<span id="mailbox-conversation"><div>Hi Will,</div>
<div><br></div>
<div>Looks like re-indexing the FASTA file did it. (I feel like I've had indexing problems before and still don't understand why it works sometimes and not others).</div>
<div><br></div>
<div>Thanks!</div></span><div class="mailbox_signature">
<br>-Konrad</div>
<br><br><div class="gmail_quote"><p>On Mon, Sep 29, 2014 at 7:06 AM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div dir="ltr">Hi Konrad,<div><br></div>
<div>I can't replicate the issue I'm afraid. A couple of things to try:</div>
<div><br></div>
<div>1) Update your ensembl-variation checkout from GitHub - there may have been a bug fix that caught this already</div>
<div><br></div>
<div>2) Download again and re-index your FASTA file</div>
<div><br></div>
<div>3) If neither of the above works, run perl with -d to jump into the Perl debugger, then:</div>
<div>- press c, enter (you might need to do this twice to skip past a breakpoint)</div>
<div>- the script should then fail and give you a backtrace of where it failed in the code hierarchy, this would help me debug.</div>
<div><br></div>
<div>
<span style="font-family:arial,sans-serif;font-size:13px">perl -d ./ensembl-tools-release-76/</span><span style="font-family:arial,sans-serif;font-size:13px">scripts/variant_effect_</span><span style="font-family:arial,sans-serif;font-size:13px">predictor/</span><a href="http://variant_effect_predictor.pl/" style="font-family:arial,sans-serif;font-size:13px">variant_effect_predictor.pl</a><span style="font-family:arial,sans-serif;font-size:13px"> --everything --vcf --allele_number --no_stats --cache --offline --dir ./vep/ --force_overwrite --fasta ./vep/homo_sapiens/76_GRCh37/</span><span style="font-family:arial,sans-serif;font-size:13px">Homo_sapiens.GRCh37.75.dna.</span><span style="font-family:arial,sans-serif;font-size:13px">primary_assembly.fa --tabix -i ./test/test.vcf.gz -o test.vep.vcf.gz --gencode_basic</span><br></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px">Regards</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px">Will McLaren</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px">Ensembl Variation</span></div>
</div>
<div class="gmail_extra">
<br><div class="gmail_quote">On 28 September 2014 20:04, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<u></u>
<div>
<span><div>Hi dev team,</div>
<div><br></div>
<div>When running v76 of VEP (with GRCh37), I'm getting a bunch of these errors (command below):</div>
<div><br></div>
<div>
<div>substr outside of string at /humgen/atgu1/fs03/konradk/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 511.</div>
<div>Use of uninitialized value $ref_allele in string eq at /humgen/atgu1/fs03/konradk/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 514.</div>
<div>Use of uninitialized value in concatenation (.) or string at /humgen/atgu1/fs03/konradk/ensembl-tools-release-76/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/Sequence.pm line 643.</div>
<div><br></div>
<div>
<div>perl ./ensembl-tools-release-76/scripts/variant_effect_predictor/<a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> --everything --vcf --allele_number --no_stats --cache --offline --dir ./vep/ --force_overwrite --fasta ./vep/homo_sapiens/76_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --tabix -i ./test/test.vcf.gz -o test.vep.vcf.gz --gencode_basic</div>
<div><br></div>
<div>Here's one line it fails on, for instance:</div>
<div><br></div>
<div><div>1       69995   .       G       C       282.63  VQSRTrancheSNP99.60to99.80      AC=1</div></div>
</div>
<div><br></div>
<div>Thanks!</div>
<span class="HOEnZb"><font color="#888888">
</font></span>
</div></span><span class="HOEnZb"><font color="#888888"><div>
<br>-Konrad</div>
</font></span>
</div>
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</div>
<br></div>
</blockquote></div><br>