Hi there,
Wondering if anyone can help with an OMA error I am having. It seems that OMA cannot access the file it requires from www.geneontology.org/ontology/gene_ontology.obo This is the error message:
Starting database conversion and checks...
Process 38697 on marvin: job nr 1 of 100
--2019-02-20 10:58:07-- http://www.geneontology.org/ontology/gene_ontology.obo
Resolving www.geneontology.org... 107.23.42.138
Connecting to www.geneontology.org|107.23.42.138|:80... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: http://geneontology.org/ontology/gene_ontology.obo [following]
--2019-02-20 10:58:07-- http://geneontology.org/ontology/gene_ontology.obo
Resolving geneontology.org... 107.23.42.138
Reusing existing connection to www.geneontology.org:80.
HTTP request sent, awaiting response... 302 Found
Location: http://purl.obolibrary.org/obo/go/gene_ontology.obo [following]
--2019-02-20 10:58:07-- http://purl.obolibrary.org/obo/go/gene_ontology.obo
Resolving purl.obolibrary.org... 52.3.123.63
Connecting to purl.obolibrary.org|52.3.123.63|:80... connected.
HTTP request sent, awaiting response... 302 Found
Location: http://snapshot.geneontology.org/ontology/gene_ontology.obo [following]
--2019-02-20 10:58:07-- http://snapshot.geneontology.org/ontology/gene_ontology.obo
Resolving snapshot.geneontology.org... 143.204.178.196, 143.204.178.95, 143.204.178.64, ...
Connecting to snapshot.geneontology.org|143.204.178.196|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2019-02-20 10:58:07 ERROR 404: Not Found.
Error, (in wget) wget failed
I have confirmed with our cluster manager that queue I am submitting to has internet access and that this problem is not due to a firewall at our end.
I have also noticed that if you copy www.geneontology.org/ontology/gene_ontology.obo directly into a browser you do indeed get a 404 not found. To manually download the file you need to start at www.geneontology.org and navigate through the website to the .obo.
I tried placing the (manually downloaded) .obo in the directory where the script was launched and the /DB and parameters.drw are located in case OMA would look for it there before attempting to download but that didnt work.
Has anyone experienced this problem or have any thoughts about a fix? Any help greatly appreciated.