Hello everyone, I hope you're doing great.

I'm trying to impute a gvcf using a PHG database. As far as I'm concerned and because of the logs (attached here) of the steps 1 and 2 in the PHG Wiki guide, It seems that I have stablished and populated the PHG db with haplotypes correctly (there is not a single 'ERROR' message in any log) . The problem comes when I run the Imputation part on a example gvcf, where I get the next error on the net.maizegenetics.pangenome.hapCalling.SNPToReadMappingPlugin - Processing record: 100_Ma100,wgsFlowcell,Ma100_.vcf.gz,wgs step:

ERROR net.maizegenetics.plugindef.AbstractPlugin - currentIndexLine must not be null

The command that I used was:

singularity exec -B ${WORKING_DIR}/:/phg/ ${WORKING_DIR}/phg_16.simg /tassel-5-standalone/run_pipeline.pl -Xmx20G -debug -configParameters imputevcfconfig.txt -ImputePipelinePlugin -imputeTarget map -localGVCFFolder /phg/inputDir/loadDB/gvcf/ -localGVCFDir /phg/inputDir/loadDB/gvcf/  -endPlugin > 08_VCF_Imputation.log

And the pipeline stops. Also, the pangenome folder at the outputDir/ is empty; and the vcfIndex file at the outputDir/ only contains the headers, and not any other information, which makes me wonder if there's any previous mistake that might be causing these problems.

I attach the logs for each step, the configure files, keys and the example gvcf in the next link:

https://drive.google.com/drive/folders/1s318N3OCQLm_okDLr5UIYjRED05jl7XK?usp=sharing

Any help or guidance would be much appreciated. If you need any other information to clarify what might be happening please let me know. Thank you!