Running nPhase partial with mapped short reads

[jdenkena]

Hi! I have an issue when trying to run nPhase partial (version v1.0.12) using both mapped long reads and mapped short reads. Running: nphase partial --sampleName $ID --reference $ref --output ~/nPhase/ --longReads $longReads --mappedLongReads $mappedLongReads.sam --mappedShortReads $mappedShortReads.bam

have me the following error: Traceback (most recent call last): File "/home/denkena/miniconda3/envs/polyploidPhasing/bin/nphase", line 8, in <module> sys.exit(main()) File "/home/denkena/miniconda3/envs/polyploidPhasing/lib/python3.8/site-packages/bin/nPhasePipeline.py", line 557, in main partialPipeline(args) File "/home/denkena/miniconda3/envs/polyploidPhasing/lib/python3.8/site-packages/bin/nPhasePipeline.py", line 375, in partialPipeline SNPVCFFile=open(SNPVCFFilePath,"r") FileNotFoundError: [Errno 2] No such file or directory: '/home/denkena/nPhase/matchedNormal_DNA/VariantCalls/shortReads/matchedNormal_DNA.SNPs.vcf'

It seems the pipeline is skipping the Variant Calling from the mapped short reads? Is there something I can do to get this to run? Thanks!