RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.XU8lGM/RM_19394.WedMay101033252023 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: 1683740004 Database = /dev/shm/rModeler.XU8lGM/GCA_027942865.1_fOdoBon6.hap1 - Sequences = 189 - Bases = 945823896 - N50 = 39502134 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 45295819-48530455 | [ 3 ] 42061183-45295818 | [ 2 ] 38826547-42061182 |** [ 8 ] 35591911-38826546 |* [ 5 ] 32357275-35591910 |* [ 4 ] 29122639-32357274 | [ 2 ] 25888003-29122638 | [ ] 22653367-25888002 | [ ] 19418731-22653366 | [ ] 16184095-19418730 | [ ] 12949459-16184094 | [ ] 9714823-12949458 | [ ] 6480187-9714822 | [ ] 3245551-6480186 | [ ] 10916-3245551 |************************************************** [ 165 ] Storage Throughput = excellent ( 1185.31 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035974 bp ( 40031474 non ambiguous ) - Num Contigs Represented = 33 - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:44 (hh:mm:ss) Elapsed Time Round Time: 00:28:05 (hh:mm:ss) Elapsed Time : 525 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 7532 repeats masked totaling 2053539 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005198 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10004198 bp After Masking: 7076412 bp Masked: 29.27 % -- Input Database Coverage: 10005198 bp out of 945823896 bp ( 1.06 % ) Sampling Time: 00:02:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:22 (hh:mm:ss) Elapsed Time, 8701 HSPs Collected Number of families returned by RECON: 1205 Round Time: 00:09:08 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 24899 repeats masked totaling 6654089 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030696 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30027196 bp After Masking: 21081784 bp Masked: 29.79 % -- Input Database Coverage: 40035894 bp out of 945823896 bp ( 4.23 % ) Sampling Time: 00:07:10 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:32:45 (hh:mm:ss) Elapsed Time, 49894 HSPs Collected Number of families returned by RECON: 4457 Round Time: 00:41:32 (hh:mm:ss) Elapsed Time : 87 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:22:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 79399 repeats masked totaling 20865088 bp(s). - TE Masking time 00:02:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018922 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 90007222 bp After Masking: 60311019 bp Masked: 32.99 % -- Input Database Coverage: 130054816 bp out of 945823896 bp ( 13.75 % ) Sampling Time: 00:26:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:29:14 (hh:mm:ss) Elapsed Time, 294175 HSPs Collected Number of families returned by RECON: 13316 Round Time: 04:09:40 (hh:mm:ss) Elapsed Time : 469 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:57:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 303436 repeats masked totaling 80462523 bp(s). - TE Masking time 00:13:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270039064 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 270019019 bp After Masking: 167476703 bp Masked: 37.98 % -- Input Database Coverage: 400093880 bp out of 945823896 bp ( 42.30 % ) Sampling Time: 01:17:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22906296 Comparison Time: 25:17:17 (hh:mm:ss) Elapsed Time, 905649 HSPs Collected Number of families returned by RECON: 45727 Round Time: 28:00:05 (hh:mm:ss) Elapsed Time : 1203 families discovered. RepeatScout/RECON discovery complete: 2297 families found Classification Time: 02:23:06 (hh:mm:ss) Elapsed Time Program Time: 35:51:36 (hh:mm:ss) Elapsed Time