Hello,

I am stuck at the initial step in the PennCNV CNV calling pipeline ie step 1.1 - generating genotype calls from raw CEL files. I have downloaded the Affymetrix power tools (APT) and the library files needed. The genotyping was done using axiom array.

The code for this step, as provided in the PennCNV (https://penncnv.openbioinformatics.org/en/latest/user-guide/affy/#-substep-11-generate-genotyping-calls-from-cel-files).

/apt-probeset-genotype --analysis-files-path /projects/cnv_calling/Axiom_UKBBv2_2/ --cel-files /projects/cnv_calling/test/b08_rawdata_cel.txt --summaries --xml-file /projects/cnv_calling/Axiom_UKBBv2_2/Axiom_UKBBv2_2.r2.apt-probeset-genotype.AxiomSS1.apt2.xml --out-dir /projects/cnv_calling/test/output/

The apt-probeset-genotype seems to run initially (goes through the xml file contents) then it throws the error in the screenshot below

I cannot figure out what this error means. I googled the error and found the cpp file for the probeset-genotype command (http://media.affymetrix.com/support/developer/powertools/changelog/ProbesetGenotypeEngine_8cpp_source.html). Here is a screenshot of the point where the error is raised

Anyone know how I can make sure only one analysis is running?

Thank you in advance for your help Jared