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PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool
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PharmCAT rare error using version 2.0.3 #119

Closed anh151 closed 1 year ago

anh151 commented 2 years ago

I am getting an error from PharmCAT on only 53 out of ~100,000 samples/files.

This is using PharmCAT version 2.0.3 and preprocessor from the development branch.


RuntimeError: Error running command /home/jupyter/workspaces/piii03variantfrequencyprojectpgxcontrolled/bin/jdk-17.0.4.1+1/bin/java -jar /home/jupyter/workspaces/piii03variantfrequencyprojectpgxcontrolled/bin/pharmcat-2.0.3-all.jar -vcf /home/jupyter/workspaces/piii03variantfrequencyprojectpgxcontrolled/pharmcat_all_positions_unphased/ready.1920431.preprocessed.vcf -o pharmcat_all_positions_unphased_output with error: java.lang.IllegalArgumentException: Comparison method violates its general contract!
    at java.base/java.util.ComparableTimSort.mergeHi(ComparableTimSort.java:870)
    at java.base/java.util.ComparableTimSort.mergeAt(ComparableTimSort.java:487)
    at java.base/java.util.ComparableTimSort.mergeForceCollapse(ComparableTimSort.java:426)
    at java.base/java.util.ComparableTimSort.sort(ComparableTimSort.java:222)
    at java.base/java.util.Arrays.sort(Arrays.java:1107)
    at java.base/java.util.Arrays.sort(Arrays.java:1301)
    at java.base/java.util.ArrayList.sort(ArrayList.java:1721)
    at java.base/java.util.Collections.sort(Collections.java:145)
    at org.pharmgkb.pharmcat.haplotype.DiplotypeMatcher.compute(DiplotypeMatcher.java:137)
    at org.pharmgkb.pharmcat.haplotype.DiplotypeMatcher.compute(DiplotypeMatcher.java:41)
    at org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher.callDpyd(NamedAlleleMatcher.java:319)
    at org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher.call(NamedAlleleMatcher.java:231)
    at org.pharmgkb.pharmcat.PharmCAT.execute(PharmCAT.java:322)
    at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:194)

If you need an example I can try and provide one.

-Andrew

BinglanLi commented 2 years ago

Hi Andrew, could you please provide an example test file so that we can figure out what might have gone wrong?

Thanks, Binglan

On Thu, Nov 3, 2022 at 2:12 PM Andrew Haddad @.***> wrote:

I am getting an error from PharmCAT on only 53 out of ~100,000 samples/files.

This is using PharmCAT version 2.0.3 and preprocessor from the development branch.

RuntimeError: Error running command /home/jupyter/workspaces/piii03variantfrequencyprojectpgxcontrolled/bin/jdk-17.0.4.1+1/bin/java -jar /home/jupyter/workspaces/piii03variantfrequencyprojectpgxcontrolled/bin/pharmcat-2.0.3-all.jar -vcf /home/jupyter/workspaces/piii03variantfrequencyprojectpgxcontrolled/pharmcat_all_positions_unphased/ready.1920431.preprocessed.vcf -o pharmcat_all_positions_unphased_output with error: java.lang.IllegalArgumentException: Comparison method violates its general contract! at java.base/java.util.ComparableTimSort.mergeHi(ComparableTimSort.java:870) at java.base/java.util.ComparableTimSort.mergeAt(ComparableTimSort.java:487) at java.base/java.util.ComparableTimSort.mergeForceCollapse(ComparableTimSort.java:426) at java.base/java.util.ComparableTimSort.sort(ComparableTimSort.java:222) at java.base/java.util.Arrays.sort(Arrays.java:1107) at java.base/java.util.Arrays.sort(Arrays.java:1301) at java.base/java.util.ArrayList.sort(ArrayList.java:1721) at java.base/java.util.Collections.sort(Collections.java:145) at org.pharmgkb.pharmcat.haplotype.DiplotypeMatcher.compute(DiplotypeMatcher.java:137) at org.pharmgkb.pharmcat.haplotype.DiplotypeMatcher.compute(DiplotypeMatcher.java:41) at org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher.callDpyd(NamedAlleleMatcher.java:319) at org.pharmgkb.pharmcat.haplotype.NamedAlleleMatcher.call(NamedAlleleMatcher.java:231) at org.pharmgkb.pharmcat.PharmCAT.execute(PharmCAT.java:322) at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:194)

If you need an example I can try and provide one.

-Andrew

— Reply to this email directly, view it on GitHub https://github.com/PharmGKB/PharmCAT/issues/119, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEEAARHL5442SOD7EVKIB4DWGQTEBANCNFSM6AAAAAARWR3VSQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Binglan Li, PhD (She/Her) Postdoctoral scholar, PharmGKB, Klein Lab Department of Biomedical Data Sciences Stanford University

anh151 commented 1 year ago

Just wanted to give an update. I tried version 2.1.2 and I'm still having the same issue

BinglanLi commented 1 year ago

Thanks for the update, Andrew. I will look into this issue this week.

On Mon, Nov 14, 2022 at 12:14 PM Andrew Haddad @.***> wrote:

Just wanted to give an update. I tried version 2.1.2 and I'm still having the same issue

— Reply to this email directly, view it on GitHub https://github.com/PharmGKB/PharmCAT/issues/119#issuecomment-1314319643, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEEAARFCOBBRBOV5K2K6FXTWIKMSTANCNFSM6AAAAAARWR3VSQ . You are receiving this because you commented.Message ID: @.***>

-- Binglan Li, PhD (She/Her) Postdoctoral scholar, PharmGKB, Klein Lab Department of Biomedical Data Sciences Stanford University