error when indexing transcroptome using salmon
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?
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did you try:
?
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.
ok.
your first version should work though (with index without the -- ) .
can you run
salmon index --help?lieven.sterck I did and returns a list of possible items (like when you do --help). and when I did :
I got this error again:
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 ;) )
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 dowhich salmon?Also, do you get the same thing if you use the command:
Rob with the which salmon command I got this:
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 fromgencode. do I have to use this option :instead of
-tit is mentioned in the result of this command:
That is very strange, as
-iand--indexshould be interchangeable. Nonetheless, I'm glad that--indexworked. 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,--gencodeis a flag that one can pass in addition to the require-toption, not a replacement for-t.