No output found after running ResFinder

[Former user]

Hello,

I ran ResFinder with the following code and it ran without any error messages:

python -m resfinder -o ${PROJECT_FOLDER}/${OUTPUT_FOLDER} -s "Escherichia Coli" \ -b "/share/groups/cohr/apps/ecoli_amr/bin/blastn" \ -k "/share/groups/cohr/apps/ecoli_amr/bin/kma" \ -l 1 -t 0.9 --acquired --point -ifq SRR10001251_1.fastq.gz SRR10001251_2.fastq.gz

However, I cannot find any output files in my output folder. Specifically, there is no such file as "ResFinder_results_table.txt", or any of the other output files described in the documentation. Do you know what may have gone wrong? And is there a "verbose" option when running ResFinder to see what's happening when I run the code?

Thank you. -Mary

[Edison Alain von Matt]

Dear Mary,

Unfortunately, I am not able to reproduce your issue.

Perhaps the path in your command is slightly different from the one you are looking in, and ResFinder has created a new folder structure according to the specified path somewhere with the output.

If that is not the case, I would either suggest reinstalling ResFinder with the following command:

pip install --upgrade --force-reinstall <package>

You could also download the git repository and run the run_resfinder.py file manually:

git clone https://bitbucket.org/genomicepidemiology/resfinder/src/master/
cd master
python src/resfinder/run_resfinder.py -o ${PROJECT_FOLDER}/${OUTPUT_FOLDER} -s "Escherichia Coli" \ -b "/share/groups/cohr/apps/ecoli_amr/bin/blastn" \ -k "/share/groups/cohr/apps/ecoli_amr/bin/kma" \ -l 1 -t 0.9 --acquired --point -ifq SRR10001251_1.fastq.gz SRR10001251_2.fastq.gz

Apart from that, we do not have a "verbose" option in ResFinder, but you could modify the src/resfinder/run_resfinder.py file to check the output paths etc.

I hope this helps to resolve your issue - please let me know if it persists.

Best

Eddy