Use of uninitialized value warning issued by plugins/Conservation.pm

rraadd88 commented 2 months ago

Describe the issue

Warnings issued but the output is generated. Therefore not sure if the output is correct.

System

VEP version: 112
VEP Cache version: 112
Perl version: 5.34.0
OS: Linux version 6.10.4-linuxkit (root@buildkitsandbox) (gcc (Alpine 13.2.1_git20240309) 13.2.1 20240309, GNU ld (GNU Binutils) 2.42) (docker in MacOS)
tabix installed: yes

Full VEP command line

vep -i input.txt -o test_conservation.txt --species homo_sapiens --assembly GRCh38 --cache --dir_cache /opt/vep/.vep --offline --plugin Conservation,/opt/vep/.vep/db/Conservation/gerp_conservation_scores.homo_sapiens.GRCh38.bw --force_overwrite

Full error message

Use of uninitialized value in subtraction (-) at /plugins/Conservation.pm line 214, <__ANONIO__> line 3.
Use of uninitialized value in subtraction (-) at /plugins/Conservation.pm line 214, <__ANONIO__> line 3.
Use of uninitialized value $values[0] in sprintf at /plugins/Conservation.pm line 250, <__ANONIO__> line 3.
Use of uninitialized value in subtraction (-) at /plugins/Conservation.pm line 214, <__ANONIO__> line 3.
Use of uninitialized value in subtraction (-) at /plugins/Conservation.pm line 214, <__ANONIO__> line 3.
Use of uninitialized value $values[0] in sprintf at /plugins/Conservation.pm line 250, <__ANONIO__> line 3.
Use of uninitialized value in subtraction (-) at /plugins/Conservation.pm line 214, <__ANONIO__> line 3.
Use of uninitialized value in subtraction (-) at /plugins/Conservation.pm line 214, <__ANONIO__> line 3.
Use of uninitialized value $values[0] in sprintf at /plugins/Conservation.pm line 250, <__ANONIO__> line 3.

Data files (if applicable)

They include:

The input file input.txt
The output file test_conservation.txt

olaaustine commented 1 month ago

Hi @rraadd88,

Hope this meets you well? Thank you for sharing your input file. I have been able to reproduce this issue. The issue is those variant do not have Conservation score but still getting 0.0 assigned. As you can see in your output file, you have some variant with conservation scoreConservation=0.000 . This issue does not impact the output for variants that have a conservation score. This issue has been rectified here VEP plugins 734 and should be available in the next release. Thank you Ola.

olaaustine commented 1 month ago

Hi @rraadd88, I am going to close this ticket now. Please feel free to open another ticket if you have any other questions/issues. Thank you Ola.

Ensembl / ensembl-vep