Closed pierrepeterlongo closed 1 year ago
Hi Pierre,
the problem you're having is due to the fact that the parsing function of the query reference graph uses the file extension to determine the file type, and the build phase at the moment does not append an extension automatically.
To fix it you can rename the file index_first_3_humans
to index_first_3_humans.fa
and the colormap file from index_first_3_humans.colors.dat
to index_first_3_humans.fa.colors.dat
.
To avoid this kind of problems in the future, you can pass an extension directly in the build phase like this:
ggcat build -c -l fof -k 25 -s 1 -o index_first_3_humans.fa
Also it's better to always specify explicitly the number of threads to use (-j
flag), as now automatically defaults to 16 threads.
Regards, Andrea
Perfect, thanks!
Oh, same problem here. Solved by adding a file extension .fasta
.
Hello,
I'm trying a few tests with ggcat and I'm having an issue at query time. Here are the used commands:
With fof linked to these files downloaded from your zenodo repository :
The computation takes 45 minutes and creates these files:
I query the created graph with this command:
It ends quickly with
Any idea ? Am I doing something wrong? Thanks ! Pierre