Closed TomasaSbaffi closed 1 year ago
Hi @TomasaSbaffi
Thanks for trying out Phamb! If you ran Vamb seperately for each coassembly, it makes sense to run Phamb seperately for each coassembly as well.
Now to your problem: It is the naming of your contigs that produce the error, specifically the "spaces" in the fasta header. I would recommend renaming your contigs and replace spaces with "_" not only to make this parsing script work but many other bioinformatic tools do not work properly with spaces in fasta headers either.
The name change should look like this: k141_1091919 flag=0 multi=5.9626 len=1318 -> k141_1091919_flag=0_multi=5.9626_len=1318
I Best, Joachim
Thank you very very much!!
Hello,
I am really happy to be trying the PHAMB pipeline on my data. I am running it on small co assemblies, I do not have a concatenated assembly but I am running the pipeline separately for each coassembly. Is this a wrong approach?
When I run the RF model I have the following error, given by python:
The head of my clusters.tsv
the head of my all.DVF.predictions.txt
Is it due to the 4 columns composing the name of the contigs? Any suggestions?
Thanks again for the great pipeline!