<div dir="ltr">Thanks! "Converted FASTA gzip file to bgzip successfully", <span id="result_box" class="short_text" lang="en"><span class="">but this time</span></span> "Indexing failed - VEP will attempt to index the file the first time you use it". Is it a critical error?</div><br><div class="gmail_quote"><div dir="ltr">ср, 23 мар. 2016 г. в 12:02, Rishi Nag <<a href="mailto:rishi@ebi.ac.uk">rishi@ebi.ac.uk</a>>:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Thanks.<br>
<br>
Change into the same directory as INSTALL.pl<br>
<br>
First check for a htslib directory being present with the ls command. If not then download and compile this:<br>
git clone -b master --depth=1 <a href="https://github.com/samtools/htslib.git" rel="noreferrer" target="_blank">https://github.com/samtools/htslib.git</a><br>
cd htslib<br>
make<br>
cd ..<br>
<br>
git clone <a href="https://github.com/Ensembl/Bio-HTS.git" rel="noreferrer" target="_blank">https://github.com/Ensembl/Bio-HTS.git</a> biodbhts<br>
You should then be able to re-run the install commands to download the sequence from this directory.<br>
<br>
Regards<br>
<br>
Rishi<br>
<br>
<br>
On 22/03/2016 18:17, Platon workaccount wrote:<br>
> VEP's install script was invoked by command perl INSTALL.pl<br>
><br>
> вт, 22 мар. 2016 г. в 15:32, Rishi Nag <<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a> <mailto:<a href="mailto:rishi@ebi.ac.uk" target="_blank">rishi@ebi.ac.uk</a>>>:<br>
><br>
><br>
>     Hi<br>
><br>
>     Thanks for raising this issue. Can you provide details on how the install script was invoked please?<br>
><br>
>     Regards<br>
><br>
>     Rishi<br>
><br>
>     On 22/03/2016 12:04, Platon workaccount wrote:<br>
>      ><br>
>      ><br>
>      > ---------- Forwarded message ---------<br>
>      > From: Platon workaccount <<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a> <mailto:<a href="mailto:platon.work@gmail.com" target="_blank">platon.work@gmail.com</a>>>><br>
>      > Date: вт, 22 мар. 2016 г. в 14:58<br>
>      > Subject: Ensembl VEP: FASTA gzip to bgzip conversion failed<br>
>      > To: <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a> <mailto:<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>>>><br>
>      ><br>
>      ><br>
>      > Hello.<br>
>      ><br>
>      > Full API end dependencies are installed (bioperl-live, ensembl, ensembl-compara, ensembl-variation, ensembl-funcgen; tabix; DBI, DBD::mysql);<br>
>      > environment is set up<br>
>      > my $API_VERSION = 84<br>
>      > ubuntu-15.10-desktop-amd64<br>
>      ><br>
>      > Error of converting sequence data:<br>
>      ><br>
>      > ? 28<br>
>      > - downloading Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz<br>
>      > - converting sequence data to bgzip format<br>
>      > Going to run:<br>
>      > ./biodbhts/scripts/convert_gz_2_bgz.sh /home/pl/.vep/homo_sapiens/84_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz ./htslib/bgzip<br>
>      > This may take some time and will be removed when files are provided in bgzip format<br>
>      > /bin/bash: ./biodbhts/scripts/convert_gz_2_bgz.sh: No such file or directory<br>
>      > FASTA gzip to bgzip conversion failed:<br>
>      ><br>
>      ><br>
>      > _______________________________________________<br>
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>      > Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
>      ><br>
><br>
>     _______________________________________________<br>
>     Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a> <mailto:<a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>><br>
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>     Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
><br>
><br>
><br>
> _______________________________________________<br>
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> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
><br>
<br>
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Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
</blockquote></div>