<div dir="ltr">Hey Priti,<div><br></div><div>I have had related problems with the FASTA index when using older versions of Perl or older BioPerl (<a href="http://lists.ensembl.org/pipermail/dev/2014-October/010492.html">http://lists.ensembl.org/pipermail/dev/2014-October/010492.html</a>). Since we were unable to update the system Perl on our cluster, the only solution was to compile Perl from source, to set it up as a local installation along with all it's libraries. Below are the commands I followed to do this. Let us know if this fixes the issue, or not.</div><div><br></div><div>~Cyriac</div><div><br></div><div>--</div><div><br></div><div># To make the commands below easier, set a temporary env variable to point to your current folder where you want to set up a local install of Perl:</div><div>export PERL_BASE="/opt/common/CentOS_6-dev/perl/"</div><div>cd $PERL_BASE</div><div><br></div><div># Download Perl source tarball into a subfolder src:<br></div><div><div>wget -P src <a href="http://www.cpan.org/src/5.0/perl-5.22.0.tar.gz">http://www.cpan.org/src/5.0/perl-5.22.0.tar.gz</a></div><div><br></div><div># Untar into properly versioned subfolder:</div><div>tar -zxf src/perl-5.22.0.tar.gz</div><div><br></div><div># Configure and build (can take a while):</div><div>cd perl-5.22.0</div><div>./Configure -des -Dprefix=$PERL_BASE/perl-5.22.0 -Dotherlibdirs=$PERL_BASE/perl-5.22.0/lib/perl5</div><div>make</div><div>make install</div><div>cd ..</div><div><br></div><div># Install dependencies of OncoKB, VEP, and other tools we use:</div><div>curl -L <a href="http://cpanmin.us">http://cpanmin.us</a> | $PERL_BASE/perl-5.22.0/bin/perl - --notest -l $PERL_BASE/perl-5.22.0 JSON::Parse XML::Parser XML::Simple Encode LWP LWP::Simple LWP::Protocol::https Archive::Extract Archive::Tar Archive::Zip CGI DBI Time::HiRes</div></div><div><br></div><div># Test running VEP using this new Perl:</div><div>$PERL_BASE/perl-5.22.0/bin/perl <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> ...<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jan 22, 2016 at 7:51 AM, Sarah Hunt <span dir="ltr"><<a href="mailto:seh@ebi.ac.uk" target="_blank">seh@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<br>
Hi Priti,<br>
<br>
We have seen this issue when there are problems with the fasta file
or it's index. If you are happy the fasta file is fine, deleting the
index file and letting VEP re-build it usually resolves the poblem.
Also, do check you are using BioPerl version 1.6.1 or later as we
have seen problems with earlier versions.<br>
<br>
Best wishes,<br>
<br>
Sarah<div><div class="h5"><br>
<br>
<div>On 21/01/2016 16:15, Priti Kumari
wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<br>
<div>
Hello,<br>
<br>
I ran two instances of VEPv83 on a large file with 50000
variants. I am getting different output, when I compare two
output files. One, example is different c. value.<br>
v1 : <br>
PTEN 0 . GRCh37 10 89692904
89692904 + Nonsense_Mutation SNP C
C T rs121909224 TUMOR NORMAL C
C <font color="#ff0000">c.388G>T</font>
p.Arg130Ter p.R130* ENST00000371953<br>
<br>
v2:<br>
PTEN 0 . GRCh37 10 89692904
89692904 + Nonsense_Mutation SNP C
C T rs121909224 TUMOR NORMAL C
C <font color="#ff0000">c.388C>T</font>
p.Arg130Ter p.R130* ENST00000371953<br>
<br>
Command used for running both instances :<br>
<br>
/usr/bin/perl
variant_effect_predictor//<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --species
homo_sapiens --assembly GRCh37 --offline --no_progress
--no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers
--domains --gene_phenotype --regulatory --canonical --protein
--biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs
1 --check_existing --check_alleles --check_ref --total_length
--allele_number --no_escape --xref_refseq --failed 1 --vcf
--minimal --flag_pick_allele --pick_order
canonical,tsl,biotype,rank,ccds,length --dir .vep/ --fasta
.vep/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
--input_file OP_VARIANT.vcf --output_file OP_VARIANT.v1.vep.vcf
--polyphen b --gmaf --maf_1kg --maf_esp --plugin
ExAC,/.vep//ExAC.r0.3.sites.minus_somatic.vcf.gz --fork 4<br>
<br>
Any idea why this is happening?<br>
Thank you,<br>
<pre cols="72">--
Priti Kumari
Bioinformatics Engineer
Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute
3 Blackfan Cir,
Center for Life Science Boston, Room 11037,
Boston, MA 02115
<a href="tel:617-632-6133" value="+16176326133" target="_blank">617-632-6133</a></pre>
<br>
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<br>
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