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Aborted Run: terminate called after throwing an instance of 'std::invalid_argument' #15

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womandrea opened this issue Jan 25, 2021 · 1 comment

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@womandrea
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I am trying to run the command

./jabba/bin/Jabba -k 75 -o ~/Jabba_Correction/ -fastq ~/...1WWL.fastq --graph ~1WWL_brownie_out.fasta

Now, the specific error I am getting is

terminate called after throwing an instance of 'std::invalid_argument'
  what():  stoi

I saw in a previous Issues thread that this had to do with the fasta file, but no note of how it was corrected is shown. The only way I've deviated from the manual is having directly gotten the de Bruijn Graph from brownie, which gave me a fastq, and converting it to a fasta with awk. Should this be causing such an issue? And if so, what would be the recommended fix for it?

@gmiclotte
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Hello

Could it be that there is a missing slash in the graph file name? It looks like ~1WWL_brownie_out.fasta should be ~/1WWL_brownie_out.fasta .

Kind regards
Giles Miclotte

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