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aquaskyline / Clairvoyante

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

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Error when no variant identified as result of low coverage

MeHelmy opened this issue · comments

commented

In case of calling SNPs and there is no sufficient coverage to support the variant,This error is raised;

elay 3 seconds before starting variant calling ...Delay 7 seconds before starting variant calling ...Delay 5 seconds before starting variant calling ...

Loading model ...
Loading model ...
Loading model ...
Traceback (most recent call last):
  File "/stornext/snfs5/next-gen/scratch/fritz/centra_programs_pipelines/conda3_64/envs/clairvoyante-1.0.0-1/bin/dataPrepScripts/ExtractVariantCandidates.py", line 316, in <module>
    main()
  File "/stornext/snfs5/next-gen/scratch/fritz/centra_programs_pipelines/conda3_64/envs/clairvoyante-1.0.0-1/bin/dataPrepScripts/ExtractVariantCandidates.py", line 312, in main
    MakeCandidates(args)
  File "/stornext/snfs5/next-gen/scratch/fritz/centra_programs_pipelines/conda3_64/envs/clairvoyante-1.0.0-1/bin/dataPrepScripts/ExtractVariantCandidates.py", line 168, in MakeCandidates
    matches.append( (refPos, SEQ[queryPos]) )

Thanks,

commented

Just to clarify it is clear that this error is provided but I think it is easier for the user if you catch it and provide some warning.
Cheers
Fritz

commented

Noted, @chaklim please look into the error