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... 188.8.131.52 Connecting to www.geneontology.org|184.108.40.206|: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... 220.127.116.11 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... 18.104.22.168 Connecting to purl.obolibrary.org|22.214.171.124|: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... 126.96.36.199, 188.8.131.52, 184.108.40.206, ... Connecting to snapshot.geneontology.org|220.127.116.11|: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.