plugin LD error: [E::hts_open_format] Failed to open file

[TriangularCell]

Hi everyone,

I encountered an error with plugin LD. The command I use is:

sudo docker run -v /home/Tools/VEP/ensembl-vep:/opt/vep/.vep:Z ensemblorg/ensembl-vep \
vep \
-i examples/homo_sapiens_GRCh38_mini.vcf \
-o test_mini \
--tab --force_overwrite \
--cache --dir_cache ./cache \
--fasta cache/homo_sapiens/113_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz \
--dir_plugins Plugins/ \
--fork 24 \
--plugin LD,1000GENOMES:phase_3:CEU,0.8

And the error message I got is:

[E::hts_open_format] Failed to open file https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/ALL.chr1_GRCh38.genotypes.20170504.vcf.gz
https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/ALL.chr1_GRCh38.genotypes.20170504.vcf.gz: Couldn't find index for file https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/ALL.chr1_GRCh38.genotypes.20170504.vcf.gz at /usr/local/lib/x86_64-linux-gnu/perl/5.34.0/Bio/DB/HTS/Tabix.pm line 53.

-------------------- EXCEPTION --------------------
MSG: ERROR: Could not write to warnings file test_mini_warnings.txt

STACK Bio::EnsEMBL::VEP::BaseVEP::warning_fh /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:894
STACK Bio::EnsEMBL::VEP::BaseVEP::warning_msg /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:817
STACK Bio::EnsEMBL::VEP::Runner::get_all_Plugins /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:913
STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:125
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:200
STACK toplevel /opt/vep/src/ensembl-vep/vep:46
Date (localtime) = Wed Apr 16 09:15:35 2025
Ensembl API version = 113

Any suggestions are apprecieated. Thanks!

[dglemos]

Hi @TriangularCell,
Thanks for sharing the full error details.

MSG: ERROR: Could not write to warnings file test_mini_warnings.txt

Can you please check the permissions for /opt/vep/? This looks like a permissions issue.

[E::hts_open_format] Failed to open file https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/ALL.chr1_GRCh38.genotypes.20170504.vcf.gz
https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/ALL.chr1_GRCh38.genotypes.20170504.vcf.gz: Couldn't find index for file https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/ALL.chr1_GRCh38.genotypes.20170504.vcf.gz at /usr/local/lib/x86_64-linux-gnu/perl/5.34.0/Bio/DB/HTS/Tabix.pm line 53.

The index file for ALL.chr1_GRCh38.genotypes.20170504.vcf.gz is available at https://ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/
It could have been a transient issue. Can you please try again?

[TriangularCell]

Thanks @dglemos for the reply!

The permission issue is now resolved but the "Failed to open file" error still occurs. I also checked the index file which is available and I have no problem with downloading the *.vcf.gz or *.vcf.gz.tbi files with wget on my server (which I think means there's no problem for my server to access these files).

Any further suggestions? Thanks very much.