nhmmer failed to run - Error: Invalid alphabet type in target for nhmmer. Expect DNA or RNA about barrnap HOT 6 OPEN

I've gotten the same error. For me, what caused the error was one sequence composed entirely of G and T nucleotides. Adding a single A and C nucleotide resulted in no error. This should be an easy :-)

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I also just ran into this problem as well.

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I also just ran into this problem as well. I added A and same problem. The Internet said it was a problem with the conda installation.

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I just stumbled upon this; in case this is still relevant @zxgsy520 there is a switch to set the alphabet type for the query and use this as "guide" in case the alphabet type cannot be guessed for the target; --dna introduced in this PR
EddyRivasLab/hmmer#252
The switch is available in nhmmer v3.3.2 installed via conda

correction: the fix in the PR has only been merged into the dev branch, the switch --dna exists in latest release but does not include the fix

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I bypassed this issue by replacing all ambiguous bases (M, K, H, et al.) to N.

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I got this issue for a genome that started with a telomere repeat and did not have all four bases in the first few hundred characters. I got around it by replacing the first four characters of each sequence with GATC and then running on the temporary file:

PREFIX=$(basename ${GENOME/.fasta/})
sed 's/^[ACGT][ACGT][ACGT][ACGT]/GATC/' $GENOME > $PREFIX.tmp.fasta

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