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Running Salmon RNA quantification with pre-computed index

Hi! I am trying to run RNA quantification through the salmon program (I am using version 1.2.1), using the pre-computed salmon index downloaded from refgenie (link can be found here). I am having a bit of trouble with the options in the command line and keep receiving error messages.

Here is the command I am passing through: salmon quant -i <directory containing index> -l A -1 <(gzip <path to .fastq.gz file>) -2 <(gzip <path to .fastq.gz file>) --validateMappings -o <output directory>

Here is what directory containing the index has in it. I am passing the directory's path into the -i option.

enter image description here

I downloaded this entire folder from the refgenie link provided above.

Here is what the error message looks like.

enter image description here

salmon rnaseq
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written by saipra003 • saipra003

This could be a memory problem. Can you monitor the RAM usage in a separate window while this is running?

You may want to copy the program output as plain text and format it using the provided buttons. Faster than taking screenshots and embedding images.

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written by Mensur Dlakic Mensur Dlakic

I don't think that I can because this command is running on a remote cluster.

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written by saipra003 • saipra003

1 answer

Hi, I was able to solve the problem by upgrading Salmon to the current version at this time (version 1.5.2). It appears that this problem might have been a bug in the previous version.

I wanted to provide a quick update for those who are looking at this issue. The above issue was indeed caused by a memory problem. If you run into this problem, you should update your salmon version and also allocate more RAM to the Salmon process.

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written by saipra003 • saipra003

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