Salmon quantification not as expected; "versionInfo.json doesn't seem to exist"
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7 weeks ago
Haad • 0

Hi everyone,

I am trying to do salmon quantification with paired-end reads. I first created the index with decoys and that went smoothly. I noticed however that no versionInfo.json file was made. I thought this would not create any issues with quantification because this .json file just specifies the salmon version (as far as I understand).

Anyway, I proceeded onto quantification, with this script that runs salmon quant for each pair out of the paired-end reads in the specified directory:

# The READS PATH here is for reading .fastq files (gzipped or otherwise from
# a given directory, but if that directory is not specified, then the fastq/
# subdirectory is used by default (assuming it exists)
READS_PATH=${1 :- fastq}
cd "$READS_PATH"
for fn in *. fastq.gz; do
printf "Filename: $fn\n" # test
base=$(echo "$fn" | sed 's/_R[12]_001.fastq.gz//')
printf "Base: ${base}\n" # test
printf "Left: ${base}_R1_001.fastq.gz\n"
printf "Right: ${base}_R2_001.fastq.gz\n\n"
salmon quant -i "$INDEX_PATH" -1 A -1 "${base}_R1_001.fastq.gz" -2 "${base}_R2_001.fastq.gz" -p 12 -- validateMappings       
-o "${QUANTS_PATH}/${base}_quant"
done

And in the messages printed to the terminal I see, for example:

"salmon quant was invoked improperly.", and:

"Exception : [Error: The index version file .../proj/index/versionInfo.json doesn't seem to exist. Please try re-building the salmon index.]"

My index folder looks like this:

contents of index folder

The indexing logs are empty, if that matters.

Any hints on why the versionInfo.json file is not being made and why it's saying that quant was invoked improperly?

[Sorry for the long question, I am just providing details that would help you help me.]

salmon • 651 views
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Hi Pierre, thanks for letting me know. I have edited my question. Please do let me know if you have any idea what might be causing the problem I have outlined in my question.

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7 weeks ago
dsull ★ 6.9k

Generally, when an output file is missing (or if files/logs are empty), it means that the program didn't finish running.

Maybe the index construction step was interrupted? Did you run out of memory or disk space? Was there an error in your input files that caused the program to terminate prematurely?

After considering these things, try running salmon index again.

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Ah yeah I think it's likely that there was no space to make those files. The program did run because just for testing purposes I had a print message that could echo out only after the index finished (it was just echo "Created index"). I will try to make more space and see if that resolves the issue.

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I resolved the issue by just making sure I had more disk space. There was nothing wrong with the script.

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