zhanxw

Can you please provide more details on input files: test.bgen, test.sample, test.ped If you can provide these files, I will debug to find out the exact problem.

Under investigation now. I will update here later.

Fixed in https://github.com/zhanxw/rvtests/commit/ff46d0af7ad49c5a81a2fad5a6a36801ff1b0854 and in master branch.

Can you check if this sample is in the vcf file? Sent from my iPhone > On May 27, 2020, at 4:49 PM, Daniel Panyard wrote: > >  >...

That depends on the content of the set file. Internally, the option `--setFile` will use the index file to read each variant specified, and the option `--geneFile` will use the...

Thanks. In this case, I don't expect `--setFile` is much slower than `--geneFile`.

Sorry for the inconvenience. Let me investigate this a bit more.

Hi Jie, For the purpose of convention, log messages go to stderr by default ( https://stackoverflow.com/a/4919110/425758). To check whether the job is successful or not, can you check the program...

Hi Jie, For the "--noweb" option, I checked rvtests in a machine without Internet access. When there was not "--noweb" option, I can see the message: "connect() error: Operation timed...

In the coming new version, RVTESTS will print "RVTESTS successfully exit" at the end. You will then be able to tell RVTESTS finished successfully from the last line of my.LOG...