Closed shalabhsuman closed 11 years ago
Shalabh;
I've been trying to reproduce this problem without success. Can you share the result of cat params.yaml
? The error indicates something is wrong with the YAML configuration file but it's tough to identify from the traceback alone.
I have used the exact same contents in the config file as provided on your site here: https://github.com/chapmanb/bcbio.variation/blob/master/config/ensemble/combine-callers.yaml
This is how cat params.yaml
looks like:
Shalabh;
It looks like something happened with the indentation in that file compared to the version on GitHub. Specifically there appears to be a space in front of the ---
line. If you edit to remove that, it should work cleanly.
The job failed again. I have sent you an email with a link to error log file. Thanks.
Shalabh; Thanks for passing along the files for testing. The code was not handling no-call genotypes which led to this error. I pushed a new version of 0.1.0-SNAPSHOT that will work cleanly on your input datasets. I took a quick look at the outputs and it looks like work needs to be done to tune to SVM classifier for multi-sample ensemble calling. That is more of a long term project, but hopefully this run will give you consolidate calls to evaluate. Thanks for all the patience getting this running and looking forward to your feedback.
Hello,
I am having 3 multi-sample VCF files (through GATK UnifiedGenotyper, FreeBayes, VarScan); and I am trying to test ensemble variant calling using the following command:
...and I get the following error (screenshot below):![screen shot 2013-08-20 at 9 51 48 am](https://f.cloud.github.com/assets/4998368/1001372/eac968ea-0a68-11e3-9c84-40a0f06ac1c0.png)
Note- For params.yaml, I am using the exact same example config file provided on your website here:(https://github.com/chapmanb/bcbio.variation/blob/master/config/ensemble/combine-callers.yaml). Also, I am using the snapshot version of the bcbio.variation jar instead of the standard one.
Please suggest.
Shalabh Suman