Indexing error using Salmon

Question

[Emilie]

Hello, I am trying to create an index utilizing Salmon/1.10.1 using the following code

salmon index -t Bos_taurus.ARS-UCD1.2.cdna.all.fa -i BT_index31 -k 31 --type quasi

However, I keep getting the following error

Exception : [Error: RapMap-based indexing is not supported in this version of salmon.] salmon index was invoked improperly.

I am running it on a Linux (CentOS 7) based server and have loaded all the modules that are needed for salmon.

I have double-checked numerous times that I am invoking the index properly and even copied the code straight from the vignette, and I am still getting this error.

I can however create an index using version Salmon/0.8.2 but I would prefer to use a newer version.

Has anyone else ran into this issue? Any suggested fixes or troubleshooting?

[Ram]

have loaded all the modules that are needed for salmon.

This could be a problem specific to your HPC. Contact your sysadmin.

Answer 1

[ATpoint]

Remove --type from your command. In recent salmon versions only one type (puff, stands for the pufferfish indexing method) of indexing method is available, and this is exactly what the error is telling. That is also why it works with that very old version. You are probably following an outdated tutorial. Current one does not mention --type, see https://salmon.readthedocs.io/en/latest/salmon.html#

[Emilie]

That fixed it! Thank you for helping me. I was in fact following an outdated tutorial.

[Ram]

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work. This will help future users that might find this post find the right answer.