I am attempting to use the netsurfp2 software to predict solvent accessibility of protein residues. The software appears to work when submitting jobs to their server, but I need to run it for many proteins locally. The alignment steps appear to work correctly, the expected intermediate files from mmseq2 are created and are well-formed. However, the result file which is supposed to contain the netsurfp2 predictions is empty when I attempt to run the program on multiple sequences. When I use it for a single sequence at a time the output is created successfully, but this is prohibitively slow for high-throughput applications. I reached out to the developers but haven't hear back, so I thought I'd check here to see if anyone has had success running netsurfp2 locally.
I think you're right. It was confusing because the MSA steps work correctly for input of multiple sequences, but probably the netsurf prediction step does not. Its unfortunate that there isn't an option to provide the MSA directly. It seems that they have that functionality on their server which does accept multiple sequences and doesn't appear to run the MSA step for each individually. I will probably have update their script to bypass the MSA step and go directly to prediction in order to run it in high-throughput. Thanks for your help!