<div dir="ltr">Thanks for troubleshooting this. I will keep at it, and try to find a better working solution.<div><br></div><div>This was done on a CentOS 6.5 server, but since I didn't have sudo rights to install Perl libs, I used perlbrew... which may be a suspect.<div><br></div><div>~Cyriac</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Oct 20, 2014 at 11:30 AM, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@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">
Hi Cyriac,<br>
<br>
As Will said, this is a Bioperl issue.<br>
<br>
The module Bio::DB::Fasta is responsible for the indexing<br>
According to the documentation
(<a href="http://search.cpan.org/dist/BioPerl-1.6.901/Bio/DB/Fasta.pm" target="_blank">http://search.cpan.org/dist/BioPerl-1.6.901/Bio/DB/Fasta.pm</a>), it
will use the AnyDBM module to know how to index the file<br>
<br>
The type of index created seems to depend on the environment you're
running in.<br>
We have noticed the creation of .pag and .dir indexes in limited
linux distributions (for example VMs) which might be missing the
required executables<br>
DB::Fasta is then unable to identify this as a correct index and
keeps re-indexing the file although nothing has changed<br>
<br>
One workaround is to manually edit your DB::Fasta file, by removing
the force_index<br>
- my $reindex = $force_reindex || $indextime < $modtime;<br>
+ my $reindex = 0; # $force_reindex || $indextime < $modtime;<br>
It does mean though that it will not pick up if your file has
changed, so you would need to edit this every time you get a new
fasta file<br>
<br>
If you can find a working solution, I would be interested to hear
about it.<br>
<br>
<br>
Regards,<br>
Magali<div><div class="h5"><br>
<br>
<div>On 20/10/2014 09:29, Will McLaren
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<p dir="ltr"> </p>
<div class="gmail_quote">Hi Cyriac,</div>
<div class="gmail_quote"><br>
</div>
<div class="gmail_quote">This is not something I've come across
before; the FASTA indexing is performed by code that we do not
maintain (the Bio::DB::Fasta module is part of the BioPerl
package).</div>
<div class="gmail_quote"><br>
</div>
<div class="gmail_quote">Which version of BioPerl are you using
(there are known issues with 1.2.3, though not this issue
AFAIK, the VEP installs 1.6.0)? And are you using a single
FASTA file or a directory containing multiple FASTA files?</div>
<div class="gmail_quote"><br>
</div>
<div class="gmail_quote">For VEP it is normal that it just
generates the .fa.index file; I have never seen the other two
you mention (perhaps they appear with a directory of files
rather than a single .fa).</div>
<div class="gmail_quote"><br>
</div>
<div class="gmail_quote">I'd try removing the indexes and
reindexing, or removing the .fa file and
re-downloading/re-generating it.</div>
<div class="gmail_quote"><br>
</div>
<div class="gmail_quote">HTH</div>
<div class="gmail_quote"><br>
</div>
<div class="gmail_quote">Will</div>
<div class="gmail_quote"><br>
</div>
<div class="gmail_quote">On 18 Oct 2014 02:33, "Cyriac Kandoth"
<<a href="mailto:kandoth@cbio.mskcc.org" target="_blank">kandoth@cbio.mskcc.org</a>>
wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Hi Devs,</div>
<div><br>
</div>
The code to check whether a FASTA index needs to be
created, looks for a file with extension ".fa.index".
However, (and this may be recent) the indexes created are
files named ".fa.index.dir" and ".fa.index.pag". I haven't
checked the code to confirm this. I'm assuming this is the
case, since VEP appears to index the FASTA everytime it
runs, unless I create a copy of ".fa.index.pag" with
extension ".fa.index".
<div>
<div>
<div><br>
</div>
<div>
<div>Cheers!<br>
</div>
<div><br>
</div>
<div>~Cyriac</div>
</div>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</div></div></div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>