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!

[OmarOakheart]

Hi, you're interpreting the error correctly. Could you first update to v1.0.14 with the following command and let me know if it still happens?

conda update -c oakheart nphase

While you do that I'll look into if I have a bug for this specific use of nphase partial, I'll let you know what I find

[jdenkena]

yes, even after updating to v1.0.14 this still happens.

[OmarOakheart]

The issue isn't glaringly obvious to me. Could you also send me your log file in the /Logs folder that should have been created? It should have some lines that can reveal what happened when nPhase tried running GATK. If you don't want to upload it to github you can email it to me

[OmarOakheart]

I received the log file. The issue is that the illumina reads were mapped to a different reference than the reference given to nPhase, and the two references didn't have a contig name in common. I'll close this issue when I've added code to identify this issue and inform the user of the best way to resolve it.