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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>
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<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>
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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 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" 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>
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</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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