I would like to run 189 SNPs through Polyphen-2 using the Batch Query facility. I submitted a job that has been sitting on the queue for over 4 days. I used the following settings:
Batch does work but their server was in "extreme" load last Friday. Maybe they are having server issues, also 189 is not that many SNPs which makes me think your job is just getting repeatedly getting pushed to the bottom of the stack.
Thanks for the info. The job submitted on 4/21 is still on the queue, so whether it is the load or server problems, it is still effectively unavailable. I am looking at other options. NIEHS SNPinfo provides the TOLERATED/DAMAGING classification, but does not provide the Polyphen score. If there are any other tools or servers that provide the Polyphen score, please post them.
Why not e-mail PolyPhen-2 server maintainers (that's me ;-) with your problem? Our compute backend is currently experiencing long delays due to large number of enormous size batches submitted vi web interface (we are talking billions of queries). We are working on a solution right now but please understand that our resources are limited. Please contact me via e-mail directly and I am sure will be able to help you with your particular batch in the meantime.
Thanks for the info. The job submitted on 4/21 is still on the queue, so whether it is the load or server problems, it is still effectively unavailable. I am looking at other options. NIEHS SNPinfo provides the TOLERATED/DAMAGING classification, but does not provide the Polyphen score. If there are any other tools or servers that provide the Polyphen score, please post them.
Also try GVS batch from UW, it provides similar information http://gvs.gs.washington.edu/SeattleSeqAnnotation/