Question: (Closed) VEP not downloading the data GRCh38
0
gravatar for pinninti1991reddy
2.4 years ago by
pinninti1991reddy60 wrote:

Hi,

Always I'm getting this error. Thanks for comments.

? 172 174 176
NB: Remember to use --merged when running the VEP with this cache!
 - downloading ftp://ftp.ensembl.org/pub/release-91/variation/VEP/homo_sapiens_merged_vep_91_GRCh38.tar.gz
 - unpacking homo_sapiens_merged_vep_91_GRCh38.tar.gz
 - converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster
 - use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later)
length() used on @array (did you mean "scalar(@array)"?) at /usr/lib/x86_64-linux-gnu/perl/5.22/IO/Compress/Zlib/Extra.pm line 166.
IO::Compress::Gzip version 2.068 required--this is only version 2.015 at /usr/share/perl/5.22/Compress/Zlib.pm line 12.
BEGIN failed--compilation aborted at /usr/share/perl/5.22/Compress/Zlib.pm line 12.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 88.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 88.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
Compilation failed in require at /usr/share/perl/5.22/base.pm line 97.
    ...propagated at /usr/share/perl/5.22/base.pm line 106.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Config.pm line 63.
Compilation failed in require at ./convert_cache.pl line 50.
BEGIN failed--compilation aborted at ./convert_cache.pl line 50.
WARNING: Failed to run convert script
NB: Remember to use --refseq when running the VEP with this cache!
 - downloading ftp://ftp.ensembl.org/pub/release-91/variation/VEP/homo_sapiens_refseq_vep_91_GRCh38.tar.gz
 - unpacking homo_sapiens_refseq_vep_91_GRCh38.tar.gz
 - converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster
 - use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later)
length() used on @array (did you mean "scalar(@array)"?) at /usr/lib/x86_64-linux-gnu/perl/5.22/IO/Compress/Zlib/Extra.pm line 166.
IO::Compress::Gzip version 2.068 required--this is only version 2.015 at /usr/share/perl/5.22/Compress/Zlib.pm line 12.
BEGIN failed--compilation aborted at /usr/share/perl/5.22/Compress/Zlib.pm line 12.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/ProteinFunctionPredictionMatrix.pm line 83.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 74.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 68.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 88.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/DBSQL/TranscriptVariationAdaptor.pm line 88.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/VariationFeature.pm line 112.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
Compilation failed in require at /home/likithreddy/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 59.
Compilation failed in require at /usr/share/perl/5.22/base.pm line 97.
    ...propagated at /usr/share/perl/5.22/base.pm line 106.
BEGIN failed--compilation aborted at /home/likithreddy/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Config.pm line 63.
Compilation failed in require at ./convert_cache.pl line 50.
BEGIN failed--compilation aborted at ./convert_cache.pl line 50.
WARNING: Failed to run convert script
 - downloading ftp://ftp.ensembl.org/pub/release-91/variation/VEP/homo_sapiens_vep_91_GRCh38.tar.gz
software error • 1.1k views
ADD COMMENTlink modified 2.4 years ago by genomax84k • written 2.4 years ago by pinninti1991reddy60
2

Start with this error: IO::Compress::Gzip version 2.068 required--this is only version 2.015

cpanm IO::Compress::Gzip
ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by ATpoint35k

Welcome back Sir

ADD REPLYlink written 2.4 years ago by Kevin Blighe60k

Hello pinninti1991reddy!

Please follow up on your questions. See C: Readgroups for a bam file ?

For this reason we have closed your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by RamRS27k
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