If baqlava is analyzing a file with a “.” character in the name it fails to create the intermediate/paths with the correct name and truncates the name at the period. The assumption is that the “.” signifies a file extension I think. The folders/files for the temp files created by humann are misnamed and it will be unable to find them for downstream step.
Hi Che,
Thank you for using BAQLaVa! That is correct, and is specified in the ‘Running BAQLaVa’ section of the user manual ( GitHub - biobakery/baqlava: Bioinformatic Application for Quantification and LAbeling of VirAl taxonomy ). Replacing “.” with “_” will solve your issue! Apologies for any confusion you’ve run into while profiling your samples with filenames that are not compatible.
Jordan
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