Open sdash-github opened 3 years ago
Andrew's comment
Hi Sudhansu- looks like gigwa is running as a tomcat application, not containerized. logs are here: /usr/local/apache-tomcat-8.5/logs
here's the last message in the gigwa.log file: 22/02 09:31:12 | ERROR | http-nio-8080-exec-3 |fr.cirad.mgdb.service.GigwaGa4ghServiceImpl 2650 | Error searching variants java.lang.NullPointerException at fr.cirad.tools.mgdb.GenotypingDataQueryBuilder.next(GenotypingDataQueryBuilder.java:774) at fr.cirad.mgdb.service.GigwaGa4ghServiceImpl.findVariants(GigwaGa4ghServiceImpl.java:838) at fr.cirad.mgdb.service.GigwaGa4ghServiceImpl.searchVariants(GigwaGa4ghServiceImpl.java:2639) at fr.cirad.web.controller.ga4gh.Ga4ghRestController.searchVariants(Ga4ghRestController.java:519) ...
not sure how much that helps. I'll note that Sam is working on loading VCF into the mines, which could be an alternate path forward.
adf
The loading part is done. I've been playing with displayers. I'm using TestMine for that project.
https://dev.lis.ncgr.org/testmine/report.do?id=5000005
Be patient, the DataTables takes a while to load initially, but it pages pretty quickly. I'm looking at some fancier displays that have lots of tools.
I'm happy to load VCFs from the DS into PeanutMine, and just use the DataTables displayer until something better comes along.
Location of data when ready to reload:
African lines (flapjack and hmp files): https://legumeinfo.org/data/public/Arachis_hypogaea/arahy.gnm1.div.LZ50/
-- Modified to replace space in names #5
US Minicore: ?? (Haven't found the data yet)
as per the email I just sent, it doesn't appear that
https://legumeinfo.org/data/public/Arachis_hypogaea/arahy.gnm1.div.LZ50/arahy.gnm1.div.LZ50.snp_chip.hmp.gz
is loading properly into gigwa (after uncompressing and renaming to have .hapmap extension).
I think the file has no spaces in the names, but throwing this error
may try reconverting to vcf before digging further into that error
There is mini core data here: https://v1.legumefederation.org/data/public/Arachis_hypogaea/aradu1_araip1.gnm1.div.2B6N/ Somewhere I have the file that I loaded way back when, probably on the machine in my office as I can't find it on the machine I'm using for teleworking.
https://peanutbase.org/germplasm/gigwa
Peggy Ozias-Akins: "We will soon have some additional data to send you to upload in peanutbase/gigwa. I cannot get anything to output from the African Breeding Lines database even when I pare down the size of the search, although it worked very quickly with the Minicore database. Could you check to see if there is a database issue?"
SD: As soon as I start using Investigate genoptype settings, even with US Minicore, it goes to perpetual search mode, "Finding matching variants ...". It doesn't even respond to Abort.
I think Gigwa is dockerized (?) and I don't have a way to look at any error messages.