<div dir="ltr">Hi Sebastian,<div><br></div><div>For some reason or other it looks as though your installation of Bio::DB::HTS is not working. You can double check by executing:</div><div><br></div><div>$ perl -MBio::DB::HTS -e1</div><div><br></div><div>This should give you an error if the module is not installed properly, and nothing if it is working OK.</div><div><br></div><div>In the case of the error, I'd try setting up Bio::DB::HTS again according to the README here: <a href="http://search.cpan.org/dist/Bio-DB-HTS/">http://search.cpan.org/dist/Bio-DB-HTS/</a></div><div><br></div><div>Having said this, it may be that you can avoid having to use it. From your command it looks as though you are not using a VEP flag that requires reading sequence data from a FASTA file (the role of Bio::DB::HTS) - those that require this are --hgvs and --check_ref.</div><div><br></div><div>You may therefore try one of two solutions:</div><div><br></div><div>1) unarchive the bgzipped FASTA file that VEP is finding, something like:</div><div><br></div><div>$ gzip -d <span style="font-size:12.8px">/opt/modules/i12g/ensembl-</span><wbr style="font-size:12.8px"><span style="font-size:12.8px">tools/85/cachedir/homo_sapiens/85_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">This will allow the code to use Bio::DB::Fasta to index the unarchived file, meaning that if you wish to use --hgvs, for example, it should work OK.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">2) move the FASTA file so that it is not picked up by VEP for indexing:</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">$ mv </span><span style="font-size:12.8px">/opt/modules/i12g/ensembl-</span><wbr style="font-size:12.8px"><span style="font-size:12.8px">tools/85/cachedir/homo_sapiens/85_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz </span><span style="font-size:12.8px">/opt/modules/i12g/ensembl-</span><wbr style="font-size:12.8px"><span style="font-size:12.8px">tools/85/cachedir/homo_sapiens/85_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz.bak</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">You could then move it back again in future if you do require it.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Hope that solves the issue for you!</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Will McLaren</span></div><div><span style="font-size:12.8px">Ensembl Variation</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 7 December 2016 at 13:12, Hollizeck, Sebastian <span dir="ltr"><<a href="mailto:Sebastian.Hollizeck@med.uni-muenchen.de" target="_blank">Sebastian.Hollizeck@med.uni-muenchen.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I installed the standalone script in my module system for usage on our server, but i cant seem to get it working with the cache.<br>
The script works with just using the --database option, but when i use the --cache i get the following error<br>
<br>
MSG: ERROR: Cannot index bgzipped FASTA file with Bio::DB::Fasta<br>
<br>
this is the full output with verbose<br>
<br>
[hollizeck@kkf0f6ee kleinPipeline]$ <a href="http://variant_effect_predictor.pl" rel="noreferrer" target="_blank">variant_effect_predictor.pl</a> --check_existing --gmaf --maf_1kg --maf_esp --maf_exac --pubmed --regulatory --species homo_sapiens --port 3337 --buffer_size 40000 --cache --minimal --sift b --polyphen b --ccds --symbol --biotype --gene_phenotype --variant_class --fork 6 --force_overwrite --filter_common --dir_cache /opt/modules/i12g/ensembl-<wbr>tools/85/cachedir -i /archive/sample_data/scn281/<wbr>scn281pa_fa.recalibrated_<wbr>variants.vcf.gz --vcf -o /archive/sample_data/scn281/<wbr>scn281pa_fa.recalibrated_<wbr>variants_vep.vcf.gz -v#---------------------------<wbr>-------#<br>
# ENSEMBL VARIANT EFFECT PREDICTOR #<br>
#-----------------------------<wbr>-----#<br>
<br>
version 85<br>
<br>
By Will McLaren (<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>)<br>
<br>
Configuration options:<br>
<br>
biotype 1<br>
buffer_size 40000<br>
cache 1<br>
ccds 1<br>
check_existing 1<br>
core_type core<br>
dir /opt/modules/i12g/ensembl-<wbr>tools/85/cachedir<br>
dir_cache /opt/modules/i12g/ensembl-<wbr>tools/85/cachedir<br>
dir_plugins /home/hollizeck/.vep/Plugins<br>
filter_common 1<br>
force_overwrite 1<br>
fork 6<br>
gene_phenotype 1<br>
gmaf 1<br>
host <a href="http://ensembldb.ensembl.org" rel="noreferrer" target="_blank">ensembldb.ensembl.org</a><br>
input_file /archive/sample_data/scn281/<wbr>scn281pa_fa.recalibrated_<wbr>variants.vcf.gz<br>
maf_1kg 1<br>
maf_esp 1<br>
maf_exac 1<br>
minimal 1<br>
numbers 1<br>
output_file /archive/sample_data/scn281/<wbr>scn281pa_fa.recalibrated_<wbr>variants_vep.vcf.gz<br>
polyphen b<br>
port 3337<br>
pubmed 1<br>
regulatory 1<br>
sift b<br>
species homo_sapiens<br>
stats HASH(0x58ccbc0)<br>
symbol 1<br>
variant_class 1<br>
vcf 1<br>
verbose 1<br>
<br>
--------------------<br>
<br>
Will only load v85 databases<br>
Species 'homo_sapiens' loaded from database 'homo_sapiens_core_85_37'<br>
Species 'homo_sapiens' loaded from database 'homo_sapiens_cdna_85_37'<br>
Species 'homo_sapiens' loaded from database 'homo_sapiens_vega_85_37'<br>
Species 'homo_sapiens' loaded from database 'homo_sapiens_otherfeatures_<wbr>85_37'<br>
Species 'homo_sapiens' loaded from database 'homo_sapiens_rnaseq_85_37'<br>
homo_sapiens_variation_85_37 loaded<br>
homo_sapiens_funcgen_85_37 loaded<br>
No ancestral database found<br>
No ontology database found<br>
No taxonomy database found<br>
No ensembl_metadata database found<br>
No production database or adaptor found<br>
2016-12-07 14:04:31 - Connected to core version 85 database and variation version 85 database<br>
2016-12-07 14:04:31 - Read existing cache info<br>
2016-12-07 14:04:32 - Auto-detected FASTA file in cache directory<br>
<br>
-------------------- EXCEPTION --------------------<br>
MSG: ERROR: Cannot index bgzipped FASTA file with Bio::DB::Fasta<br>
<br>
STACK Bio::EnsEMBL::Variation::<wbr>Utils::FastaSequence::setup_<wbr>fasta /opt/modules/i12g/ensembl-<wbr>tools/85/modules/Bio/EnsEMBL/<wbr>Variation/Utils/FastaSequence.<wbr>pm:194<br>
STACK main::configure /opt/modules/i12g/ensembl-<wbr>tools/85/bin/<a href="http://variant_effect_predictor.pl:835" rel="noreferrer" target="_blank">variant_effect_<wbr>predictor.pl:835</a><br>
STACK toplevel /opt/modules/i12g/ensembl-<wbr>tools/85/bin/<a href="http://variant_effect_predictor.pl:146" rel="noreferrer" target="_blank">variant_effect_<wbr>predictor.pl:146</a><br>
Date (localtime) = Wed Dec 7 14:04:32 2016<br>
Ensembl API version = 85<br>
------------------------------<wbr>---------------------<br>
<br>
This looks like the program does not select the Bio:DB:HTS module but it is present and also in the perl path<br>
<br>
[hollizeck@kkf0f6ee kleinPipeline]$ ll /opt/modules/i12g/ensembl-<wbr>tools/85/modules/Bio/DB/HTS.pm<br>
-rw-rw-rw- 1 root root 77700 Sep 21 18:44 /opt/modules/i12g/ensembl-<wbr>tools/85/modules/Bio/DB/HTS.pm<br>
[hollizeck@kkf0f6ee kleinPipeline]$ echo $PERL5LIB<br>
/opt/modules/i12g/perl/5.24.0/<wbr>perl5lib/lib/perl5:/opt/<wbr>modules/i12g/ensembl-tools/85/<wbr>modules<br>
<br>
I do not know, if I even look at the right spot.<br>
Can you please help me to debug this further?<br>
<br>
Is there any way to specify which plugin to use?<br>
<br>
<br>
Sebastian Hollizeck<br>
Bioinformatics<br>
<br>
Dr. von Hauner Children's Hospital<br>
Kubus Research Center<br>
Lindwurmstraße 2a<br>
D-80337 München<br>
phone +49 89-4400-57488<br>
fax +49 89-4400-57979<br>
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</blockquote></div><br></div>