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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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problem in running pggb with empty file #129

Closed anna176577 closed 2 years ago

anna176577 commented 3 years ago

Hi All,

I am running pggb using: pggb -i input.fa -w 100000 -s 100000 -p 80 -a 100 -n 24 -k 8 -I 0.6 -R 0.2 -t 16 -v -L -o out

It produces all the files but the input.paf file is empty. The 1-D graph not not look correct and there is no 2-D graph output. Thank you!

AndreaGuarracino commented 3 years ago

Hi @anna176577, it seems you are using a pretty old version of pggb, For example, the -a is not supported anymore (I've just updated the README, where that parameter was still mentioned). Could you please update your installation, remove that parameter, and retry?

In case you still have problems, it could be useful to know what level of divergence you expect between the sequences in your dataset.

anna176577 commented 3 years ago

Hi @AndreaGuarracino, I updated pggb version and used these parameters: pggb -i input.fa -s 100000 -p 80 -n 24 -k 8 -I 0.6 -R 0.2 -t 16 -v -o out

It is running but taking much longer as it took with the previous version. I only see alog file and an ymlfile. The paffile is not made yet. Could you please suggest if there is something wrong with the parameters? Thank you!

AndreaGuarracino commented 3 years ago

Hi @anna176577, sorry for the delay, your run is probably over (hopefully). Nothing wrong, but the identity threshold is pretty low (-p 80), so you are exploring also regions with higher divergence which take more time to be aligned.

How did it end?

AndreaGuarracino commented 2 years ago

Hopefully, it ended well.