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Hi all
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<div>I found an interesting corner case for another VEP "fork of death" problem. I managed to replicate it fairly successfully, but haven't had a chance to pin it down. </div>
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<div>The scenario is: I'm using a subset of COSMIC in a fairly large (700k variants) input file. I'm using both --hgvs and --check_ref, and they seem to interact. Using --hgvs alone works. Using both in non-fork mode I get sometimes got errors about reference
alleles and variant alleles being the same. In fork mode the same parameters throw an error, possibly as the errors leak into data communications. What is odd is that these errors went away when --check_ref was not used, and that when I checked the lines reporting
errors, the alleles were in fact different. It is as if something accessed or revealed by --check_ref is being modified behind the scenes, triggering the HGVS errors. </div>
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<li>Succeeds: perl -X /Users/swatt/ensembl/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl --format ensembl --offline --no_progress --canonical --check_existing --force_overwrite --numbers --buffer_size 5000 --sift b --polyphen b
--compress gzcat --fasta /Users/swatt/fasta --input_file vep1.txt --output_file vep1.vep_output --hgvs --fork 8 </li><li>Fails (Fork of Death): perl -X /Users/swatt/ensembl/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl --format ensembl --offline --no_progress --canonical --check_existing --force_overwrite --numbers --buffer_size 5000 --sift b
--polyphen b --compress gzcat --fasta /Users/swatt/fasta --input_file vep1.txt --output_file vep1.vep_output --hgvs --fork 8 --check_ref</li><li>Succeeds (probably, eventually, but it takes a very long time): perl -X /Users/swatt/ensembl/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl --format ensembl --offline --no_progress --canonical --check_existing --force_overwrite
--numbers --buffer_size 5000 --sift b --polyphen b --compress gzcat --fasta /Users/swatt/fasta --input_file vep1.txt --output_file vep1.vep_output --hgvs --check_ref</li></ul>
<div>The only options that seem to determine these behaviours are --fork, --check_ref, and --hgvs, but I haven't exhaustively factored out the other options. </div>
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<div>Despite this, I can now complete the full file in fork mode on OSX, and that saves me many hours. So thanks for all the great work on these issues so far. </div>
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<div>I'm happy to provide data files and other info if required. If anybody has any tips in debugging this, I may get time to peek further into the perl code and figure out where things go funny. </div>
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<div>Configuration info:</div>
<div>OSX - Lion</div>
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<div>perl - 5.16.1 (not system perl, built using perlbrew)</div>
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<div>Ensembl/VEP version 72</div>
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<p style="margin-bottom: 0px; ">All the best</p>
<div>Stuart</div>
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<b>Stuart Watt, PhD</b></div>
<p style="font-family: Verdana, sans-serif; font-size: 8pt; margin-top: 0px; ">Scientific Associate</p>
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<b>Ontario Institute for Cancer Research</b></p>
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Toronto, Ontario, Canada M5G 0A3</p>
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<a href="http://www.oicr.on.ca">www.oicr.on.ca</a></p>
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