erro for ksd

[lfp-a]

When I use the steps of ksd, the following error will appear, and all codeml files are empty files, how to solve it?

WARNING No codeml result for GF00003411 due to no resolved nucleotides codeml.py:234 INFO Analysing family GF00003415 core.py:2873 WARNING No codeml result for GF00003412 due to no resolved nucleotides codeml.py:234 INFO Analysing family GF00003416 core.py:2873 WARNING No codeml result for GF00003413 due to no resolved nucleotides codeml.py:234 INFO Analysing family GF00003417 core.py:2873 WARNING No codeml result for GF00003414 due to no resolved nucleotides codeml.py:234 WARNING No codeml result for GF00003415 due to no resolved nucleotides codeml.py:234

[heche-psb]

Hi, there was a bug in v2.0.21. I have fixed the bug and replaced it with v2.0.22. Could you reinstall and try again?

[lfp-a]

Thank you very much. I'll try it right away

[lfp-a]

I have just installed a new version of 2.022. but I still have the following errors

15:12:31 WARNING No codeml result for GF00000092 due to no resolved nucleotides codeml.py:234 WARNING No codeml result for GF00000093 due to no resolved nucleotides codeml.py:234 WARNING No codeml result for GF00000094 due to no resolved nucleotides codeml.py:234 15:12:48 WARNING No codeml result for GF00000001 due to no resolved nucleotides codeml.py:234 15:12:48 INFO Saving to sample.ksd/sample.fasta.tsv.ks.tsv cli.py:493 INFO Making plots cli.py:495 INFO No valid Ks values for plotting

[heche-psb]

Hi, this is not an error I think. It just shows that there is no Ks value can be estimated from those families because of in-frame stop codon in the alignment file that codeml couldn't handle, even though it looks like the stripped alignment length is non-zero. How many familes have you given as input in total? Did you only give those 4 large families? If you use --cds option at dmd step and ksd step, it might be another solution.

[lfp-a]

I don't think it's going to be this way, the comdel files in the running result are empty, I'm the cds of the entire transcriptional group data, thousands of family, and the final comdel is all empty

[heche-psb]

Could you share me with your cds file? I will try to reproduce your error.

[lfp-a]

I'll send the attachment to your mailbox

[lfp-a]

Can you provide your email address? I just replied to the email but was returned

[heche-psb]

This is my university email address Hengchi.Chen@UGent.be

[lfp-a]

It has been sent, please check it

[heche-psb]

run_log.txt As you can see, I can't reproduce your error. Are you using paml v4.9j and install the wgd from this github repository?

[lfp-a]

Thank you very much for your help. I have re-installed paml4.9 and now it can be used, but there are new errors like the following

This is wgd v2.0.22 cli.py:32 qt.qpa.xcb: could not connect to display localhost:12.0 qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted (core dumped)

[heche-psb]

This error is typically encountered in Linux systems when there is a problem with the X Window System. You can try echo $DISPLAY. It should return something like ":0.0". If it's not set or set incorrectly, you may need to configure your X server. Or you may need to install or reinstall the Qt libraries or the xcb plugin specifically.

[lfp-a]

Thank you very much. I changed the software of the linked server to MobaXterm and it can be used

[heche-psb]

No problem. Thanks for your interest in wgd v2 :-)