运行Partitionfinder2时出错

[wangyan48691412]

尊敬的张老师： 在运行Partitionfinder2时，第52循环提示存在以下错误： ERROR | 2023-05-22 19:56:21,154 | main | A program that Partitionfinder uses failed. Output follows, in case it's helpful for finding the problem ERROR | 2023-05-22 19:56:21,154 | main | Assertion failed! Program: D:\biosoft\phylosuite\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite\plugins\partitionfinder-2.1.1\programs\raxml.exe File: optimizeModel.c, Line 123 Expression: rate >= RATE_MIN && rate <= RATE_MAX ERROR | 2023-05-22 19:56:21,154 | main | Warning: tree evaluation with CAT model of rate heterogeneity Only compare likelihood values for identical rate category assignments CAT-based Branch lengths are on average shorter by factor 0.5 than GAMMA-based branch lengths ... but highly correlated with GAMMA branch lengths Warning, you specified a working directory via "-w" Keep in mind that RAxML only accepts absolute path names, not relative ones! IMPORTANT WARNING: Sequences zizania_aquatica_168472191229365 and zizania_palustris_168472357313243 are exactly identical IMPORTANT WARNING Found 1 sequence that is exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. An alignment file with sequence duplicates removed has already been printed to file .\analysis\phylofiles\a250ca8f6a6080488e06c813be18dbaf.phy.reduced Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" This is RAxML version 8.2.7 released by Alexandros Stamatakis on March 10 2016. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Alignment has 20 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.00% RAxML Branch length scaler and other model parameter optimization up to an accuracy of 1.000000 log likelihood units Using 1 distinct models/data partitions with individual per partition branch length optimization All free model parameters will be estimated by RAxML ML estimate of 25 per site rate categories Likelihood of final tree will be evaluated and optimized under GAMMA GAMMA Model parameters will be estimated up to an accuracy of 1.0000000000 Log Likelihood units Partition: 0 Alignment Patterns: 20 Name: No Name Provided DataType: DNA Substitution Matrix: GTR RAxML was called as follows: D:\biosoft\phylosuite\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite\plugins\partitionfinder-2.1.1\programs\raxml.exe -f B -s .\analysis\phylofiles\a250ca8f6a6080488e06c813be18dbaf.phy -t .\analysis\start_tree\RAxML_result.BLTREE -m GTRCAT -V -n a250ca8f6a6080488e06c813be18dbaf_GTR.txt -w D:\biosoft\phylosuite\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite\myWorkPlace\GenBank_File\files\PartFind_results\2023_05_22-19_38_16\analysis\phylofiles -e 1.0 -O 请问如何处理

[dongzhang0725]

试试用modelfinder选分区模型把

wangyan48691412 @.***> 于2023年5月22日周一 20:46写道：

尊敬的张老师： 在运行Partitionfinder2时，第52循环提示存在以下错误： ERROR | 2023-05-22 19:56:21,154 | main | A program that Partitionfinder uses failed. Output follows, in case it's helpful for finding the problem ERROR | 2023-05-22 19:56:21,154 | main | Assertion failed! Program: D:\biosoft\phylosuite\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite\plugins\partitionfinder-2.1.1\programs\raxml.exe File: optimizeModel.c, Line 123 Expression: rate >= RATE_MIN && rate <= RATE_MAX ERROR | 2023-05-22 19:56:21,154 | main | Warning: tree evaluation with CAT model of rate heterogeneity Only compare likelihood values for identical rate category assignments CAT-based Branch lengths are on average shorter by factor 0.5 than GAMMA-based branch lengths ... but highly correlated with GAMMA branch lengths Warning, you specified a working directory via "-w" Keep in mind that RAxML only accepts absolute path names, not relative ones! IMPORTANT WARNING: Sequences zizania_aquatica_168472191229365 and zizania_palustris_168472357313243 are exactly identical IMPORTANT WARNING Found 1 sequence that is exactly identical to other sequences in the alignment. Normally they should be excluded from the analysis. An alignment file with sequence duplicates removed has already been printed to file .\analysis\phylofiles\a250ca8f6a6080488e06c813be18dbaf.phy.reduced Using BFGS method to optimize GTR rate parameters, to disable this specify "--no-bfgs" This is RAxML version 8.2.7 released by Alexandros Stamatakis on March 10 2016. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) Alignment has 20 distinct alignment patterns Proportion of gaps and completely undetermined characters in this alignment: 0.00% RAxML Branch length scaler and other model parameter optimization up to an accuracy of 1.000000 log likelihood units Using 1 distinct models/data partitions with individual per partition branch length optimization All free model parameters will be estimated by RAxML ML estimate of 25 per site rate categories Likelihood of final tree will be evaluated and optimized under GAMMA GAMMA Model parameters will be estimated up to an accuracy of 1.0000000000 Log Likelihood units Partition: 0 Alignment Patterns: 20 Name: No Name Provided DataType: DNA Substitution Matrix: GTR RAxML was called as follows: D:\biosoft\phylosuite\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite\plugins\partitionfinder-2.1.1\programs\raxml.exe -f B -s .\analysis\phylofiles\a250ca8f6a6080488e06c813be18dbaf.phy -t .\analysis\start_tree\RAxML_result.BLTREE -m GTRCAT -V -n a250ca8f6a6080488e06c813be18dbaf_GTR.txt -w D:\biosoft\phylosuite\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite_v1.2.3_Win64_with_plugins\PhyloSuite\myWorkPlace\GenBank_File\files\PartFind_results\2023_05_22-19_38_16\analysis\phylofiles -e 1.0 -O 请问如何处理

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