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:
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.]
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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.