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Sorry Will I forgot to copy "-check_existing" from command (it was
on new line)<br>
<br>
Regards,<br>
Guillermo<br>
<br>
<div class="moz-cite-prefix">On 12/06/15 15:26, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX1hTD+NcVUwxxa1XfnkUCS70Z2arYr4G0Xjddg5T02Y6w@mail.gmail.com"
type="cite">
<div dir="ltr">That command shouldn't even execute the line of
code that is reporting that warning. Please double check.
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 12 June 2015 at 14:21, Guillermo
Marco Puche <span dir="ltr"><<a moz-do-not-send="true"
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 the command:<br>
<ul>
<li><a moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">variant_effect_predictor.pl</a> -i
example_GRCh38.vcf -o annotation_example_GRCh38.vcf
-database -hgvs -cache -dir_cache
/home/gmarco/ensembl_80/cache </li>
</ul>
I've tried on another machine (machine2) and I dont' get
the error. Gonna try to re-install the exact same version
of Perl on both machines. If this continues failing then
I've no idea what's going on.<br>
Tried both version of bioperl 1.2.3 and 1.6.1 on both
machines and both work good on machine2 and show warnings
on machine1.<br>
Tried both versions of tabix 0.2.5 and 0.2.6 on both
machines and both work good on machine2 and show warnings
on machine1.
<ul>
<li>Machine1 Warnings:<br>
This is perl 5, version 14, subversion 4 (v5.14.4)
built for x86_64-linux<br>
</li>
</ul>
<ul>
<li>Machine2 NO warnings:<br>
This is perl 5, version 18, subversion 2 (v5.18.2)
built for x86_64-linux-gnu-thread-multi (with 41
registered patches, see perl -V for more detail)<br>
</li>
</ul>
Maybe it's not a perl issue. Then I've no clue what could
be causing the issue.<br>
<br>
Regards,<br>
Guillermo.
<div>
<div class="h5"><br>
<br>
<br>
<br>
<div>On 12/06/15 15:04, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Just to clarify, what command are you
running that gives the original error/warning?
<div><br>
</div>
<div>I can't recreate the issue, sorry!</div>
<div><br>
</div>
<div>Will<br>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 11 June 2015 at 12:28,
Guillermo Marco Puche <span dir="ltr"><<a
moz-do-not-send="true"
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>
Completely deleted cache, re-downloaded and
ran <a moz-do-not-send="true"
href="http://convert_cache.pl"
target="_blank">convert_cache.pl</a> as
you suggest in b) warnings still appear.<br>
<br>
If I try to reprocess again a cache already
processed with <a moz-do-not-send="true"
href="http://convert_cache.pl"
target="_blank">convert_cache.pl</a> I
get:<br>
<br>
<blockquote><small><a moz-do-not-send="true"
href="http://convert_cache.pl"
target="_blank">convert_cache.pl</a>
-d /share/references/vep -s homo_sapiens
-v 80_GRCh38 --force_overwrite</small><br>
<small>2015-06-11 13:25:43 - Processing
homo_sapiens</small><br>
<small>2015-06-11 13:25:43 - Processing
version 80_GRCh38</small><br>
<small>2015-06-11 13:25:43 - Processing
_var cache type</small><br>
<small>[>
] [ 2% ]ERROR: tabix failed</small><br>
<small>[ti_index_core] the file out of
order at line 300</small><br>
</blockquote>
First run on fresh cache doesn't fail.<br>
I've tried with tabix 0.2.5 and tabix 0.2.6
both versions have the exact same results.<br>
<br>
As I said I'm getting warnings when using
cache <b>even if I don't index it </b>previously
with <a moz-do-not-send="true"
href="http://convert_cache.pl"
target="_blank">convert_cache.pl</a><br>
<br>
Regards,<br>
Guillermo.
<div>
<div><br>
<br>
<div>On 11/06/15 12:40, Will McLaren
wrote:<br>
</div>
<blockquote type="cite">
<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
moz-do-not-send="true"
href="http://convert_cache.pl"
target="_blank">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
moz-do-not-send="true"
href="http://convert_cache.pl"
target="_blank">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
moz-do-not-send="true"
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><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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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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