Salmon Script Troubleshooting for RNA Seq Data

Question

[makylakb]

Hello!

I am working on a Slurm sbatch bash script to perform RNAseq analysis with Salmon in an HPC environment.

I keep receiving the error "salmon quant was invoked improperly" but can't figure out where my error is.

Can anyone spot any errors to help me figure this out?

Script and slurm.out error are attached.

[Arup Ghosh]

Make sure the index was created properly. Similar issue has been discussed in the following thread.

https://github.com/COMBINE-lab/salmon/issues/197

[GenoMax]

1. Problem appears to be the fact that mates2 value is being concatenated at the end of mates1. It is not immediately apparent as to why that is happening. That is leaving values of mates2 blank. Check the values of fq1 and fq2 and make sure they are coming through properly.
2. There may be one more directory inside that long index directory name Pdac_Barhee...._normalized_index. You should add that name at the end of the long string for the salmon index.