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Hello again!
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<div class="">I tried set the following in the JSON file:</div>
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</div>
<div class="">
<div class=""> {</div>
<div class=""> "id": "1000genomes_phase3",</div>
<div class=""> "species": "homo_sapiens",</div>
<div class=""> "assembly": "GRCh38",</div>
<div class=""> "type": "local",</div>
<div class=""> "strict_name_match": 1,</div>
<div class=""> "filename_template": "~/src/ensembl-vcf/",</div>
<div class=""> "chromosomes": [</div>
<div class=""> "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14",</div>
<div class=""> "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y"</div>
<div class=""> ],</div>
<div class=""> "sample_prefix": "1000GENOMES:phase_3:"</div>
<div class=""> },</div>
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</div>
<div class="">But I get this error message:</div>
<div class="">MSG: ERROR: VCF file ~/src/ensembl-vcf/ not found</div>
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<div class="">I downloaded all the hg38 files you linked to in the folder ~/src/ensembl-vcf/. When you say that I need to change filename_template to the path where the files were downloaded, is it the full path of all the 48 files rather than the path to
the folder they are in?</div>
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<div class="">Best,</div>
<div class="">Johanne</div>
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<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">
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<div dir="ltr" class="">Hi Johanne,
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<div class="">It looks like the API is intermittently losing connection to the remote VCF files hosted on our FTP site.</div>
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<div class="">You can bypass this connection by downloading the files to your local machine:</div>
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<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>
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</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>
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</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>
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<div class="">Regards</div>
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</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,
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<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>
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<div class="">The different error messages are:</div>
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<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>
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<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>
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<div class="">Also, if I use the GRCh37 database:</div>
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</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>
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</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>
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<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>
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<div class="">Best,</div>
<div class="">Johanne Håøy Horn</div>
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</blockquote>
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</blockquote>
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