# VEP Error On Some Files

**URL:** <https://discuss.hail.is/t/vep-error-on-some-files/1731>\
**Category:** Hail Query & hailctl\
**Created:** [October 7, 2020, 10:35am UTC](https://discuss.hail.is/t/vep-error-on-some-files/1731 "2020-10-07T10:35:02Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Haseeb1](https://avatars.discourse-cdn.com/v4/letter/h/df705f/32.png) [@Haseeb1](https://discuss.hail.is/u/Haseeb1)\
**Post date:** [October 7, 2020, 10:35am UTC](https://discuss.hail.is/t/vep-error-on-some-files/1731/1 "2020-10-07T10:35:02Z")

</div>

I am facing this error while applying VEP, VEp was successfully running on different chromosome file of same database but on chr6 this error came,

File “/opt/conda/default/lib/python3.6/site-packages/hail/backend/spark\_backend.py”, line 42, in deco  
‘Error summary: %s’ % (deepest, full, hail. **version** , deepest)) from None  
hail.utils.java.FatalError: HailException: VEP command ‘/vep --format vcf --json --everything --allele\_number --no\_stats --cache --offline --minimal --assembly GRCh38 --fasta /opt/vep/.vep/homo\_sapiens/95\_GRCh38/Homo\_sapiens.GRCh38.dna.toplevel.fa.gz --plugin LoF,loftee\_path:/opt/vep/Plugins/,gerp\_bigwig:/opt/vep/.vep/gerp\_conservation\_scores.homo\_sapiens.GRCh38.bw,human\_ancestor\_fa:/opt/vep/.vep/human\_ancestor.fa.gz,conservation\_file:/opt/vep/.vep/loftee.sql --dir\_plugins /opt/vep/Plugins/ -o STDOUT’ failed with non-zero exit status 2  
VEP Error output:  
Smartmatch is experimental at /opt/vep/Plugins/de\_novo\_donor.pl line 175.  
Smartmatch is experimental at /opt/vep/Plugins/de\_novo\_donor.pl line 214.  
Smartmatch is experimental at /opt/vep/Plugins/splice\_site\_scan.pl line 191.  
Smartmatch is experimental at /opt/vep/Plugins/splice\_site\_scan.pl line 194.  
Smartmatch is experimental at /opt/vep/Plugins/splice\_site\_scan.pl line 238.  
Smartmatch is experimental at /opt/vep/Plugins/splice\_site\_scan.pl line 241.  
Can’t call method “feature” on an undefined value at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/BaseVariationFeatureOverlapAllele.pm line 196.