ExecutionException due to UnexpectedStateException: Multiple Phenotypes for Gene CYP2C9

[ngslabex]

I have faced with this error: Where could I go wrong? Thanks.

[BinglanLi]

Hi @ngslabex, thank you for sharing the issue with us.

Could you please share a mock VCF (removing the personal identifiable information)? It will help us replicate the error and resolve the issue.

[ngslabex]

Thank you very much for your quick response and interest. @BinglanLi

I share it immediately.

https://drive.google.com/file/d/1s_jkmkmIdi1WILyrzp-69O5nZn1SJLPB/view?usp=sharing

[markwoon]

@ngslabex Could you please provide the command line you're using to run PharmCAT? What options are you providing?

[ngslabex]

@ngslabex Could you please provide the command line you're using to run PharmCAT? What options are you providing?

I have used prompt that: @markwoon

docker run --rm  \
    -v /home/user/Desktop:/pharmcat/data \
    pgkb/pharmcat ./pharmcat_pipeline \
    data/sample.vcf.bgz \
    -v --reporter-extended

[markwoon]

We understand the problem and have a fix in place. Hope to release a new version next week.

[ngslabex]

We understand the problem and have a fix in place. Hope to release a new version next week.

Thanks for your support and solution. Has the new version release date been announced?

[whaleyr]

@ngslabex The new release has the fix for your problem. Please download v2.12.0

[lacek]

The issue occurs again in v2.13.0.

I am able to reproduce issue with sample.vcf.bgz in https://github.com/PharmGKB/PharmCAT/issues/180#issuecomment-2040575437 with below command:

./pharmcat_vcf_preprocessor.py -refFna /mnt/data/ref/Homo_sapiens_assembly38.fasta -s EO_EO --vcf sample.vcf.bgz -o . -bf test
java -jar pharmcat.jar -vcf test.preprocessed.vcf.bgz -s EO_EO -rt EO_EO -o . -bf test -reporterJson

The same commands works with v2.12.0

[whaleyr]

Found the problem. It was related to the new FDA content. I have a fix for this on the development branch and it will be included in the next release.

[lacek]

Thank you @whaleyr !

Do you have an ETA for the next release?

[whaleyr]

"Soon"

We have a couple other data updates coming through from PharmVar and CPIC. Once those have landed we'll cut the release, within the next week or two, I assume.