Closed npavlovikj closed 3 years ago
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)
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:
"gr1.csv" has 1077 rows and looks like:
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