Error: The index version file /labs/Resources/MMUL_10/index.salmon/versionInfo.json doesn’t seem to exist. Please try re-building the salmon index.]

[kalanir]

Issue with salmon for bulk RNA-seq

The following code was run to invoke salmon:

docker run --rm -v /labs/Resources/mmulatta/MMUL_10:/mnt/indexdir/ resources/salmon salmon index -t /mnt/indexdir/gentrome.fa -d /mnt/indexdir/decoys.txt -p 8 -i /mnt/indexdir/index.salmon

however, everytime I run it, I get the following error: Exception : [Error: The index version file /labs/khatrilab/Resources/mmulatta/MMUL_10/index.salmon/versionInfo.json doesn’t seem to exist. Please try re-building the salmon index.]

when in fact, the file exists. the gentrome.fa and decoys.txt files were created by following this tutorial (clearly changing the genome to mmulatta) https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/

Why is salmon not finding the index file that's clearly present in the given folder path?

[hariiyer16]

Hello kalanir. Were you able t resolve this. I am facing the same problem for some time now. Thank you.

[kalanir]

@hariiyer16 I have not! The index works in an older version of salmon but not the newer one even though it was built in a way that should be usable by the newer Salmon version.

[rob-p]

@kalanir,

Can you please direct me to the files you used to build the index? Is the docker image above the one from docker hub? I would be hopeful, if this happens in docker, we could track down what's going on. When you say it works with an older version, can you tell me whst version works for you with this index?

Thanks, Rob

[rob-p]

Though I don't know exactly the reference you used, I just attempted to index and quantify using the latest docker image combinelab/salmon:latest, and it worked properly on the host machine on which it was being run (and ubuntu 16.10 box) with a gentrome created from vM25 and GRCm38. So, the difficulty must be due either to the specific reference being used or to the specifics of the machine on which the commands are being run.

[ACastanza]

I suspect you're running this on a Mac, correct? I had the same issue, Salmon would index for the better part of a day, use ~30 gb of swap space, then die (killed 9 message). The versionInfo.json error is slightly misleading, most likely what happened is that the indexing didn't finish and since that file is only created if it finishes correctly, that's the error you get. Running the indexing with the same code, with similar resources completed on our AWS node so I wonder if this is a Mac specific problem...