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?
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
Is the command you can run to update the modules.