[ensembl-dev] bgzf_read_block message in stderr

William McLaren wm2 at ebi.ac.uk
Tue Dec 5 09:41:40 GMT 2017

Hi Andrew,

A few of pieces of information would be useful:

- a particular variant or location you’re querying that recreates the issue
- the code and context from which you’re making the call
- whether you’re using remotely accessed VCFs or locally downloaded (if you don’t know then it’s likely the VCFs are being accessed remotely)


Will McLaren
Ensembl Variation

On 4 December 2017 at 5:31:07 pm, andrew126 at mac.com (andrew126 at mac.com) wrote:


In using API 90, when recovering all available allele frequencies for a particular variation feature, occassionally this message is shown in stderr:  

[W::bgzf_read_block] EOF marker is absent. The input is probably truncated  

That message seems to correlate with some allele frequencies not being found/reported by my script (in my case, the gnomAD frequencies).  

That is, when that message is not seen in stderr, I recover gnomAD frequencies for a particular variation feature; but when the message is seen, then it can look like that same variation feature doesn't have any gnomAD frequencies (even though it does).  

Is there any way to make such an event fatal to any API script? I'd much rather have my script fail/exit under such errors, than to not have it fail and risk believing such allele frequencies don't exist.  


Please let me know if any other information would be useful.  



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