Hi there,

GWideCodeML successfully run. However, the final results data in .tsv were empty without any real data. Warning occurred as shown in gwidecodeml.log, see below:
WARNING :: LnL value was not found at x.alt.txt/ x.null.txt for all genes analyzed.
That's the reason why no data was generated in the final output files. I have checked the input files, nothing seems wrong to me. FYI, I have posted the log file below. Could anyone help me out? Thanks a lot!

part of gwidecodeml.log, as below:
INFO :: Starting GWideCodeML analysis... ROUND NAME: r01
WARNING :: Found duplicated genome tags in fasta files. 1 fasta files won't be analyzed
WARNING :: Discarded fasta files: ['group_1030.fna']
INFO :: These alignments won't be analyzed:
INFO :: group_1030.fna
INFO :: Starting analysis of 22 alignments
INFO :: Control files successfully created, GWidecodeml is ready for codeml performance
INFO :: Running codeml null hypothesis on btuD_2
INFO :: Running codeml alternative hypothesis on btuD_2
...(same for the remaining genes, not shown here)
INFO :: Codeml has finished, output files successfully created. Running LRTs...
WARNING :: LnL value was not found at btuD_2_r01_alt.txt. Please, check.
WARNING :: LnL value was not found at btuD_2_r01_null.txt. Please, check.
WARNING :: LRT not performed because the value LnL is missing in btuD_2_r01_alt.txt btuD_2_r01_null.txt files
....(same for the remaining genes, not shown here)
INFO :: Total nr. of genes rejecting null hypothesis: 0
INFO :: dnds option selected. Omega values will be written to an output file.
INFO :: Round name r01 finished
INFO :: GWideCodeML successfully run. Please, check results files: ['results_r01_SM.tsv']

Thanks!
Li

Hey Dev, just came across this nice tool that I'm starting to try, and as a feature request comment, it would be handy to count with a fourth preset nested analysis for Clade Model (M2a_rel vs Clade model C). ;)

Traceback (most recent call last):
File "/home/zhangyanan/miniconda3/envs/gwcodeml/bin/gwidecodeml", line 33, in
sys.exit(load_entry_point('gwidecodeml==1.1', 'console_scripts', 'gwidecodeml')())
File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/main.py", line 82, in main
File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/pkg_utils/utils.py", line 55, in dup_tags
File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/biopython-1.78-py3.6-linux-x86_64.egg/Bio/SeqIO/init.py", line 607, in parse
return iterator_generator(handle)
File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/biopython-1.78-py3.6-linux-x86_64.egg/Bio/SeqIO/FastaIO.py", line 183, in init
super().init(source, mode="t", fmt="Fasta")
File "/home/zhangyanan/miniconda3/envs/gwcodeml/lib/python3.6/site-packages/biopython-1.78-py3.6-linux-x86_64.egg/Bio/SeqIO/Interfaces.py", line 47, in init
self.stream = open(source, "r" + mode)

I'm using a species tree generated by OrthoFinder and the genome tags correspond to the names in my codon-aware alignment file. Here's the command and the output:

gwidecodeml -tree SpeciesTree_unrooted.txt -work_dir ~/HGT/flexible.dNdS/Orthogroup_Sequences/single.copy.fasta/codon.aware.alignments -cds .pal2nal -model BS -p 5 -branch branch_labels.csv -dnds

Traceback (most recent call last):
  File "/home/janani/anaconda3/envs/gwcodeml/bin/gwidecodeml", line 33, in <module>
    sys.exit(load_entry_point('gwidecodeml==1.1', 'console_scripts', 'gwidecodeml')())
  File "/home/janani/anaconda3/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/__main__.py", line 134, in main
  File "/home/janani/anaconda3/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/pkg_utils/utils.py", line 136, in prepare_codeml
  File "/home/janani/anaconda3/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/pkg_utils/utils.py", line 527, in prune_tree
  File "/home/janani/anaconda3/envs/gwcodeml/lib/python3.6/site-packages/ete3/coretype/tree.py", line 532, in prune
    start, node2path = self.get_common_ancestor(to_keep, get_path=True)
  File "/home/janani/anaconda3/envs/gwcodeml/lib/python3.6/site-packages/ete3/coretype/tree.py", line 928, in get_common_ancestor
    raise TreeError("Nodes are not connected!")
ete3.coretype.tree.TreeError: 'Nodes are not connected!'

Happy to send any files that might be helpful in troubleshooting.

Hello everyone!

While reviewing the folders generated after running the GWideCodeML, I noticed that empty files alt.txt and null.txt were created for many sequences. Because of this, it is not possible to generate LRT tests for these files, and I also don't know their dN/dS value. I checked different sequences for which these files were generated, and when compared to those for which they were not, I cannot discern any differences. Has anyone experienced something similar? Thanks in advance.

Dear lauguma,

WGideCodeML is a great work. However, when I set only one species as foreground, error appears as below:

Traceback (most recent call last):
File "/DATA5/software/miniconda/envs/gwcodeml/bin/gwidecodeml", line 33, in
sys.exit(load_entry_point('gwidecodeml==1.1', 'console_scripts', 'gwidecodeml')())
File "/DATA5/software/miniconda/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/main.py", line 134, in main
File "/DATA5/software/miniconda/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/pkg_utils/utils.py", line 141, in prepare_codeml
File "/DATA5/software/miniconda/envs/gwcodeml/lib/python3.6/site-packages/gwidecodeml-1.1-py3.6.egg/gwidecodeml/pkg_utils/utils.py", line 517, in mark_branches
AttributeError: 'str' object has no attribute 'node_id'

This error alos happens in the example, when only one species selected as foreground. How to set only one species as foreground ?

Best,
Leon
[email protected]

I tried running the example and after one hour it did not ended. I then removed most some fna leaving just four alignments and it still never ends.

When I check one of the gene folders this is what I get:
total 56
-rw-r--r-- 1 r users 0 May 12 13:04 2NG.dN
-rw-r--r-- 1 r users 0 May 12 13:04 2NG.dS
-rw-r--r-- 1 r users 0 May 12 13:04 2NG.t
lrwxrwxrwx 1 r users 29 May 29 2020 codeml.ctl -> /usr/lib/paml/data/codeml.ctl
-rw-r--r-- 1 r users 0 May 12 13:04 lnf
-rw-r--r-- 1 r users 0 May 12 13:04 rst
-rw-r--r-- 1 r users 0 May 12 13:04 rst1
-rw-r--r-- 1 r users 0 May 12 13:04 rub
-rw-r--r-- 1 r users 2202 May 12 13:04 YBL102W_alt.ctl
-rw-r--r-- 1 r users 2203 May 12 13:04 YBL102W_null.ctl
-rw-r--r-- 1 r users 17559 May 12 13:04 YBL102W.phy
-rw-r--r-- 1 r users 22387 May 12 13:04 YBL102W_r01_null.txt
-rw-r--r-- 1 r users 230 May 12 13:04 YBL102W.tree

Log file :
2022-05-12 13:04:21,361 :: INFO :: Working directory: /home/r/Software/GWideCodeML/example_data
2022-05-12 13:04:21,361 :: INFO :: Multiple branch testing selected: 2 branches will be analyzed as foreground branches.
2022-05-12 13:04:21,361 :: INFO :: Total number of alignments provided: 4
2022-05-12 13:04:21,362 :: INFO :: Model selected: BS
2022-05-12 13:04:21,362 :: INFO :: Species tree: /home/r/Software/GWideCodeML/example_data/spp_unrooted_tree.nwk
2022-05-12 13:04:21,362 :: INFO :: Nr. of threads: 6
2022-05-12 13:04:21,362 :: INFO :: Starting GWideCodeML analysis... ROUND NAME: r01
2022-05-12 13:04:21,371 :: INFO :: Applying filters...
2022-05-12 13:04:21,371 :: INFO :: Minimum number of outgroup species: 3
2022-05-12 13:04:21,373 :: INFO :: 0 alignments removed by min. outgroup filter.
2022-05-12 13:04:21,373 :: INFO :: Minimum number of clade-of-interest species: 3
2022-05-12 13:04:21,376 :: INFO :: 0 alignments removed by min. clade-of-interest filter.
2022-05-12 13:04:21,376 :: INFO :: Starting analysis of 4 alignments
2022-05-12 13:04:21,443 :: INFO :: Control files successfully created, GWidecodeml is ready for codeml performance
2022-05-12 13:04:21,468 :: INFO :: Running codeml null hypothesis on YFR016C
2022-05-12 13:04:21,468 :: INFO :: Running codeml null hypothesis on YEL063C
2022-05-12 13:04:21,469 :: INFO :: Running codeml null hypothesis on YBR167C
2022-05-12 13:04:21,469 :: INFO :: Running codeml null hypothesis on YBL102W

Any suggestions on how to make the software faster ? If I provide more threads even though only four alignments are given would it help ?

Thank you for this tool anyway !!

Hi,

I was trying to use GWideCodeML. I got the following error: UnboundLocalError: local variable 'log' referenced before assignment.

I took a piece of code -- for instance function lnl(codeml_in) -- and then reran with and without initializing local variable "log" in the function lnl((), I was able reproduce the error by not initializing the log variable.

Can you let me know if there is a bug (the one I mention) in the program?

Best,
Niraj

Hi!

I'm following the conda install instructions, however I get

Traceback (most recent call last):                                                                                                                                  
  File "setup.py", line 7, in <module>                                                                                                                              
    long_description = fh.read()                                                                                                                                    
  File "/miniconda3/envs/gwcodeml/lib/python3.6/encodings/ascii.py", line 26, in decode                                                   
    return codecs.ascii_decode(input, self.errors)[0]                                                                                                               
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 1727: ordinal not in range(128)      

The cause seems to be some characters in the README.md file. I think it's the í Macías, when I delete that it works.

Hi Laura,

In the log file (gwidecodeml.log), I see the following information.

INFO :: Total nr. of genes rejecting null hypothesis: 1033

However, when I check the results_r01_BS.tsv file there are only 239 genes.

Could you please let me know if the number of genes reported in the results_r01_BS.tsv file has to equal to be equal to the number shown in the log file?

Regards,
Niraj

Hi,
Congratulations on the program! It is a great contribution to work with genomic data.
I have run the branch model several times and always I get the outputs but not the .tsv file with the LRTs. Should I indicate a special flag or should it be generated automatically?

The analysis I ran it as follows:
gwidecodeml -model BM -work_dir $WD -cds .cd.msa -tree species_tree.nwk -dnds -branch branch1.csv -p 10

Best,
Daly