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ExecutionException due to UnexpectedStateException: Multiple Phenotypes for Gene CYP2C9 #180

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ngslabex opened this issue Apr 5, 2024 · 11 comments
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ExecutionException due to UnexpectedStateException: Multiple Phenotypes for Gene CYP2C9 #180

ngslabex opened this issue Apr 5, 2024 · 11 comments

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@ngslabex
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ngslabex commented Apr 5, 2024

I have faced with this error:
Where could I go wrong?
Thanks.
image
@BinglanLi
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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
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ngslabex commented Apr 5, 2024

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
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markwoon commented Apr 6, 2024

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

@ngslabex
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ngslabex commented Apr 6, 2024

@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 added a commit that referenced this issue Apr 6, 2024
@markwoon
fix(reporter): avoid exception for multiple phenotypes or activity sc…
da65834 
…ores for warfarin

Fix-for: #180
@markwoon
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markwoon commented Apr 6, 2024

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

@ngslabex
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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?

markwoon pushed a commit that referenced this issue Apr 23, 2024
@semantic-release-bot
chore(release): 2.12.0
0585c29 
## [2.12.0](v2.11.0...v2.12.0) (2024-4-23)

### Features

* **pharmcat:** support more than one outside call file ([154ac49](154ac49))
* **pipeline:** add the feature of bypassing the gVCF check to the pipeline ([d38005e](d38005e))

### Bug Fixes

* add json2tsv script ([dfabdc1](dfabdc1))
* **namedallelematcher:** improve VCF warnings ([1659e21](1659e21))
* **pharmcat:** add to path in docker container to fix running scripts ([57a956b](57a956b))
* **phenotyper:** strip gene symbol prefix from outside call diplotype alleles ([940f6cf](940f6cf))
* **reporter:** add "Activity Value" prefix to formatted function ([8735554](8735554))
* **reporter:** avoid exception for multiple phenotypes or activity scores for warfarin ([da65834](da65834)), closes [#180](#180)
* **reporter:** fix display of function/activity in variant position section ([2181f31](2181f31))
* **reporter:** no tags for CPIC warfarin report ([3842c1f](3842c1f))
@whaleyr
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whaleyr commented May 3, 2024

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

@lacek
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lacek commented Jul 10, 2024

The issue occurs again in v2.13.0.

I am able to reproduce issue with sample.vcf.bgz in #180 (comment) 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 whaleyr reopened this Jul 10, 2024
whaleyr added a commit that referenced this issue Jul 10, 2024
@whaleyr
fix(reporter): fix phenotype check by querying only phenotype-related…
b666953 
… genes in an annotation

Fix-for: #180
@whaleyr
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whaleyr commented Jul 10, 2024

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
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lacek commented Jul 11, 2024

Thank you @whaleyr !

Do you have an ETA for the next release?

@whaleyr
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whaleyr commented Jul 11, 2024

"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.

markwoon pushed a commit that referenced this issue Jul 19, 2024
@semantic-release-bot
chore(release): 2.14.0
a172280 
## [2.14.0](v2.13.0...v2.14.0) (2024-07-19)

### Features

* **data:** make all allele definitions import from PharmGKB ([47da939](47da939))
* **data:** update to PharmVar v6.1.3 ([e4b8fc2](e4b8fc2))

### Bug Fixes

* **data:** fix downloading new guidance data ([a1007c0](a1007c0))
* **diplotype-comparator:** update string delimiter ([e10a2ea](e10a2ea))
* **namedallelematcher:** fix exception thrown while sorting diplotype matches ([093f5b2](093f5b2))
* **namedallelematcher:** handle CYP2D6 and HLA outside calls with sub-alleles gracefully ([dcaa055](dcaa055))
* **reporter:** fix how allele presence phenotypes are shown in final report ([2f00c6c](2f00c6c))
* **reporter:** fix missing PMID in report citation data ([81a0df2](81a0df2)), closes [#187](#187)
* **reporter:** fix multiple version check logic ([3af2726](3af2726))
* **reporter:** fix phenotype check by querying only phenotype-related genes in an annotation ([b666953](b666953)), closes [#180](#180)
* **reporter:** warn if multiple versions found ([9bb2a55](9bb2a55))
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5 participants
@markwoon @whaleyr @lacek @BinglanLi @ngslabex