Database = /dev/shm/rModeler.WUWnDB/GCF_028858705.1_bGruAme1.mat - Sequences = 930 - Bases = 1257837975 - N50 = 126354548 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 205210557-219868338 | [ 1 ] 190552776-205210556 | [ ] 175894995-190552775 | [ ] 161237214-175894994 | [ 1 ] 146579434-161237214 | [ ] 131921653-146579433 | [ ] 117263872-131921652 | [ 1 ] 102606091-117263871 | [ ] 87948310-102606090 | [ ] 73290530-87948310 | [ 2 ] 58632749-73290529 | [ 1 ] 43974968-58632748 | [ ] 29317187-43974967 | [ 4 ] 14659406-29317186 | [ 8 ] 1626-14659406 |************************************************** [ 912 ] Storage Throughput = excellent ( 1123.94 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40140671 bp ( 40027463 non ambiguous ) - Num Contigs Represented = 80 - Sequence extraction : 00:02:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:08 (hh:mm:ss) Elapsed Time Round Time: 00:28:32 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1343 repeats masked totaling 573672 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10074760 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 10034370 bp After Masking: 9247132 bp Masked: 7.85 % -- Input Database Coverage: 10074760 bp out of 1257837975 bp ( 0.80 % ) Sampling Time: 00:02:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:15:05 (hh:mm:ss) Elapsed Time, 406 HSPs Collected Number of families returned by RECON: 212 Round Time: 00:18:01 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4490 repeats masked totaling 1990138 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30105911 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30033093 bp After Masking: 27608037 bp Masked: 8.07 % -- Input Database Coverage: 40180671 bp out of 1257837975 bp ( 3.19 % ) Sampling Time: 00:03:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292230 Comparison Time: 00:40:45 (hh:mm:ss) Elapsed Time, 9301 HSPs Collected Number of families returned by RECON: 1504 Round Time: 00:44:52 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15143 repeats masked totaling 6072046 bp(s). - TE Masking time 00:01:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90314455 bp Num Contigs Represented = 148 Non ambiguous bp: Initial: 90028473 bp After Masking: 82293945 bp Masked: 8.59 % -- Input Database Coverage: 130495126 bp out of 1257837975 bp ( 10.37 % ) Sampling Time: 00:18:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2618616 Comparison Time: 07:07:31 (hh:mm:ss) Elapsed Time, 41810 HSPs Collected Number of families returned by RECON: 8482 Round Time: 07:44:31 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:55 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:51:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 58909 repeats masked totaling 22596737 bp(s). - TE Masking time 00:04:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270877484 bp Num Contigs Represented = 355 Non ambiguous bp: Initial: 270039716 bp After Masking: 241402324 bp Masked: 10.60 % -- Input Database Coverage: 401372610 bp out of 1257837975 bp ( 31.91 % ) Sampling Time: 01:10:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23595015 Comparison Time: 59:06:05 (hh:mm:ss) Elapsed Time, 202025 HSPs Collected Number of families returned by RECON: 53147 Round Time: 61:24:59 (hh:mm:ss) Elapsed Time : 236 families discovered. RepeatScout/RECON discovery complete: 380 families found Classification Time: 00:38:08 (hh:mm:ss) Elapsed Time Program Time: 71:19:04 (hh:mm:ss) Elapsed Time