<div dir="ltr">Hi Kirsley,<div><br>You do not need to specify the config file manually with "--config cache/vep.ini" if your --dir parameter is set to "cache".</div><div><br></div><div>The VEP looks for a config file called vep.ini in the cache directory (default is $HOME/.vep but it looks like you've changed it to ./cache/) and loads this automatically; you are then manually telling it to load the same file again, so the configuration gets duplicated for things configured as arrays i.e. plugins and custom files.</div><div><br></div><div>Either rename your ini file and specify it manually, or leave it as it is and remove "--config cache/vep.ini" from your command.</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 22 July 2015 at 22:01, Kirsley CHENNEN <span dir="ltr"><<a href="mailto:kchennen@unistra.fr" target="_blank">kchennen@unistra.fr</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">
Hi Will,<br>
There seems to be a bug in VEP (v81) for the use of
Plugins and custom annotations. When theses parameters are specified
in a config file, it seems that VEP imports them twice! This is even
worse for custom annotations, as they are ouput twice and in a
concatenated form! However, they behave normally, if the parameters
are given in command line. Is it the only solution?<br>
<br>
<br>
Plugin example:<br>
-------------------------<br>
* In config file:<br>
plugin Blosum62<br>
<br>
<br>
* Shell log:<br>
[15-07-22 22:43:57] > ./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --config
cache/vep.ini -i example_GRCh37.vcf<br>
...<br>
version 81<br>
<br>
By Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)<br>
<br>
Configuration options:<br>
<br>
##<br>
allele_number 1<br>
assembly GRCh37<br>
config cache/vep.ini<br>
core_type core<br>
dir
xxxxx/ensembl-tools/scripts/variant_effect_predictor/cache<br>
dir_plugins
xxxxx/ensembl-tools/scripts/variant_effect_predictor/cache/Plugins<br>
force_overwrite 1<br>
fork 10<br>
host <a href="http://ensembldb.ensembl.org" target="_blank">ensembldb.ensembl.org</a><br>
input_file example_GRCh37.vcf<br>
minimal 1<br>
offline 1<br>
phased 1<br>
plugin Blosum62 Blosum62 <font color="#ff0000"><====</font> <br>
port 3306<br>
species homo_sapiens<br>
stats HASH(0x42c7728)<br>
stats_text 1<br>
terms SO<br>
variant_class 1<br>
verbose 1<br>
<br>
--------------------<br>
<br>
2015-07-22 22:44:10 - Read existing cache info<br>
2015-07-22 22:44:10 - Auto-detected FASTA file in cache directory<br>
2015-07-22 22:44:10 - Checking/creating FASTA index<br>
2015-07-22 22:44:10 - Loaded plugin: Blosum62 <font color="#ff0000"><====</font><br>
2015-07-22 22:44:10 - Loaded plugin: Blosum62 <font color="#ff0000"><====</font><br>
2015-07-22 22:44:10 - Starting...<br>
2015-07-22 22:44:10 - Detected format of input file as vcf<br>
2015-07-22 22:44:10 - Read 173 variants into buffer<br>
2015-07-22 22:44:10 - Calculating consequences<br>
[===============================================] [ 100% ]<br>
2015-07-22 22:44:11 - Writing output<br>
2015-07-22 22:44:11 - Processed 173 total variants (173 vars/sec,
173 vars/sec total)<br>
2015-07-22 22:44:11 - Wrote stats summary to
variant_effect_output.txt_summary.txt<br>
2015-07-22 22:44:11 - Finished!<br>
<br>
<br>
<br>
* In ouput file:<br>
...<br>
## BLOSUM62 : BLOSUM62 substitution score for the reference and
alternative amino acids <font color="#ff0000"><====</font><br>
## BLOSUM62 : BLOSUM62 substitution score for the reference and
alternative amino acids <font color="#ff0000"><====</font><br>
#Uploaded_variation Location Allele Gene Feature
Feature_type Consequence cDNA_position <br>
...<br>
<br>
<br>
<br>
<br>
<br>
<br>
Custom example:<br>
-------------------------<br>
* In config file:<br>
custom
xxxxx/vep/ucsc_encode/All_hg19_RS.bw,GERP_RS,bigwig<br>
<br>
<br>
* Shell log:<br>
[15-07-22 22:43:57] > ./<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> --config
cache/vep.ini -i example_GRCh37.vcf<br>
...<br>
version 81<br>
<br>
By Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)<br>
...<br>
custom
xxxxx/vep/ucsc_encode/All_hg19_RS.bw,GERP_RS,bigwig
xxxxx/vep/ucsc_encode/All_hg19_RS.bw,GERP_RS,bigwig<br>
...<br>
<br>
* In ouput file:<br>
...<br>
## GERP_RS : xxxxx/vep/ucsc_encode/All_hg19_RS.bw (exact)<br>
## GERP_RS : xxxxx/vep/ucsc_encode/All_hg19_RS.bw (exact)<br>
<br>
...<br>
<br>
<br>
Best,<br>
Kirsley<br>
<br>
<br>
<br>
</div>
</blockquote></div><br></div>