Hello!
I'm using the MAFToGVCFPlugin to convert MAF files into GVCF files using the "phg_latest.sif". I have used this plugin without issue before using the below arguments:
module load singularity
singularity exec phg_latest.sif /tassel-5-standalone/run_pipeline.pl \
-Xmx300g \
-MAFToGVCFPlugin \
-referenceFasta ${REFfasta} \
-mafFile Sb313_${REFname}_anchorwave.maf \
-sampleName Sb313_${REFname} \
-gvcfOutput Sb313_${REFname}_anchorwave.gvcf \
-fillGaps true
However, I'm now getting this error message:
ERROR net.maizegenetics.plugindef.AbstractPlugin - VariantInfo start <= previous end at 03:213777. Previous end was 215202
Looking at my MAF file, the first coordinates (head -n 3 MAF.file) are:
##maf version=1
a score=-11514
s Chr03 213776 10031 + 74386277 CTAACACGCCTCTGGTACAAACTTGA
This suggests to me that the MAF might need to be sorted? But this seems odd given this was not needed in the past when I've used this and others in my lab who've been using this have not run into this error or needed to sort their MAFs. I have been unable to locate in the documentation a potential cause for this error. I have tried using a different image of phg and different MAF files, but I get the same error.
Any guidance would be greatly appreciated! Thank you!
