Empty output files with k-mer GWAS

[npavlovikj]

Hi,

I am running Scoary with manually created k-mer file. While the job finishes ok, the output file is empty, and I don't see any errors. I have 60 different datasets for which the same occurs, so I believe I am either misusing the options, not properly formatting the k-mer file, or exceeding the array.

I used Scoary 1.6.16 with Python 3.6 installed using conda, and the command I use is:

scoary -s 2 -t gr1.csv -g gr1_matrix_kmer.csv --threads 16 \
    -o scoary_out_gr1 --delimiter ',' -c I EPW

"gr1.csv" has 1077 rows and looks like:

,serovar_phenotype
DRR106950,0
ERR023784,0

while "gr1_matrix_kmer.csv" has 1077 columns and 718522 rows, where the first column is the k-mer, and remaining columns are the samples (thus the -s 2 option).

I would really appreciate your input on this. If you need any additional information, or you have any ideas why I am not getting any output, please let me know.

Thank you, Natasha

[AdmiralenOla]

Hi Natasha,

Sounds strange. Could you try running with -p 1.0 to check that your results aren't simply being filtered due to having a Fisher p-value >=0.05?

If that doesn't work I would gladly take a look at your files if you send them to me at olbb@fhi.no (You can just do a tiny subset of the rows in the kmer presence/absence file)