"Internal error writing BLAST format"


I am trying to import some LAST-generated alignments of long reads against a protein reference database into Megan. I first use the sort-last-maf program to sort the generated alignments:

tools/sort-last-maf -i input.maf -o input.sorted.maf

I then try to generate an RMA file with the following command:

blast2rma -i input.sorted.maf -f LastMAF -o input.sorted.rma -lg -alg longReads --acc2taxa a2t.mapping

, where a2t.mapping is a file that specifies the taxon ID for each protein sequence in the reference database.

When following this procedure, I get a lot of error messages of the following form:

Internal error writing BLAST format: qEnd=1675, should be: 1687
Internal error writing BLAST format: qEnd=118, should be: 119
Internal error writing BLAST format: qEnd=4743, should be: 4744

Any advice?

Best wishes and thanks in advance,


could you please give me access to a small example file and I will look into this

Of course - here we go:


…/tools/blast2rma -i alignments.maf.sorted.maf.short -f LastMAF -o test -alg longReads -lg --acc2taxa DB.fa.megan.fpa.taxonMapping

… should produce 23 error messages.

You must specify the blast mode using this (blast2rma “guesses” the wrong mode):

-bm BlastX

This did it! Thank you very much!

Best wishes,