MINTIE -p assemblyFasta= line in params.txt

-p assemblyFasta= in params.txt being interpreted with non-empty value. Makes the pipeline assume that an assembly has been provided. Tried setting to '',"","''" etc. but that wasn't interpreted correctly by bpipe. Suggest removing this line from the default params.txt file?

Oct 18 '25 22:10 nadiadavidson

Which version of bpipe are you running? I believe this was due to a change between bpipe versions in the way that parameters values are handled from text files.

Oct 19 '25 23:10 mcmero

Thanks Marek, I'm using the bpipe version that came with the conda installation, version 0.9.13. Is this version too new or too old? Is there a way to constrain during installation? I can't see it in the requirements.txt file. I can see bpipe 0.9.9.5 in the installation script, but I'm not sure that's used with the conda method of installing.

Cheers, Nadia.

Oct 20 '25 09:10 nadiadavidson

Try version 0.9.12, you can constrain this like so (with minite env loaded):

mamba install -c conda-forge -c bioconda bpipe=0.9.12

I really should pin the right version in mintie's bioconda recipe however, I will run some tests and check which version avoids this bug.

Oct 21 '25 04:10 mcmero

I've tried testing in a fresh environment using the bpipe version that is installed by default (0.9.13) and couldn't replicate the error. Can you post the run command and output?

Oct 26 '25 23:10 mcmero

This should be fixed in MINTIE v0.4.3. Please reopen with an error log if you run into the problem again with this version.

Nov 11 '25 03:11 mcmero