Over the past couple of days I have been running a workflow for basic data analysis of samples which looks like this:
Trimmomatic -> SPAdes -> MLST & ABRIcate
The past 6 samples that I ran through this workflow have been perfectly fine however with my most recent sample the Trimmomatic stage completes but the next step of SPAdes assembly does not activatev and sits on ‘waiting to run’. Is this a known issue or has anyone else run into this problem? I’ve tried to run the trimmed reads into SPAdes serparately too but the same issue occurs.
Thanks for any help!