Corset error

Question

[scarey]

Hello,

I'm getting this error when I'm trying to make count matrices with corset and the Trinity 'align_and_estimate_abundance.pl script.

Output:

Running Corset Version 1.09
Setting sample groups:Gynophore,Gynophore,Gynophore,Gynophore,Filament,Filament,Filament,Filament, 2 groups in total

Setting sample names to:Gynophore_Rep1,Gynophore_Rep2,Gynophore_Rep3,Gynophore_Rep4,Filament_Rep1,Filament_Rep2,Filament_Rep3,Filament_Rep4

The number of sample names passed (via the -n option), 8, does not match the number of samples, 1. Please check how many values you have passed.

The input is the following:

mkdir corset
cd corset

while read SAMPLE_LINE; do
        SAMPLE=$(echo "$SAMPLE_LINE" | cut -f2)
        FILE=../DE_analysis/"$SAMPLE"/bowtie2.bam
        cp "$FILE" "$SAMPLE".bam
        corset -r true-stop "$SAMPLE".bam &
done < ../"$SAMPLE_DESCR_FILE"
wait

SAMPLE_GROUPS=$(cut -f1 ../"$SAMPLE_DESCR_FILE" | tr "\n" "," | sed '$s/,$/\n/')

REPLICATE_LIST=$(cut -f2 ../"$SAMPLE_DESCR_FILE" | tr "\n" "," | sed '$s/,$/\n/')

echo "Clustering contigs with Corset..."

corset -g "$SAMPLE_GROUPS" -n "$REPLICATE_LIST" -i corset *.corset-reads

I don't understand what I'm missing here. No issues with older versions of Trinity and Corset. Please forgive the formatting.

Please be gentle, I'm mostly just a biologist.

Shane

[WouterDeCoster]

Please try before the corset command to take a look at the variables by adding

echo $SAMPLE_GROUPS
echo $REPLICATE_LIST

the error indicates that one of these is just one element, while it should be 8, or so it seems.

[scarey]

echo $SAMPLE_GROUPS

Gynophore,Gynophore,Gynophore,Gynophore,Filament,Filament,Filament,Filament

echo $REPLICATE_LIST Gynophore_Rep1,Gynophore_Rep2,Gynophore_Rep3,Gynophore_Rep4,Filament_Rep1,Filament_Rep2,Filament_Rep3,Filament_Rep4

Two sample groups with 4 replicates a piece. I don't know where the 1 is coming from.