error when indexing transcroptome using salmon

Question

[Sara]

I have made a singularity container for the salmon v1.6.0 and I am working with centOS. I am trying to make an index file for human transcript using this command:

salmon index -t hg19_EnsenmblGenes_sequence_ensenmbl.fasta -i Ensembl_hg19_salmon_index

But I am getting this error:

Version Info: This is the most recent version of salmon.
exception : [the option '--index' is required but missing]. Exiting.

Then I tried this command:

salmon --index -t hg19_EnsenmblGenes_sequence_ensenmbl.fasta -i Ensembl_hg19_salmon_index

Then I got this error:

Version Info: This is the most recent version of salmon. salmon was invoked improperly. For usage information, try salmon --help Exiting.

Do you know how I can fix the issue?

[Rob]

Your command looks correct, and the error message is referring, somehow, to the options parser not finding the option for where to place the index -i = --index. Can you do which salmon?

Also, do you get the same thing if you use the command:

salmon index -t hg19_EnsenmblGenes_sequence_ensenmbl.fasta --index Ensembl_hg19_salmon_index

[Sara]

Rob with the which salmon command I got this:

/usr/local/bin/salmo

but the version of salmon is the latest which is: salmon v1.6.0. when I run the command you mentioned it works (still running). but I got my reference file from gencode. do I have to use this option :

--gencode

instead of -t

it is mentioned in the result of this command:

salmon index -- help

[Rob]

That is very strange, as -i and --index should be interchangeable. Nonetheless, I'm glad that --index worked. Regarding using --gencode, this is recommended if you want the output to make use of simplified transcript names (everything up to the first | in the fasta header for each transcript). If you want the full (looong) name, then you can leave off the --gencode. It will have no effect on the actual results of quantification, apart from the name used in the output files for the transcripts. Also, --gencode is a flag that one can pass in addition to the require -t option, not a replacement for -t.

[lieven.sterck]

did you try:

For usage information, try salmon --help

?

[Sara]

lieven.sterck yes I did. in the help shows the command I used. that is why I am confused! I should also mention that I used that without singularity as well and got the same error.

[lieven.sterck]

ok.

your first version should work though (with index without the -- ) .

can you run salmon index --help ?

[Sara]

lieven.sterck I did and returns a list of possible items (like when you do --help). and when I did :

salmon index --gencode gencode.v39.transcripts.fa

I got this error again:

Version Info: This is the most recent version of salmon.
exception : [the option '--index' is required but missing]. Exiting.

[lieven.sterck]

long shot, but do you have write permissions for the location where you want to write/put/create the index?

and do follow Rob 's advise and suggestions (can't get any better than direct from the developers ;) )