Closed jos4uke closed 3 years ago
Hi @jos4uke , am I correct in assuming that you're running this on SLURM? There is currently an issue with running GimmeMotifs in a process-safe manner. You have to delete the cache directory (which has become corrupted): ~/.cache/gimmemotifs
.
After, you can try the work-around mentioned in the first FAQ entry here: https://gimmemotifs.readthedocs.io/en/master/faq.html#faq
Hi @simonvh
thanks for your reply. I will try your suggestions and tell if it is ok for me.
Best
hi @simonvh
your suggestions fixed my issue on SLURM. Nevertheless, I encountered a new issue at denovo reporting step. I will open a new issue. thanks again
Best
Added a more informative warning, see 50103d4
Hi @simonvh
I ran
gimme motifs
on motif database JASPAR2020_plants, but it seems the way I set the command line may be wrong as I got this errorsqlite3.DatabaseError: file is not a database
:As you can see, I didn't suffix the motifs database file name with
.pfm
extension as seen in your documentation forJASPAR2020_vertebrates
orHOMER
.I checked for
JASPAR2020_plants
motifs database location in my installation. It was installed as well along with all the other motifs databases in/opt/share/FLOCAD/userspace/jtran1/miniconda3/envs/gimmemotifs/lib/python3.8/site-packages/data/motif_databases/
(see Additional information for the path to included motifs database installed via conda).And also checked for the configuration file (see Additional information for my config file content) for the default motifs databases location parameter:
motif_databases = motif_databases
. It matched the folder name in my installation.But seems gimme motifs didn't know where to search for the motifs database on my installation.
Is it the right way to set the motifs database, when this one is included with gimme motifs? Or maybe I need to setup the configuration file differently so gimme motifs know where to find it? Can you help please?
Thanks in advance
@jos4uke
Step to reproduce:
Expected behavior A clear and concise description of what you expected to happen.
Error logs
Installation information:
bash mamba create -n gimmemotifs python=3 gimmemotifs
Additional information:
I installed gimme motifs using conda. And searching for all included motifs databases, I found them installed under:
/opt/share/FLOCAD/userspace/jtran1/miniconda3/envs/gimmemotifs/lib/python3.8/site-packages/data/motif_databases/
And here is the config file content: