CHASMplus Async RuntimeWarning and Blank Results File

Question

[brunods1001]

I encountered the following error when running CHASMplus on a VCF file. My specific code was:

cravat -n GIBX29_run -t text -a chasmplus chasmplus_COAD cosmic dbsnp gnomad loftool mutpred1 biogrid abraom cgc cgl civic clinvar -d $HOME/rnaseq/data/cravat GIBx29_somatic_filtered.vcf

Which resulted in:

 Input file(s): /home/ec2-user/rnaseq/GIBx29_somatic_filtered.vcf
    Running annotators...
            chasmplus: started at Tue Aug 13 12:31:16 2019
            chasmplus: finished at Tue Aug 13 12:32:16 2019
            chasmplus: runtime 59.079s
        annotator(s) finished in 59.162s
    Running aggregator...
        Variants                        finished in 11.269s
        Genes                           finished in 0.017s
        Samples                         finished in 8.298s
        Tags                            finished in 12.349s
    Running postaggregators...
        Tag Sampler (tagsampler)        finished in 10.856s
        VCF Info (vcfinfo)              finished in 14.273s
    Running reporter...
        Text Reporter (textreporter)    /home/ec2-user/.local/lib/python3.7/site-packages/cravat/cravat_report.py:198: RuntimeWarning: coroutine 'Reporter.write_table_row' was never awaited
      self.write_table_row(new_datarow)
    RuntimeWarning: Enable tracemalloc to get the object allocation traceback
    finished in 3350.097s
    Finished normally. Runtime: 3458.260s

I expected my TSV results to contain annotations, but it was blank; file size = 1.1kb.

I researched the RuntimeWarning and found this suggestion on stackoverflow. I added "await" to line 198 in cravat_report.py and ran the code again.

The RuntimeWarning was no longer present. I am currently awaiting the program to finish and will post updates when it does.

Has anyone encountered this issue? Is there a solution I'm missing?

Thank you.

EDIT: Success!!! I hope this can help others who may face the same issue.

cat GIBX29_run_2.tsv | head
#CRAVAT Report
#Created at Tuesday 08/13/2019 13:45:52
#Report level: variant
#
Variant Annotation                                                          CHASMplus           VCF Info                            
UID Chrom   Position    Ref Base    Alt Base    Note    Coding  Hugo    Transcript  Sequence Ontology   Protein Change  All Mappings    Sample Count    Samples Tags    P-value Score   Transcript  All results Phred   VCF filter  Zygosity    Alternate reads Total reads Variant AFHaplotype block ID    Haplotype strand ID
1   chr1    14542   A   G                               1   GIBx29-cancer                           clustered_events;germline;panel_of_normals  het 15  25  0.593       
2   chr1    14574   A   G                               1   GIBx29-cancer                           clustered_events;germline;panel_of_normals  het 23  39  0.586       
3   chr1    14590   G   A                               1   GIBx29-cancer                           clustered_events;germline;haplotype;panel_of_normals    het 23  37  0.615       
4   chr1    14599   T   A                               1   GIBx29-cancer                           clustered_events;germline;haplotype;panel_of_normals    het 23  36  0.632

Answer 1

[slcrick]

Sorry there was a text reporter version with a bug. If you install the newest version of textreporter, that error will go away.

[kyle.moad2]

cravat-admin update

Is the command you can run to update the modules.