From emboss-bug :
> I found a bug in the header parsing of needle. See the inputs and outputs included below. Note how in the output there is no sequence accession for input 1.
> *************Input 1********************
>> OMNI|NTL01AP01841||5105472| 247aa long hypothetical protein taxon:272557
> ************Input2***********************
>> pva1.model.393_00196
>
> **************Output*****************
> #=======================================
> #
> # Aligned_sequences: 2
> # 1:
> # 2: pva1.model.393_00196
This relates to how non-standard NCBI FASTA headers are parsed,
especially where they have missing fields.
We will check and make sure the next release has something to report in
the header.