# No space left on device - export\_vcf

**URL:** <https://discuss.hail.is/t/no-space-left-on-device-export-vcf/447>\
**Category:** Help \[0.1\]\
**Created:** [March 29, 2018, 1:24am UTC](https://discuss.hail.is/t/no-space-left-on-device-export-vcf/447 "2018-03-29T01:24:17Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![eipVCCRI](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/eipvccri/32/111_2.png) [@eipVCCRI](https://discuss.hail.is/u/eipVCCRI)\
**Post date:** [March 29, 2018, 1:24am UTC](https://discuss.hail.is/t/no-space-left-on-device-export-vcf/447/1 "2018-03-29T01:24:17Z")

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Hi there,

I’m trying to export a vds to VCF but I’m getting an "hail.java.FatalError: IOException: No space left on device  
" error.

I have plenty of space on the drive I’m writing to, so not sure where the limitation maybe.

vds.write("/Burden\_data/WGS\_CHD\_Burden\_samples.vds",overwrite=True) #  
vds.export\_vcf("/Burden\_data/WGS\_CHD\_Burden\_samples.vcf.bgz") #

The vds.write is fine and I can see the vds file is created (file size 547MB), but the export\_vcf fails. Given the size of the vds, the VCF should not be that large.

In starting my spark-submit I set a driver-memory of 22G  
and I have pointed my $SPARK\_WORKER\_DIR and $SPARK\_LOCAL\_DIRS to filespace of 400GB.

hope someone can help.  
Thanks for your assistance in advance.  
Eddie

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [March 29, 2018, 1:25am UTC](https://discuss.hail.is/t/no-space-left-on-device-export-vcf/447/2 "2018-03-29T01:25:32Z")

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What’s the hail temp dir (passed on hail context)?

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<div class="post-metadata">

**Author:** ![eipVCCRI](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/eipvccri/32/111_2.png) [@eipVCCRI](https://discuss.hail.is/u/eipVCCRI)\
**Post date:** [March 29, 2018, 1:29am UTC](https://discuss.hail.is/t/no-space-left-on-device-export-vcf/447/3 "2018-03-29T01:29:46Z")

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I have a vanilla HailContext()

hc = HailContext() #

I see from the doc that it defaults to /tmp

class hail.HailContext(sc=None, app\_name=‘Hail’, master=None, local=‘local[\*]’, log=‘hail.log’, quiet=False, append=False, parquet\_compression=‘snappy’, min\_block\_size=1, branching\_factor=50, tmp\_dir=’/tmp’)

I will amend it to a specific location.

thanks.

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**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [March 29, 2018, 1:42am UTC](https://discuss.hail.is/t/no-space-left-on-device-export-vcf/447/4 "2018-03-29T01:42:26Z")

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yep, that would do it. export\_vcf needs to write file shards before it serially concatenates them all together, and I think the shards were blowing out /tmp.