<div dir="ltr">Hi Guillermo,<div><br></div><div>The info.txt looks fine. My guess is something's gone wrong in the conversion stage which has corrupted the column structure in one of the converted files.</div><div><br></div><div>I downloaded the cache afresh and ran the <a href="http://convert_cache.pl">convert_cache.pl</a> script and I'm afraid I don't see the same error.</div><div><br></div><div>I'd try</div><div><br></div><div>a) run <a href="http://convert_cache.pl">convert_cache.pl</a> again (you may need to add the --force_overwrite option)</div><div><br></div><div>b) remove the existing one and download the cache again</div><div><br></div><div>Will</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 11 June 2015 at 08:21, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
Hi Will,<br>
<br>
This is info.txt content in
[cache_dir]/homo_sapiens/80_GRCh38/info.txt<br>
<br>
<br>
<small># CACHE UPDATED 2015-06-11 09:12:21<br>
sift b<br>
cell_types
HeLa-S3,GM06990,U2OS,CD4,IMR90,HL-60,HepG2,Lymphoblastoid,CD133,CD36,K562,GM12878,HUVEC,NHEK,H1ESC,MultiCell,K562b,NH-A,HSMM,HMEC,A549,AG04449,AG04450,AG09309,AG09319,AG10803,Caco-2,Chorion,CMK,GM10847,GM12801,GM12864,GM12865,GM12872,GM12873,GM12874,GM12875,GM12891,GM12892,GM15510,GM18505,GM18507,GM18526,GM18951,GM19099,GM19193,GM19238,GM19239,GM19240,H7ESC,H9ESC,HAEpiC,HCF,HCM,HCPEpiC,HCT116,HEEpiC,HEK293b,HEK293,HepG2b,HGF,HIPEpiC,HNPCEpiC,HRCEpiC,HRE,HRPEpiC,Jurkat,LHSR,MCF7,Medullo,Melano,NB4,NHBE,NHDF-neo,NHLF,NT2-D1,Panc1,PanIslets,PFSK1,SAEC,SKMC,SKNMC,SKNSHRA,Th1,Th2,WERIRB1,RPTEC,ProgFib,HSMMtube,Osteobl,MCF10A-Er-Src,HPAEpiC,Fibrobl,GM12878-XiMat,BJ,NHDF-AD,Monocytes-CD14+,DND-41<br>
var_type tabix<br>
user ensro<br>
host genebuild9<br>
variation_cols
chr,variation_name,failed,somatic,start,end,allele_string,strand,minor_allele,minor_allele_freq,clin_sig,phenotype_or_disease,pubmed,AFR,AMR,EAS,EUR,SAS,AA,EA<br>
port 3306<br>
build all<br>
polyphen b<br>
regulatory 1<br>
assembly GRCh38<br>
species homo_sapiens<br>
source_polyphen 2.2.2<br>
source_sift sift5.2.2<br>
source_COSMIC 71<br>
source_ESP 20141103<br>
source_gencode GENCODE 22<br>
source_HGMD-PUBLIC 20144<br>
source_genebuild 2014-07<br>
source_regbuild 13.0<br>
source_assembly GRCh38.p2<br>
source_dbSNP 142<br>
source_ClinVar 20150306</small><br>
<br>
Regards,<br>
Guillermo<div><div class="h5"><br>
<br>
<div>On 10/06/15 20:41, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote type="cite">
<div>Hi Will,<br>
<br>
I got the exact same warnings with 79_GRCh38 cache (indexed
previosuly with convert_cache)<br>
Then I decided to try with 80_GRCh38 cache and API version 80. I
didn't index it and I'm getting the same warnings. Tomorrow I'll
index 80_GRCh38 cache and report "info.txt".<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
El 10/06/2015 a las 17:59, Will McLaren escribió:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>Did you say you had run <a href="http://convert_cache.pl" target="_blank">convert_cache.pl</a> in an
earlier email?</div>
<div><br>
</div>
<div>This may be the issue here. Can you send on the content
of the file [cache_dir]/homo_sapiens/80_GRCh37/info.txt</div>
<div><br>
</div>
<div>It may be you need to re-run the convert_cache script,
possibly after downloading the original cache again.</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 10 June 2015 at 15:40, Guillermo
Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Dear devs,<br>
<br>
I'm experiencing the following warnings when using vep
local cache with variant_effect_predictor script:<br>
<br>
<blockquote>
<pre>Argument "-/C" isn't numeric in numeric eq (==) at /share/apps/src/ensembl_80-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 6218.</pre>
<pre>Use of uninitialized value in split at /share/apps/src/ensembl_80-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 6223.</pre>
</blockquote>
<br>
If no cache is used warnings disappear.<br>
<br>
Input VCF: example_GRCh38.vcf (inside <a href="https://github.com/Ensembl/ensembl-tools/archive/release/80.zip" target="_blank">https://github.com/Ensembl/ensembl-tools/archive/release/80.zip</a>)<br>
Cache downloaded from: <a href="ftp://ftp.ensembl.org/pub/release-80/variation/VEP/homo_sapiens_vep_80_GRCh38.tar.gz" target="_blank">ftp://ftp.ensembl.org/pub/release-80/variation/VEP/homo_sapiens_vep_80_GRCh38.tar.gz</a><br>
<br>
Best regards,<br>
Guillermo.<br>
</div>
<br>
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