Open bbimber opened 4 months ago
I have also encountered such a problem!Have you solved this problem? Does this mean there is not enough memory?
Honestly we gave up on GLNexus. We ended up taking the per-sample VCFs produced by DeepVariant (VCF, not gVCF), and merged them directly.
Hello -
I am trying to run GLNExus to combine gVCFs produced by DeepVariant. The input is 16 single-sample gVCFs, aligned to the rhesus macaque genome. I split the job to run one contig at a time, and I find that chromosome 1 consistently gives a std::bad_alloc error. Below is the command and output. Can you suggest any debugging steps I could try?
In the command, contig.bed is a one-line bed file specifying chromosome 1.
The output is the following:
When I run this same pattern for any of the other contigs the tool runs fine. Any help would be appreciated.