Question: OMA standalone:"Error, (in ReadFastaWithNames) length(seqs) = length(refs), assertion failed"
gravatar for johan.aranberg
2.0 years ago by
johan.aranberg0 wrote:

Hi I used OMA standalone to identify orthologs in two fasta files with aa sequences. When I ran the analysis on macOS 64-bit, there was no issue in initializing the analysis, but because it takes too long I wanted to use a more powerful computer. The computer I have available is running on windows, so I have the OMA standalone running in a virtualbox with Bio-linux 8.0.7. when I start the OMA analysis I get this error:

"Error, (in ReadFastaWithNames) length(seqs) = length(refs), assertion failed"

In a previous post the following reason for the error is given: "*at least one of the fasta files could not be properly parsed. The number of sequences is not equal to the number of IDs" OMA Orthology Error Message Since the analysis with the same fasta files is running in macOS, I don't think there is an issue with the selected fasta-files. Any suggestions to what could be going wrong?

Best regards Johan

oma • 547 views
ADD COMMENTlink written 2.0 years ago by johan.aranberg0

sounds to me like it could be an issue with the newline format. is the data on a shared windows folder? you could try to run dos2unix on these fasta files. To rule out some issues with Bio-linux (I've never used it), you could also try to export a small dataset from the omabrowser and check if it works with that.

ADD REPLYlink written 2.0 years ago by adrian.altenhoff700
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