I'm about to go to sleep so I won't be able to run some of your tests until the morning

taxonomy.tab is 800kb, the smaller $tempFile is 250,000kb, the larger is 10gb. When I use a 23,000kb $tempFile, the program completes sucessfully on both a Mac and PC

The problem does occur when $tempFile gets too large. $tempfile is format "$annotativeInformation\t$aminoacidSequence\t$taxonomyCode\n". The following is an example of one line of $tempFile. >sp|P48255|ABCX_CYAPA Probable ATP-dependent transporter ycf16 OS=Cyanophora paradoxa GN=ycf16 PE=3 SV=1 MSTEKTKILEVKNLKAQVDGTEILKGVNLTINSGEIHAIMGPNGSGKSTFSKILAGHPAYQVTGGEILFKNKNLLELEPEERARAGVFLAFQYPIEIAGVSNIDFLRLAYNNRRKEEGLTELDPLTFYSIVKEKLNVVKMDPHFLNRNVNEGFSGGEKKRNEILQMALLNPSLAILDETDSGLDIDALRIVAEGVNQLSNKENSIILITHYQRLLDYIVPDYIHVMQNGRILKTGGAELAKELEIKGYDWLNELEMVKK CYAPA

What I mean by the script failing is that, the hash %taxR is messed up, as shown in the 3 examples of output (2 good, 1 bad) which causes the program to not forward any lines of $tempFile to the rest of the program. There is no error. For the program to progress, some of the hash values must equal 1

$filter is true if there is a value for $taxR{$curLineΐ]} which is built near the top

checkSeq(@curLine) is the rest of my program which works no matter where I test it, if I set $filter to be equal to 1, the program doesn't work because $filter is never set to 1 because the hash seems to break when $tempFile is too large

I use strict but I haven't used warning, I'll have to check that