here is the problem log
(base) lindh@R740xd:/data/02_work/lindh/work/05_TQS/09_chromosome/04_new/04_wgd/00_raw$ wgd ksd --n_threads 8 -mp 1000 -o ../02_ks/00_tqs_cds.ksd/ ../01_mcl/00_tqs_cds.dmd/00_tqs_cds.fa.mcl 00_tqs_cds.fa
2024-06-27 21:38:53: INFO codeml stdout: AAML in paml version 4.10.7, June 2023
2024-06-27 21:38:53: INFO codeml stderr: error: file name empty.
2024-06-27 21:38:53: INFO codeml found
2024-06-27 21:38:53: INFO mafft stdout:
2024-06-27 21:38:53: INFO mafft stderr: v7.525 (2024/Mar/13)
2024-06-27 21:38:53: INFO FastTree stdout:
2024-06-27 21:38:53: INFO FastTree stderr: Unknown or incorrect use of option --version
FastTree protein_alignment > tree
FastTree < protein_alignment > tree
FastTree -out tree protein_alignment
FastTree -nt nucleotide_alignment > tree
FastTree -nt -gtr < nucleotide_alignment > tree
FastTree < nucleotide_alignment > tree
FastTree accepts alignments in fasta or phylip interleaved formats
Common options (must be before the alignment file):
-quiet to suppress reporting information
-nopr to suppress progress indicator
-log logfile -- save intermediate trees, settings, and model details
-fastest -- speed up the neighbor joining phase & reduce memory usage
(recommended for >50,000 sequences)
-n to analyze multiple alignments (phylip format only)
(use for global bootstrap, with seqboot and CompareToBootstrap.pl)
-nosupport to not compute support values
-intree newick_file to set the starting tree(s)
-intree1 newick_file to use this starting tree for all the alignments
(for faster global bootstrap on huge alignments)
-pseudo to use pseudocounts (recommended for highly gapped sequences)
-gtr -- generalized time-reversible model (nucleotide alignments only)
-lg -- Le-Gascuel 2008 model (amino acid alignments only)
-wag -- Whelan-And-Goldman 2001 model (amino acid alignments only)
-quote -- allow spaces and other restricted characters (but not ' ) in
sequence names and quote names in the output tree (fasta input only;
FastTree will not be able to read these trees back in)
-noml to turn off maximum-likelihood
-nome to turn off minimum-evolution NNIs and SPRs
(recommended if running additional ML NNIs with -intree)
-nome -mllen with -intree to optimize branch lengths for a fixed topology
-cat # to specify the number of rate categories of sites (default 20)
or -nocat to use constant rates
-gamma -- after optimizing the tree under the CAT approximation,
rescale the lengths to optimize the Gamma20 likelihood
-constraints constraintAlignment to constrain the topology search
constraintAlignment should have 1s or 0s to indicates splits
-expert -- see more options
For more information, see http://www.microbesonline.org/fasttree/
2024-06-27 21:38:53: WARNING Output directory exists, will possibly overwrite
2024-06-27 21:38:54: INFO Translating CDS file
Traceback (most recent call last):
File "/data/02_work/lindh/software/Mamba/bin/wgd", line 33, in
sys.exit(load_entry_point('wgd==1.2', 'console_scripts', 'wgd')())
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return _callback(*args, **kwargs)
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/wgd-1.2-py3.10.egg/wgd_cli.py", line 629, in ksd
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/wgd-1.2-py3.10.egg/wgd_cli.py", line 725, in ksd
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/wgd-1.2-py3.10.egg/wgd/utils.py", line 363, in translate_cds
TypeError: ProgressBar.init() got an unexpected keyword argument 'max_value'
thank for you apply
here is the problem log
(base) lindh@R740xd:/data/02_work/lindh/work/05_TQS/09_chromosome/04_new/04_wgd/00_raw$ wgd ksd --n_threads 8 -mp 1000 -o ../02_ks/00_tqs_cds.ksd/ ../01_mcl/00_tqs_cds.dmd/00_tqs_cds.fa.mcl 00_tqs_cds.fa
2024-06-27 21:38:53: INFO codeml stdout: AAML in paml version 4.10.7, June 2023
2024-06-27 21:38:53: INFO codeml stderr: error: file name empty.
2024-06-27 21:38:53: INFO codeml found
2024-06-27 21:38:53: INFO mafft stdout:
2024-06-27 21:38:53: INFO mafft stderr: v7.525 (2024/Mar/13)
2024-06-27 21:38:53: INFO FastTree stdout:
2024-06-27 21:38:53: INFO FastTree stderr: Unknown or incorrect use of option --version
FastTree protein_alignment > tree
FastTree < protein_alignment > tree
FastTree -out tree protein_alignment
FastTree -nt nucleotide_alignment > tree
FastTree -nt -gtr < nucleotide_alignment > tree
FastTree < nucleotide_alignment > tree
FastTree accepts alignments in fasta or phylip interleaved formats
Common options (must be before the alignment file):
-quiet to suppress reporting information
-nopr to suppress progress indicator
-log logfile -- save intermediate trees, settings, and model details
-fastest -- speed up the neighbor joining phase & reduce memory usage
(recommended for >50,000 sequences)
-n to analyze multiple alignments (phylip format only)
(use for global bootstrap, with seqboot and CompareToBootstrap.pl)
-nosupport to not compute support values
-intree newick_file to set the starting tree(s)
-intree1 newick_file to use this starting tree for all the alignments
(for faster global bootstrap on huge alignments)
-pseudo to use pseudocounts (recommended for highly gapped sequences)
-gtr -- generalized time-reversible model (nucleotide alignments only)
-lg -- Le-Gascuel 2008 model (amino acid alignments only)
-wag -- Whelan-And-Goldman 2001 model (amino acid alignments only)
-quote -- allow spaces and other restricted characters (but not ' ) in
sequence names and quote names in the output tree (fasta input only;
FastTree will not be able to read these trees back in)
-noml to turn off maximum-likelihood
-nome to turn off minimum-evolution NNIs and SPRs
(recommended if running additional ML NNIs with -intree)
-nome -mllen with -intree to optimize branch lengths for a fixed topology
-cat # to specify the number of rate categories of sites (default 20)
or -nocat to use constant rates
-gamma -- after optimizing the tree under the CAT approximation,
rescale the lengths to optimize the Gamma20 likelihood
-constraints constraintAlignment to constrain the topology search
constraintAlignment should have 1s or 0s to indicates splits
-expert -- see more options
For more information, see http://www.microbesonline.org/fasttree/
2024-06-27 21:38:53: WARNING Output directory exists, will possibly overwrite
2024-06-27 21:38:54: INFO Translating CDS file
Traceback (most recent call last):
File "/data/02_work/lindh/software/Mamba/bin/wgd", line 33, in
sys.exit(load_entry_point('wgd==1.2', 'console_scripts', 'wgd')())
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return _callback(*args, **kwargs)
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/wgd-1.2-py3.10.egg/wgd_cli.py", line 629, in ksd
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/wgd-1.2-py3.10.egg/wgd_cli.py", line 725, in ksd
File "/data/02_work/lindh/software/Mamba/lib/python3.10/site-packages/wgd-1.2-py3.10.egg/wgd/utils.py", line 363, in translate_cds
TypeError: ProgressBar.init() got an unexpected keyword argument 'max_value'
thank for you apply