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wgd dmd #31
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Hi, are you up to a whole paranome? that a simple command |
Hi. Many thanks for the quick reply. Yes, I am tying to do a whole paranome. I run the command "wgd dmd cds.fa" but it didnt produce "familes" file. do I need to pass the dmd output dir to ks? |
Hi, the "familes" file is what you get as the result from the |
Thanks a lot for your prompt answers. So, if I understand you correctly, the file My goal from this analysis is to identify and date the WGD event(s) in my genome. towards this goal, do you think using the protein sequences will perform better than the cds sequences. |
I wend ahead and tested
`` `` |
To construct a Ks distribution, a cds file is essential. Protein file can be used in the final phylogenetic dating step, but optionally. The
The log seems to indicate that you didn't preinstall |
Thanks. I was thinking of using the protein file with When I use the cds as input for Do i need to trim the sequences or for some reasons, installing using conda on our HPC is not working and they had to install the tool from the source using the described method:
We installed PAML withing the wgd environment, which seems to be working. But when I run the `` `` the error log from yesterday is not showing up, so it seems that PAML is working, but the
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Hi, as I marked in the requirement on |
Hi,
I even tried on local linux machine. I installed it via pip and got successful installation messages as follows:
but when I started
I even tried to install from the bioconda channel |
Hi, the log information "FileNotFoundError: [Errno 2] No such file or directory: 'FastTree': 'FastTree'" indicates that you haven't installed the software |
Hello .. all my attempts were in conda environment specific for this program. For now, I want to understand whether the following "warning" indicates an installation issues:
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Hi, the log is not an indication of any installation issue but a normal log informing that the stripped alignment (i.e., after dropping all gap-containing sites) length is zero such that no |
Thank you! I think it might be working at last. the Assuming it will finish successfully this time, do you think the default command |
Hi, yes I think it will be sufficient and note that increasing the number of threads will significantly speed up the process because it is equal to the number of gene families that can be analyzed by |
Hello, -ap, --anchorpoints, the anchor points datafile, default None By now I have got all parts of the pipeline to work. |
Another question: |
Hi, |
Hello:
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Hi, I didn't encounter this type of error on my test dataset before. Could you please share me with your input files? I will try to reproduce your error. |
Yes. Please find the attached files. |
Hi, the |
Sorry.. added it |
Hi, I did reproduce your error, which is due to an unanticipated failure of finding peak in the segment-guided Ks GMM analysis when it is mapped back to anchor pairs. I have now fixed the error and updated it in |
Many thanks. will the installation still work with conda? do I need to rebuild the environment again? |
also, do I need redo the ks, dmd, syn, and mix analyses? |
Since I only modified the concerned part of code, you only need to update the version of |
The updated version In your example of Aquilegia coerulea, you used the |
Hi, |
Hi, thanks for the clarification. I run
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Hi, I haven't encoutered the condition that the |
I think the problem has to do the memory allocation. When I run the job with ``
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Hi, I think setting the number of thread as 1 and allocating the job with sufficient memory is the solution. |
I don't see any memory flags in the command line options. is there a way to calculate there required memory based on the OG families? |
This step involves external softwares for instance |
Hi,
I trying to analysis a single species using WGD V2. In the species delineation step, I am sure how to generate the families file that I need in the Ks step. I tried all relevant wgd dmd options, but none of them writes a "families" single file. I am sure I am missing something here. I'd really appreciate your answers.
best,
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