Encountered error about more than two alleles seen for 2 bit compression
Dan Weeks
Mega2 v4.6.1 Windows
ERROR: More than two alleles seen for 2 bit compression. 1/5 stored. 1/2 now seen.
WARNING: An error occurred while attempting to run 'mega2log2html.pl'.
WARNING: Can not find 'mega2log2html.pl' run log. (__tmp__)
WARNING: Unable to create html-formatted run summary.
Using STR data so I am not sure if I should be using an earlier version, or if the ERROR: message is ok.
Dan Weeks
In the latest update to Mega2, we made it much more memory efficient and, in the process, set the default compression mode to handle only 2 alleles.
If you want to run markers with more than 2 alleles, you need to adjust the "Genotype compression" option from 2 bits to 2 bytes in the initial input menu. See Section 11.11 of the Mega2 documentation (below).
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11.11 Input menu item: Compression
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Please enter compression value 1, 2, or 3 (2 bits, 2 bytes, or 16 bytes) >
This is an integer value: 1, 2, or 3. The default value is 1. In this case, each pair of alleles is represented internally with two bits, the same as the PLINK compressed binary “bed” representation. This technique does not provide enough space to represent microsatellite markers or half-typed genotypes (where one allele is unknown). For these data sets, the compression value of 2 should be adequate. It provides for up to 256 alleles. The compression value of 3 is left for historical comparisons - it should never be necessary.
Note that in the 2 byte mode, if the input data are in Linkage format and all allele labels are integers, those integers will be used as is, which means that an allele with the label ’257’ would not work. However, if the input data are in Annotated format, then allele labels are treated as strings, and will be recoded to sequential integers.
Dan Weeks
In the latest update to Mega2, we made it much more memory efficient and, in the process, set the default compression mode to handle only 2 alleles.
If you want to run markers with more than 2 alleles, you need to adjust the "Genotype compression" option from 2 bits to 2 bytes in the initial input menu. See Section 11.11 of the Mega2 documentation (below).