search

PROBIC / mGEMS

mGEMS Genomic epidemiology with mixed samples
MIT License
16 stars 1 forks source link

`Error: basic_string` when using mSWEEP abundances with bootstrap iterations in them as input #9

Closed tmaklin closed 3 years ago

tmaklin commented 4 years ago

mGEMS will crash with the error message Error: basic_string if the program is called with an input abundances file (-a option) that contains bootstrap iterations from mSWEEP version 1.4.0 or earlier (abundances file created using the --iters option when running mSWEEP). The crash is caused by an extra empty line at the end of the abundances file, which does not exist in abundances files that have been produced without the mSWEEP bootstrapping option.

Since the issue is in mSWEEP, a workaround for successfully running mGEMS when bootstrapped abundances are used is to delete the empty line from the end of the input files.

However, mGEMS should produce more informative error messages if the input files contain nonsense or are in the wrong format. Closing this issue requires adding better error messages for such cases.

tmaklin commented 3 years ago

mSWEEP has fixed this in https://github.com/PROBIC/mSWEEP/pull/10, resolving this issue.