<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div>Hi Johannes,</div><div><br class=""><blockquote type="cite" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class="">
</div>
<div class="">Another thing: I have noticed that when I run the same script, with the same list of rsids as input, I get different outputs of variants in LD if I use hg38 and hg19. There are more LD-variants found with hg19, while I thought that it would be
the other way around, or similar amount. Do you know why?</div></div></blockquote><div><br class=""></div><div>We haven’t noticed any major differences for LD computation between the different assemblies. Could you please share some examples which we can use for looking into this? </div><div><br class=""></div><br class=""><blockquote type="cite" class=""><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div class=""><br class="">
</div>
<div class="">I previously got errors with variants mapping to alternate loci on hg38, and your colleague suggested that I only use loci mapped to the reference genome: next unless ($vf->slice->is_reference); Could this affect the amount of SNPs from LD in
hg38? Have you fixed the issue?</div>
<div class=""><br class=""></div></div></div></blockquote><div><br class=""></div><div>This shouldn’t have an effect on the number of variants that are returned. We will limit LD computation for variants on the reference sequence only for the next release 85 planned for late July.</div><div><br class=""></div><div><br class=""></div><div>Thank you,</div><div>Anja</div><br class=""><blockquote type="cite" class=""><div class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">
</div>
<div class="">Best,</div>
<div class="">Johanne</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">23. mai 2016 kl. 11.57 skrev Will McLaren <<a href="mailto:wm2@ebi.ac.uk" class="">wm2@ebi.ac.uk</a>>:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Johanne,
<div class=""><br class="">
</div>
<div class="">It looks like the API is intermittently losing connection to the remote VCF files hosted on our FTP site.</div>
<div class=""><br class="">
</div>
<div class="">You can bypass this connection by downloading the files to your local machine:</div>
<div class=""><br class="">
</div>
<div class="">GRCh38: <a href="ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/" class="">
ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/</a><br class="">
</div>
<div class="">GRCh37: <a href="ftp://ftp.ensembl.org/pub/grch37/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/" class="">
ftp://ftp.ensembl.org/pub/grch37/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/</a><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">You will then need to edit [module_path]/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json, changing the "filename_template" entry to the path where you downloaded the files, and "type" from "remote" to "local".</div>
<div class=""><br class="">
</div>
<div class="">Regarding the warning message, this should not affect your analyses in any way, but I have put in a fix on release/84 of ensembl-variation to suppress it.</div>
<div class=""><br class="">
</div>
<div class="">Regards</div>
<div class=""><br class="">
</div>
<div class="">Will McLaren</div>
<div class="">Ensembl Variation</div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On 21 May 2016 at 12:57, Johanne Håøy Horn <span dir="ltr" class="">
<<a href="mailto:johannhh@ifi.uio.no" target="_blank" class="">johannhh@ifi.uio.no</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Dear ensembl dev team,
<div class=""><br class="">
</div>
<div class="">I have been using your variation API for some time now, and get a range of errors from time to time, without knowing exactly why. It is not because of the scripts, I think, as the same script producing the error can work just fine if I run it
again.</div>
<div class=""><br class="">
</div>
<div class="">The different error messages are:</div>
<div class="">
<div class=""><font face="Courier New" class="">/Parser/BaseVCF4.pm line 891, <IN> line 5.</font></div>
<div class=""><font face="Courier New" class="">Use of uninitialized value in list assignment at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 891, <IN> line 5.</font></div>
<div class=""><span style="white-space:pre-wrap" class=""><font face="Courier New" class=""></font></span></div>
<div class=""><font face="Courier New" class="">connect: Operation timed out</font></div>
<div class=""><font face="Courier New" class="">[kftp_connect_file] 350 Restarting at 654385206. Send STORE or RETRIEVE to initiate transfer</font></div>
<div class=""><font face="Courier New" class=""> </font></div>
<div class=""><font face="Courier New" class="">[kftp_connect_file] 227 Entering Passive Mode (193,62,203,85,220,250).</font></div>
<div class=""><font face="Courier New" class="">Tabix::tabix_query: t is not of type tabix_tPtr at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm line 70.</font></div>
<div class=""><font face="Courier New" class=""> </font></div>
<div class=""><font face="Courier New" class="">[kftp_connect_file] 227 Entering Passive Mode (193,62,203,85,157,134).</font></div>
<div class=""><font face="Courier New" class="">[main] fail to open the data file.</font></div>
<div class=""><font face="Courier New" class="">Can't use an undefined value as an ARRAY reference at /Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm line 730.</font></div>
</div>
<div class=""><br class="">
</div>
<div class="">Usually just one of these error occur at a time. I suspect it might have something to do with the connection between my computer and the ensembl database, as the first error at least always show up in repeats when I lose my Internet connection.
However, are all of them caused by Internet trouble? I have checked that the MySQL instance is up and running, and can visit web pages through a browser when some of the errors occur. Could it be something on the server/database side?</div>
<div class=""><br class="">
</div>
<div class="">Also, if I use the GRCh37 database:</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""><font face="Courier New" class="">$registry->load_registry_from_db(</font></div>
<div class=""><font face="Courier New" class=""> -host => '<a href="http://ensembldb.ensembl.org/" target="_blank" class="">ensembldb.ensembl.org</a>',</font></div>
<div class=""><font face="Courier New" class=""> -user => 'anonymous',</font></div>
<div class=""><font face="Courier New" class=""> -port => 3337,</font></div>
<div class=""><font face="Courier New" class="">);</font></div>
</div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class="">I get this warning/printout:</div>
<div class=""><font face="Courier New" class="">Use of uninitialized value $nums{"."} in numeric comparison (<=>) at /Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm line 770, <IN> line 6.</font></div>
<div class=""><font face="Courier New" class=""><br class="">
</font></div>
<div class="">I use version 84 of the Ensembl API, OS X 10.11.5, and the script I use when all of these errors occur, is attached. Note that the attached script by default uses hg38, but will produce the last printout mentioned when switching to hg37.</div>
<div class=""><br class="">
</div>
<div class="">And something different I have been wondering about:</div>
<div class="">The VCF files that are downloaded locally (ALL.chr1.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi, for instance) - should they be deleted and re-downloaded from time to time to get the latest 1000G
data? And where exactly are the VCFs downloaded from? Is it dbSNP, as indicated in the file name?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Johanne Håøy Horn</div>
<div class=""></div>
</div>
<br class="">
_______________________________________________<br class="">
Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank" class="">
http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank" class="">
http://www.ensembl.info/</a><br class="">
<br class="">
</blockquote>
</div>
<br class="">
</div>
_______________________________________________<br class="">
Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">
http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">
Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""></body></html>