# Hail command stalls or "no space left on device" with VEP annotation

**URL:** <https://discuss.hail.is/t/hail-command-stalls-or-no-space-left-on-device-with-vep-annotation/2686>\
**Category:** Hail Query & hailctl\
**Created:** [June 1, 2022, 4:19pm UTC](https://discuss.hail.is/t/hail-command-stalls-or-no-space-left-on-device-with-vep-annotation/2686 "2022-06-01T16:19:07Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![djw](https://avatars.discourse-cdn.com/v4/letter/d/45deac/32.png) [@djw](https://discuss.hail.is/u/djw)\
**Post date:** [June 1, 2022, 4:19pm UTC](https://discuss.hail.is/t/hail-command-stalls-or-no-space-left-on-device-with-vep-annotation/2686/1 "2022-06-01T16:19:08Z")

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Hi all,

I am trying to work with a VEP-annotated version of the Genebass variant-level summary statistics. When I try to work with the VEP-annotated version, Hail either stalls (the progress bar stops) or I get `FatalError: IOException: No space left on device` – despite not trying to write out any file to storage, as you can see from the code below.

Does this sound like insufficient memory/RAM, or some other issue? If memory, what would be optimal parameters to set up a VM with `hailctl` for this case? My current configuration is the hailctl default (`hailctl dataproc start cluster_name`)

Here is example code which generates the error (it runs fine if you exclude the `annotate_rows` command):

```auto
#load genebass variants
genebass_variant = hl.read_matrix_table('path_to_genebass_variants’)
genebass_variant = genebass_variant.key_rows_by(genebass_variant.markerID)

#Filter variants
vep_ht = hl.read_table("path_to_genebass_vep_hailtable”)
vep_ht = vep_ht.key_by("markerID")
genebass_variant = genebass_variant.filter_rows(genebass_variant.annotation == "missense")
genebass_variant = genebass_variant.annotate_rows(vep = vep_ht[genebass_variant.markerID].vep)
genebass_variant = genebass_variant.filter_rows(genebass_variant.gene == "PCSK9")
genebass_variant.entries().show(10)

```

Thank you! -Dan

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<div class="post-metadata">

**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\
**Post date:** [June 2, 2022, 2:00pm UTC](https://discuss.hail.is/t/hail-command-stalls-or-no-space-left-on-device-with-vep-annotation/2686/2 "2022-06-02T14:00:02Z")

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It’s hard to know exactly what the problem is without the full stack trace, but my guess is that Spark is using HDFS to re-order your data in the `key_by`. You can avoid that by explicitly initializing Hail and specifying a temporary directory:

```auto
hl.init(tmp_dir='gs://my-bucket/tmp')

```

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<div class="post-metadata">

**Author:** ![danking](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/danking/32/43_2.png) [@danking](https://discuss.hail.is/u/danking)\
**Post date:** [June 2, 2022, 2:01pm UTC](https://discuss.hail.is/t/hail-command-stalls-or-no-space-left-on-device-with-vep-annotation/2686/3 "2022-06-02T14:01:29Z")

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Also, I recommend against using the `entries()`. That is an inefficient representation of the entries of a matrix table. If you want to look at the entries of a matrix table, just show the matrix table itself:

```auto
genebass_variant.show()

```