<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">I’ve been investigating some inconsistent behavior with VEP, and finally traced it to an out of memory error that was simply being swallowed up. In load_dumped_transcript_cache in VEP.pm, we sometimes run out of memory, which causes the `open` to fail. We do see the warning message "Could not find cache for …”, but since our pipelines are largely automated, warning messages don’t mean very much to us. The variants in these regions end up falsely annotated as Intergenic, when many of them should have a transcript annotation. It would be nice to expose this type of error condition more obviously.<div>For example, the line:</div><div><pre class="fragment" style="font-family: monospace, fixed; font-size: 9pt; margin: 4px 8px 4px 2px; line-height: 15px; border: 1px solid rgb(196, 207, 229); padding: 4px 6px; overflow: auto; word-wrap: break-word; background-color: rgb(251, 252, 253);">open my $fh, $config->{compress}.<span class="stringliteral" style="font-size: 1em; color: rgb(0, 32, 128);">" "</span>.$dump_file.<span class="stringliteral" style="font-size: 1em; color: rgb(0, 32, 128);">" |"</span> or <span class="keywordflow" style="font-size: 1em; color: rgb(224, 128, 0);">return</span> undef;</pre><div>could be changed to</div><div><pre class="fragment" style="margin: 4px 8px 4px 2px; border: 1px solid rgb(196, 207, 229); padding: 4px 6px; overflow: auto; word-wrap: break-word; background-color: rgb(251, 252, 253);"><font face="monospace, fixed"><span style="font-size: 9pt; line-height: 15px;">open my $fh, $config->{compress}.</span></font><span class="stringliteral" style="font-family: monospace, fixed; font-size: 1em; line-height: 15px; color: rgb(0, 32, 128);">" "</span><font face="monospace, fixed"><span style="font-size: 9pt; line-height: 15px;">.$dump_file.</span></font><span class="stringliteral" style="font-family: monospace, fixed; font-size: 1em; line-height: 15px; color: rgb(0, 32, 128);">" |"</span><font face="monospace, fixed"><span style="font-size: 9pt; line-height: 15px;"> or </span></font><font color="#e08000"><font face="monospace, fixed"><span style="font-size: 9pt; line-height: 15px;">die </span><span style="line-height: 15px;">“ERROR $!"</span></font></font><font face="monospace, fixed"><span style="font-size: 9pt; line-height: 15px;">;</span></font></pre><div><br></div></div><div>I can’t think of a time when we would want to ignore a failure to open a file handle.</div></div><div><br></div><div>thanks!</div><div><br></div><div>Allison Regier</div>
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